bluuebunny/crossref_metadata_2025 huggingface dataset:
Urban–rural links in relaunching left-behind places: the case of Portuguese municipalities
Authors: Alamá-Sabater Luisa , Márquez Miguel Á , Tortosa-Ausina Emili , Cravo Júlia
Published: November 2024

During the last few decades, the gap between the most prosperous metropolitan areas and the rural areas has widened, especially since the 2008 crisis. This gap has been particularly relevant in relation to population and employment. However, the bi-directional links in terms of population and employment between rural places and the most urbanized areas have been partly overlooked by the literature. At the same time, recent studies have brought the plight of “left-behind” areas to the forefront, highlighting rural as well as other types of “left-behind” places as focal points of discontent. In the context of the debate on left-behind areas, and in an attempt to address the decline in population and employment that they are experiencing, this article proposes a strategy based on the spatial interactions among the different types of territories. Specifically, we develop a spatial econometric model capable of testing all interactions among different territorial typologies based on their degree of urbanization. We apply the model to 278 continental municipalities in Portugal during the period 2010–8. The model estimates have implications for understanding the dynamics of territorial interactions in Portugal, highlighting the crucial role of semi-urban municipalities. The results reveal the positive and significant connections between change in employment in semi-urban municipalities and population change in both neighboring rural and urban municipalities. The findings suggest that semi-urban/rural diffusion should be promoted as a policy approach to left-behind rural places in Portugal.
Bootstrap Inference for Group Factor Models
Authors: Gonçalves Sílvia , Koh Julia , Perron Benoit
Published: November 2024

Andreou et al. (2019) have proposed a test for common factors based on canonical correlations between factors estimated separately from each group. We propose a simple bootstrap test that avoids the need to estimate the bias and variance of the canonical correlations explicitly and provide high-level conditions for its validity. We verify these conditions for a wild bootstrap scheme similar to the one proposed in Gonçalves and Perron (2014). Simulation experiments show that this bootstrap approach leads to null rejection rates closer to the nominal level in all of our designs compared to the asymptotic framework.
Graph-Based Methods for Forecasting Realized Covariances
Authors: Zhang Chao , Pu Xingyue , Cucuringu Mihai , Dong Xiaowen
Published: November 2024

We forecast the realized covariance matrix of asset returns in the U.S. equity market by exploiting the predictive information of graphs in volatility and correlation. Specifically, we augment the Heterogeneous Autoregressive model via neighborhood aggregation on these graphs. Our proposed method allows for the modeling of interdependence in volatility (also known as spillover effect) and correlation, while maintaining parsimony and interpretability. We explore various graph construction methods, including sector membership and graphical LASSO (for modeling volatility), and line graph (for modeling correlation). The results generally suggest that the augmented model incorporating graph information yields both statistically and economically significant improvements for out-of-sample performance over the traditional models. Such improvements remain significant over horizons up to 1 month ahead, but decay in time. The robustness tests demonstrate that the forecast improvements are obtained consistently over the different out-of-sample sub-periods and are insensitive to measurement errors of volatilities.
The afterlife of ISDS awards: post-award settlements and the limits of transparency reforms
Authors: Chernykh Yuliya , Sattorova Mavluda
Published: November 2024

Post-award settlements in investor–state dispute settlement (ISDS) remain largely unstudied. One of the reasons for this gap in knowledge is the lack of transparency in the post-award phase of the relationship between investors and host states. The primary objective of this article is to use novel empirical data to explore the transparency gaps and absences in the post-award phase of ISDS. We seek to challenge the prevailing notions of finality of ISDS awards and highlight the need to re-think the end goals of transparency considering the significant public policy implications post-award agreements may engender. The veil of secrecy that continues to shroud the world of post-award settlements raises a number of issues that go to the heart of the ongoing debate about the workings of ISDS, its legitimacy and the role of openness and accountability therein.
Impact of probiotic Bacillus sp. dietary supplementation on pancreatic and intestinal activities in seabream Sparus aurata
Authors: Yıldırım Şükrü , Suzer Cüneyt , Fırat Kürşat , Saka Şahin , Hekimoğlu Müge , Çoban Deniz , Korkut Ali Yıldırım , Köse İbrahim , Antepli Onurkan , Gökvardar Alize , Perçin Fatih
Published: November 2024

The main objective of this study was to investigate the effects of commercial probiotic Bacillus sp. supplementation on seabream Sparus aurata larviculture under culture conditions. In this context, Bacillus was supplemented via rotifer feeding and water and its effects on pancreatic and intestinal enzyme activities as well as aquaculture parameters were evaluated during early life development. In the experimental group, as probiotic three Bacillus sp. spores were introduced via rotifer and larval culture tanks, while the larvae in control group did not feed any probiotic supplementation. At the end of the experiment on 40 days after hatching, the probiotic-supplemented group exhibited better growth performance and there were statistically differences in between groups of probiotic-treated and control regarding growth parameters (P < 0.01), despite insignificant survival rate (P > 0.05). In terms of enzymatic expressions, S. aurata larvae receiving probiotic supplementation through rotifers demonstrated noteworthy (P < 0.05) enhancements in specific activities of pancreatic and intestinal enzymes, except for amylase (P > 0.05), when compared to the control group. It is concluded that the administration of Bacillus sp. as probiotic bacteria through rotifer supplementation and water intake demonstrates significant positive impacts on both growth parameters and specific activities of main pancreatic and intestinal enzymes of seabream larvae.
Molecular characterization of Staphylococcus aureus from nasal samples of healthy pet cats
Authors: Bezzi Amel , Antri Kenza , Bachtarzi Mohamed Azzedine , Martins-Simoes Patricia , Youenou Benjamin , Gourari Samir , Nateche Farida , Tristan Anne
Published: November 2024

The objective of this study was to characterize Staphylococcus aureus isolates recovered from the nasal samples of healthy pet cats in Algiers province. A total of 138 nasal swabs were collected. Antimicrobial susceptibility was conducted using the disk-diffusion method and the VITEK-2 susceptibility system. Whole genome sequencing was performed to identify multiple-locus sequence typing, antimicrobial and virulence genes. Staphylococcus aureus isolates were detected in 23 cats. Among these, 11 were methicillin-resistant S. aureus (MRSA) (one isolate/sample). Three sequence types (ST6, ST5, and ST1) were identified in MRSA, with the predominance of ST6 (n = 7). Seven distinct STs [ST398, ST97, ST15, ST7, ST291, ST5043, and a new ST, (ST9219)] were detected in methicillin-sensitive S. aureus. All MRSA isolates harbored the mecA gene and SCCmec-type-IVa. MRSA exhibited resistance to tetracycline [n = 3/tet(L) and tet(M); n = 1/tet(K)], kanamycin-tobramycin [n = 3/ant(4′)-Ia), amikacin-kanamycin (n = 1/aph(3′)-IIIa], and erythromycin-clindamycin [n = 1/erm(C)]. Seven S. aureus isolates were multidrug resistant. All the isolates were negative for lukS/lukF-PV and tst-1 genes, while 20 isolates were IEC-positive. This study revealed a diversity of genetic lineages in S. aureus strains isolated from nasal samples of pet cats, including multidrug-resistant and toxigenic strains. The presence of IEC-positive S. aureus suggests possible human–animal transmission.
Biochemical characterization of HcrF from Limosilactobacillus fermentum, a NADH-dependent 2-ene reductase with activity on hydroxycinnamic acids
Authors: Gaur Gautam , Gänzle Michael
Published: November 2024

In fermented plant foods, phenolic compounds are metabolized by 2-ene reductases, which reduce double bonds adjacent to an aromatic rings in phytochemicals, including hydroxycinnamic acids, isoflavones, and flavones. Only few 2-ene reductases of lactic acid bacteria were characterized, including the hydrocinnamic reductases HcrB and Par1, and the daidzein reductase of Lactococcus lactis. This study aimed to characterize HcrF, a homologue of HcrB, in Limosilactobacillus fermentum. HcrF was purified after cloning in Escherichia coli and purification by affinity chromatography. HcrF was optimally active at 30°C–40°C and pH 7.0 and required both flavin mononucleotide and nicotinamide adenine dinucleotide as co-factors. Ferulic, caffeic, p-coumaric, and sinapic acids but not trans-cinnamic acids were reduced to dihydro derivatives. The maximum reaction velocity Vmax of HcrF was highest for ferulic acid. On a phylogenetic tree of 2-ene reductases, HcrF clustered most closely with the hydroxycinnamic acid reductase HcrB of Lactiplantibacillus plantarum. The hydroxycinnamic acid reductase Par1 of Furfurilactobacillus milii and flavone or isoflavone reductases were only distantly related to HcrF. In summary, current knowledge does not allow to predict the substrate specificity of 2-ene reductases on the basis of the protein sequence; this study adds HcrF to the short list of enzymes with known substrate specificity.
Eccentric mergers in AGN discs: influence of the supermassive black hole on three-body interactions
Authors: Fabj Gaia , Samsing Johan
Published: November 2024

There are indications that stellar-origin black holes (BHs) are efficiently paired up in binary black holes (BBHs) in active galactic nucleus (AGN) disc environments, which can undergo interactions with single BHs in the disc. Such binary–single interactions can potentially lead to an exceptionally high fraction of gravitational-wave mergers with measurable eccentricity in LIGO/Virgo/KAGRA. We here take the next important step in this line of studies by performing post-Newtonian N-body simulations between migrating BBHs and single BHs set in an AGN disc-like configuration, with a consistent inclusion of the central supermassive black hole (SMBH) in the equations of motion. With this set-up, we study how the fraction of eccentric mergers varies in terms of the initial size of the BBH semimajor axis relative to the Hill sphere, as well as how it depends on the angle between the BBH and the incoming single BH. We find that the fraction of eccentric mergers is still relatively large, even when the interactions are notably influenced by the gravitational field of the nearby SMBH. However, the fraction as a function of the BBH semimajor axis does not follow a smooth functional shape, but instead shows strongly varying features that originate from the underlying phase-space structure. The phase-space further reveals that many of the eccentric mergers are formed through prompt scatterings. Finally, we present the first analytical solution to how the presence of an SMBH in terms of its Hill sphere affects the probability for forming eccentric BBH mergers through chaotic three-body interactions.
Analysing the dynamics of the Kepler-90 planetary system
Authors: Gaslac Gallardo D M , Giuliatti Winter S M , Winter O , Callegari N , Muñoz-Gutiérrez M A
Published: November 2024

Kepler-90 system has a set of eight planets in a hierarchical structure. In this work, we used frequency analysis to study several Kepler-90 analogues to analyse in detail how the values of the eccentricity of each planet can alter the stability of the system. The system was formed by the star and eight planets for three different intervals of eccentricity ($e$). Our results show that for the first and second intervals, all the systems are stable. However, no set of Kepler-90 systems with large values of $e$ survived up to $10^5$ orbits of Kepler-90h. In the low-eccentricity interval, planets Kepler-90b and Kepler-90c were found to be in a 5:4 mean motion resonance, and the pair Kepler-90g and Kepler-90h in a 3:2 mean motion resonance, although these two pairs are in resonance in different Kepler-90 analogues. In the medium-eccentricity interval, only the pair Kepler-90g and Kepler-90h is in resonance. Kepler-90b and Kepler-90c are in quasi-resonance 5:4; the critical angle circulates and librates intermittently in different periods of time. The results statistically indicate that these resonances directly affect the most of them. The influence covers a wide range of possibilities: (i) a strong resonant mean motion coupling added to a coupling of the longitude of the pericentres; (ii) just a single resonant argument librating; (iii) intermittent behaviour, interleaving libration, and circulation of the resonant arguments; and (iv) the quasi-resonant influence due to the near commensurability.
Reactivity of chondritic meteorites under H2-rich atmospheres: formation of H2S
Authors: Cabedo V , Pareras G , Allitt J , Rimola A , Llorca J , Yiu H H P , McCoustra M R S
Published: November 2024

Current models of chemical evolution during star and planetary formation rely on the presence of dust grains to act as a third body. However, they generally ignore the reactivity of the dust grains themselves. Dust grains present in the protoplanetary phase will evolve as the Solar system forms and, after protoplanets have appeared, they will be constantly delivered to their surfaces in the form of large aggregates or meteorites. Chondritic meteorites are mostly unaltered samples of the dust present in the first stages of the Solar system formation, which still arrive nowadays to the surface of Earth and allow us to study the properties of the materials forming the early Solar system. These materials contain, amongst others, transition metals that can potentially act as catalysts, as well as other phases that can potentially react in different astrophysical conditions, such as FeS. In this work, we present the reactivity of chondritic meteorites under H$_{2}$-rich atmospheres, particularly towards the reduction of FeS for the formation of H$_{2}$S and metallic Fe during the early phases of the planetary formation. We present the obtained results on the reaction rates and the percentage of FeS available to react in the materials. Additionally, we include a computational study of the reaction mechanism and the energetics. Finally, we discuss the implications of an early formation of H$_{2}$S in planetary surfaces.
From particles to pixels: how many particles do I really need to construct stellar kinematic mock observational measurements?
Authors: Harborne K E , Lagos C del P , Croom S M , van de Sande J , Ludlow A , Remus R S , Kimmig L C , Power C
Published: November 2024

This work considers the impact of resolution in the construction of mock observations of simulated galaxies. In particular, when building mock integral field spectroscopic observations from galaxy formation models in cosmological simulations, we investigate the possible systematics that may arise given the assumption that all galaxies above some stellar mass limit will provide unbiased and meaningful observable stellar kinematics. We build a catalogue of N-body simulations to sample the range of stellar particle resolutions within the EagleRef0050N0752 simulation box and examine how their observable kinematics vary relative to a higher-resolution N-body control. We use these models to compile a table of the minimum number of particles-per-pixel to reach a given uncertainty in the fitted line-of-sight velocity distribution parameters. Further, we introduce a Voronoi-binning module to the mock observation code, SimSpin, in order to meet these minimum numbers. Using Eagle, we show the impact of this shot noise on the observed spin–ellipticity plane and the recovery of this space when observations are binned with increasing numbers of particles. In conclusion, we advise binning mock images to meet at least 200 particles-per-pixel to avoid systematically under-estimating the velocity dispersion along a given line-of-sight. We demonstrate that this is important for comparing galaxies extracted from the same simulation, as well as between simulations of varying mass resolution and observations of real galaxies.
The structure of the stellar halo of the Andromeda galaxy explored with the NB515 for Subaru/HSC – I. New insights on the stellar halo up to 120 kpc
Authors: Ogami Itsuki , Tanaka Mikito , Komiyama Yutaka , Chiba Masashi , Guhathakurta Puragra , Kirby Evan N , Wyse Rosemary F G , Filion Carrie , Gilbert Karoline M , Escala Ivanna , Mori Masao , Kirihara Takanobu , Tanaka Masayuki , Ishigaki Miho N , Hayashi Kohei , Lee Myun Gyoon , Sharma Sanjib , Kalirai Jason S , Lupton Robert H
Published: November 2024

We analyse the M31 halo and its substructure within a projected radius of 120 kpc using a combination of Subaru/HSC NB515 and Canada France Hawaii Telescope/MegaCam g and i bands. We succeed in separating M31’s halo stars from foreground contamination with $\sim$90 per cent accuracy by using the surface gravity sensitive NB515 filter. Based on the selected M31 halo stars, we discover three new substructures, which associate with the Giant Southern Stream (GSS) based on their photometric metallicity estimates. We also produce the distance and photometric metallicity estimates for the known substructures. While these quantities for the GSS are reproduced in our study, we find that the north-western stream shows a steeper distance gradient than found in an earlier study, suggesting that it is likely to have formed in an orbit closer to the Milky Way. For two streams in the eastern halo (Stream C and D), we identify distance gradients that had not been resolved. Finally, we investigate the global halo photometric metallicity distribution and surface brightness profile using the NB515-selected halo stars. We find that the surface brightness of the metal-poor and metal-rich halo populations, and the all population can be fitted to a power-law profile with an index of $\alpha =-1.65\pm 0.02$, $-2.82\pm 0.01$, and $-2.44\pm 0.01$, respectively. In contrast to the relative smoothness of the halo profile, its photometric metallicity distribution appears to be spatially non-uniform with non-monotonic trends with radius, suggesting that the halo population had insufficient time to dynamically homogenize the accreted populations.
MIGHTEE: the continuum survey Data Release 1
Authors: Hale C L , Heywood I , Jarvis M J , Whittam I H , Best P N , An Fangxia , Bowler R A A , Harrison I , Matthews A , Smith D J B , Taylor A R , Vaccari M
Published: November 2024

The MeerKAT International GHz Tiered Extragalactic Exploration Survey (MIGHTEE) is one of the large survey projects using the MeerKAT telescope, covering four fields that have a wealth of ancillary data available. We present Data Release 1 of the MIGHTEE continuum survey, releasing total intensity images and catalogues over $\sim$20 deg$^2$, across three fields at $\sim$1.2–1.3 GHz. This includes 4.2 deg$^2$ over the Cosmic Evolution Survey (COSMOS) field, 14.4 deg$^2$ over the XMM Large-Scale Structure (XMM-LSS) field and deeper imaging over 1.5 deg$^2$ of the Extended Chandra Deep Field South (CDFS). We release images at both a lower resolution (7–9 arcsec) and higher resolution ($\sim 5$ arcsec). These images have central rms sensitivities of $\sim 1.3-$2.7 $\mu$Jy beam$^{-1}$ ($\sim 1.2-$3.6 $\mu$Jy beam$^{-1}$) in the lower (higher) resolution images, respectively. We also release catalogues comprised of $\sim$144 000 ($\sim$114 000) sources using the lower (higher) resolution images. We compare the astrometry and flux-density calibration with the Early Science data in the COSMOS and XMM-LSS fields and previous radio observations in the CDFS field, finding broad agreement. Furthermore, we extend the source counts at the $\sim$10 $\mu$Jy level to these larger areas ($\sim 20$ deg$^2$) and, using the areal coverage of MIGHTEE we measure the sample variance for differing areas of sky. We find a typical sample variance of 10 –20 per cent for 0.3 and 0.5 deg2 subregions at $S_{1.4} \le 200$$\mu$Jy, which increases at brighter flux densities, given the lower source density and expected higher galaxy bias for these sources.
The cooler past of the intracluster medium in TNG-cluster
Authors: Rohr Eric , Pillepich Annalisa , Nelson Dylan , Ayromlou Mohammadreza , Péroux Céline , Zinger Elad
Published: November 2024

The intracluster medium (ICM) today is comprised largely of hot gas with clouds of cooler gas of unknown origin and lifespan. We analyse the evolution of cool gas (temperatures $\lesssim 10^{4.5}$ K) in the ICM of 352 galaxy clusters from the TNG-Cluster simulations, with present-day mass $\sim 10^{14.3-15.4}\, {\rm M}_\odot$. We follow the main progenitors of these clusters over the past $\sim 13$ billion years (since $z\lesssim 7$) and find that, according to TNG-Cluster, the cool ICM mass increases with redshift at fixed cluster mass, implying that this cooler past of the ICM is due to more than just halo growth. The cool cluster gas at $z\lesssim 0.5$ is mostly located in and around satellite galaxies, while at $z\gtrsim 2$ cool gas can also accrete via filaments from the intergalactic medium. Lower-mass and higher-redshift clusters are more susceptible to cooling. The cool ICM mass correlates with the number of gaseous satellites and inversely with the central supermassive black hole (SMBH) mass. The average number of gaseous satellites decreases since $z=2$, correlating with the decline in the cool ICM mass over cosmic time, suggesting a link between the two. Concurrently, kinetic SMBH feedback shifts the ICM temperature distribution, decreasing the cool ICM mass inside–out. At $z\approx 0.5$, the predicted Mg ii column densities are in the ballpark of recent observations, where satellites and other haloes contribute significantly to the total Mg ii column density. Suggestively, a non-negligible amount of the ICM cool gas forms stars in situ at early times, reaching $\sim 10^{2}\, {\rm M}_\odot \, {\rm ~yr^{-1}}$ and an H $\alpha$ surface brightness of $\sim 10^{-17}\, {\rm ~erg\, s^{-1}\, cm^{-2}\, arcsec^{-2}}$ at $z\approx 2$, detectable with Euclid and JWST.
Ionizing properties of galaxies in JADES for a stellar mass complete sample: resolving the cosmic ionizing photon budget crisis at the Epoch of Reionization
Authors: Simmonds C , Tacchella S , Hainline K , Johnson B D , Puskás D , Robertson B , Baker W M , Bhatawdekar R , Boyett K , Bunker A J , Cargile P A , Carniani S , Chevallard J , Curti M , Curtis-Lake E , Ji Z , Jones G C , Kumari N , Laseter I , Maiolino R , Maseda M V , Rinaldi P , Stoffers A , Übler H , Villanueva N C , Williams C C , Willott C , Witstok J , Zhu Y
Published: November 2024

We use NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) to study the ionizing properties of a sample of 14 652 galaxies at $3 \le z_{\rm {phot}} \le 9$, 90 per cent complete in stellar mass down to log(M$_{\star }$/[M$_{\odot }])\approx 7.5$. Out of the full sample, 1620 of the galaxies have spectroscopic redshift measurements from the literature. We use the spectral energy distribution fitting code Prospector to fit all available photometry and infer galaxy properties. We find a significantly milder evolution of the ionizing photon production efficiency ($\xi _{\rm {ion}}$) with redshift and UV magnitude than previously reported. Interestingly, we observe two distinct populations in $\xi _{\rm {ion}}$, distinguished by their burstiness (given by SFR$_{10}$/SFR$_{100}$). Both populations show the same evolution with z and M$_{\rm {UV}}$, but have a different $\xi _{\rm {ion}}$ normalization. We convolve the more representative $\log (\xi _{\rm {ion}} (z,\text{M}_{\rm {UV}}))$ relations (accounting for $\sim 97$ % of the sample), with luminosity functions from literature, to place constraints on the cosmic ionizing photon budget. By combining our results, we find that one of our models can match the observational constraints from the Ly $\alpha$ forest at $z\lesssim 6$. We conclude that galaxies with M$_{\rm {UV}}$ between $-16$ and $-20$, adopting a reasonable escape fraction, can produce enough ionizing photons to ionize the Universe, without exceeding the required ionizing photon budget.
Clinical application of machine-based deep learning in patients with radiologically presumed adult-type diffuse glioma grades 2 or 3
Authors: Gómez Vecchio Tomás , Neimantaite Alice , Thurin Erik , Furtner Julia , Solheim Ole , Pallud Johan , Berger Mitchel , Widhalm Georg , Bartek Jiri , Häggström Ida , Gu Irene Y H , Jakola Asgeir Store
Published: November 2024

Background

Radiologically presumed diffuse lower-grade glioma (dLGG) are typically non or minimal enhancing tumors, with hyperintensity in T2w-images. The aim of this study was to test the clinical usefulness of deep learning (DL) in IDH mutation prediction in patients with radiologically presumed dLGG.

Methods

Three hundred and fourteen patients were retrospectively recruited from 6 neurosurgical departments in Sweden, Norway, France, Austria, and the United States. Collected data included patients’ age, sex, tumor molecular characteristics (IDH, and 1p19q), and routine preoperative radiological images. A clinical model was built using multivariable logistic regression with the variables age and tumor location. DL models were built using MRI data only, and 4 DL architectures used in glioma research. In the final validation test, the clinical model and the best DL model were scored on an external validation cohort with 155 patients from the Erasmus Glioma Dataset.

Results

The mean age in the recruited and external cohorts was 45.0 (SD 14.3) and 44.3 years (SD 14.6). The cohorts were rather similar, except for sex distribution (53.5% vs 64.5% males, P-value = .03) and IDH status (30.9% vs 12.9% IDH wild-type, P-value <.01). Overall, the area under the curve for the prediction of IDH mutations in the external validation cohort was 0.86, 0.82, and 0.87 for the clinical model, the DL model, and the model combining both models’ probabilities.

Conclusions

In their current state, when these complex models were applied to our clinical scenario, they did not seem to provide a net gain compared to our baseline clinical model.
Expenditure behaviour of pensioners: exploring differences between breadwinners and non-breadwinners
Authors: Muñiz-Fernández Álvaro , Cabanillas-Jiménez Guillermo
Published: November 2024

This article examines the expenditure behaviours of households headed by pensioners who are financially responsible for other household members. By analysing household-level consumption data from the Spanish Family Income Survey from 2018 to 2021, our findings reveal that pensioner-led households with dependents exhibit a 10.2 per cent reduction in total spending compared to pensioner-led households without dependents. Moreover, expenditure on durable and non-durable goods is lower by 10.4 and 8.8 per cent, respectively. We find no heterogeneous effects across income levels or with cohort-fixed effects.
Effectiveness of military spending in reducing the intensity of armed conflict in Sub-Saharan Africa
Authors: AYA Idrissa Aladji
Published: November 2024

This study empirically examines the effectiveness of military spending in reducing the intensity of armed conflict in Sub-Saharan Africa. We use a dynamic probit model, and the results show that military spending reduces the intensity of conflict. It significantly reduces low-intensity conflicts more than high-intensity conflicts. Additionally, the effectiveness of military spending depends on its level and the quality of institutions. Finally, the analysis of transmission channels shows that military spending affects conflict intensity mainly through the channel of military capabilities. We conducted several tests and robustness checks to ensure the validity of our results.
Does gender matter for trade policy? Evidence from contingent protection
Authors: Bros Catherine , Lochard Julie , Upadhayay Neha B
Published: November 2024

Do female heads of government make different policy choices? In this article, we show that gender matters in the definition of international trade policy. We focus on an increasingly used instrument of trade policy, namely contingent protection, that is decided unilaterally by governments. Using panel data covering 149 countries over the period 1995–2019, we provide evidence that female heads of government have been significantly more intensive users of contingent protection. Our results suggest that this gender effect is unlikely to stem from gendered preferences against free trade but rather from an incentive for female heads of government to overcome gender stereotypes in international relations.
Donor-Derived Infections: A Journey From Evidence to Policy
Authors: Beechar Vivek B , Pouch Stephanie M , La Hoz Ricardo M
Published: November 2024

The prevalence of donor-derived Bartonella quintana infection poses an emerging issue in solid organ transplantation. Further studies are needed to validate criteria for donor screening to prevent transmission without negatively affecting organ utilization.
Development and Characterization of a 13-Plex Binding Assay to Detect Shigella Antibodies in Human Samples
Authors: Vezzani G , Mancini F , Raso M M , Giannelli C , Nappini R , Gasperini G , Rappuoli R , Berlanda Scorza F , Iturriza M , Micoli F , Rossi O
Published: November 2024

Shigella is the leading bacterial cause of diarrhea worldwide, with increasing levels of antibiotic resistance. The greatest burden is among children aged <5 years in low- and middle-income countries, and efforts are ongoing to develop vaccines against this pathogen. One of the challenges associated with the development of a vaccine against Shigella is the need for a multivalent vaccine covering the most prevalent Shigella serotypes. Epidemiologic studies to better understand the prevalence of the Shigella serotypes and inform vaccination schedules are very useful, with clinical data showing the ability of vaccines to elicit cross-reactive antibodies. Here, we set up a Luminex-based method able to reproducibly measure antibodies specific to 13 Shigella antigens in human sera. This method will allow the rapid collection of large amounts of data based on the analysis of serum samples from vaccinated individuals or people naturally exposed to Shigella, supporting the development of a vaccine against this disease.
Disrupted nitric oxide homeostasis impacts fertility through multiple processes including protein quality control
Authors: Treffon Patrick , Vierling Elizabeth
Published: November 2024

Plant fertility is fundamental to plant survival and requires the coordinated interaction of developmental pathways and signaling molecules. Nitric oxide (NO) is a small, gaseous signaling molecule that plays crucial roles in plant fertility as well as other developmental processes and stress responses. NO influences biological processes through S-nitrosation, the posttranslational modification of protein cysteines to S-nitrosocysteine (R-SNO). NO homeostasis is controlled by S-nitrosoglutathione reductase (GSNOR), which reduces S-nitrosoglutathione (GSNO), the major form of NO in cells. GSNOR mutants (hot5-2/gsnor1) have defects in female gametophyte development along with elevated levels of reactive nitrogen species and R-SNOs. To better understand the fertility defects in hot5-2, we investigated the in vivo nitrosoproteome of Arabidopsis (Arabidopsis thaliana) floral tissues coupled with quantitative proteomics of pistils. To identify protein-SNOs, we used an organomercury-based method that involves direct reaction with S-nitrosocysteine, enabling specific identification of S-nitrosocysteine–containing peptides and S-nitrosated proteins. We identified 1,102 endogenously S-nitrosated proteins in floral tissues, of which 1,049 were unique to hot5-2. Among the identified proteins, 728 were novel S-nitrosation targets. Notably, specific UDP-glycosyltransferases and argonaute proteins are S-nitrosated in floral tissues and differentially regulated in pistils. We also discovered S-nitrosation of subunits of the 26S proteasome together with increased abundance of proteasomal components and enhanced trypsin-like proteasomal activity in hot5-2 pistils. Our data establish a method for nitrosoprotein detection in plants, expand knowledge of the plant S-nitrosoproteome, and suggest that nitro-oxidative modification and NO homeostasis are critical to protein quality control in reproductive tissues.
Changes in diabetes care and management practices during the COVID-19 pandemic
Authors: Vashist Kushagra , Frediani Jennifer K , Weber Mary Beth , Ali Mohammed K , Narayan K M Venkat , Patel Shivani A
Published: November 2024

Background

We examined changes in diabetes care and management practices before and during the COVID-19 pandemic.

Methods

Population-based data regarding four diabetes-related healthcare engagement and four self-management indicators were obtained from adults with diabetes surveyed in 19 US States and Washington DC through the Behavioral Risk Factor Surveillance System. Using logistic regression, we estimated changes in the prevalence of each indicator, overall and by sociodemographic subgroups in 2019 (before the pandemic) and 2021 (during the pandemic).

Results

Between 2019 and 2021, the prevalence of biannual HbA1c tests reduced by 2.6 percentage points (pp; 95% confidence interval: −4.8, −0.4), from 75.4% to 73.1%, and prevalence of annual eye exams fell by 4.0 pp (−6.2, −2.8), from 72.2% to 68.7%. The composite indicator of engagement with healthcare for diabetes control fell by 3.5 pp (−5.9, −1.1), from 44.9% to 41.9%. Of self-management behaviors, avoidance of smoking increased by 2.0 pp (0.4, 3.6) from 84.7% to 87.1%.

Conclusions

The findings suggest a deterioration of the uptake of evidence-based, preventive health services requiring laboratory services and clinical examination for diabetes control during the pandemic. On the other hand, smoking rates decreased, suggesting potential positive impacts of the pandemic on health behaviors in people with diabetes.
Simulation-based inference of the sky-averaged 21-cm signal from CD-EoR with REACH
Authors: Saxena Anchal , Meerburg P Daniel , Weniger Christoph , Acedo Eloy de Lera , Handley Will
Published: November 2024

The redshifted 21-cm signal from the cosmic dawn and epoch of reionization carries invaluable information about the cosmology and astrophysics of the early Universe. Analysing data from a sky-averaged 21-cm signal experiment requires navigating through an intricate parameter space addressing various factors such as foregrounds, beam uncertainties, ionospheric distortions, and receiver noise for the search of the 21-cm signal. The traditional likelihood-based sampling methods for modelling these effects could become computationally demanding for such complex models, which makes it infeasible to include physically motivated 21-cm signal models in the analysis. Moreover, the inference is driven by the assumed functional form of the likelihood. We demonstrate how simulation-based inference through truncated marginal neural ratio estimation (TMNRE) can naturally handle these issues at a reduced computational cost. We estimate the posterior distribution on our model parameters with TMNRE for simulated mock observations, incorporating beam-weighted foregrounds, physically motivated 21-cm signal, and radiometric noise. We find that maximizing information content by analysing data from multiple time slices and antennas significantly improves the parameter constraints and enhances the exploration of the cosmological signal. We discuss the application of TMNRE for the current configuration of the REACH experiment and demonstrate its potential for exploring new avenues.
Data inaccuracy quantification and uncertainty propagation for bibliometric indicators
Authors: Donner Paul
Published: November 2024

This study introduces an approach to estimate the uncertainty in bibliometric indicator values that is caused by data errors. This approach utilizes Bayesian regression models, estimated from empirical data samples, which are used to predict error-free data. Through direct Monte Carlo simulation—drawing many replicates of predicted data from the estimated regression models for the same input data—probability distributions for indicator values can be obtained which provide the information on their uncertainty due to data errors. It is demonstrated how uncertainty in base quantities, such as the number of publications of certain document types of a unit of analysis and the number of citations of a publication, can be propagated along a measurement model into final indicator values. Synthetic examples are used to illustrate the method and real bibliometric research evaluation data is used to show its application in practice. Though in this contribution we just use two out of a larger number of known bibliometric error categories and therefore can account for only some part of the total uncertainty due to inaccuracies, the latter example reveals that average values of citation impact scores of publications of research groups need to be used very cautiously as they often have large margins of error resulting from data inaccuracies.
How qualitative criteria can improve the assessment process of interdisciplinary research proposals
Authors: Schölvinck Anne-Floor , Uygun-Tunç Duygu , Lakens Daniël , Vaesen Krist , Hessels Laurens K
Published: November 2024

Despite the increasing recognition for the scientific and societal potential of interdisciplinary research, selection committees struggle with the evaluation of interdisciplinary proposals. Interdisciplinary proposals include a wider range of theories and methods, involve a more diverse team, pose a higher level of uncertainty, and their evaluation requires expertise from multiple disciplines. In this study, we investigate the possibility to support the evaluation of interdisciplinary research proposals with measures of interdisciplinary research quality. Based on the literature, we curated a set of qualitative criteria and bibliometric indicators. Subsequently, we examined their feasibility using interviews with interdisciplinary researchers and a re-assessment session of a grant-allocation procedure. In the re-assessment session members of an original evaluation panel assessed four original research proposals again, but now supported with our measures. This study confirmed the potential of qualitative criteria to assess the interdisciplinarity or research proposals. These indicators helped to make explicit what different people mean with interdisciplinary research, which improved the quality of the discussions and decision-making. The utility of bibliometric indicators turned out to be limited, due to technical limitations and concerns about unintended side effects.
A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy
Authors: Shahid Aniqa , Jones Bradley R , Duncan Maggie C , MacLennan Signe , Dapp Michael J , Kuniholm Mark H , Aouizerat Bradley , Archin Nancie M , Gange Stephen , Ofotokun Igho , Fischl Margaret A , Kassaye Seble , Goldstein Harris , Anastos Kathryn , Joy Jeffrey B , Brumme Zabrina L
Published: November 2024

Hypermutated proviruses, which arise in a single Human Immunodeficiency Virus (HIV) replication cycle when host antiviral APOBEC3 proteins introduce extensive guanine to adenine mutations throughout the viral genome, persist in all people living with HIV receiving antiretroviral therapy (ART). However, hypermutated sequences are routinely excluded from phylogenetic trees because their extensive mutations complicate phylogenetic inference, and as a result, we know relatively little about their within-host evolutionary origins and dynamics. Using >1400 longitudinal single-genome-amplified HIV env-gp120 sequences isolated from six women over a median of 18 years of follow-up—including plasma HIV RNA sequences collected over a median of 9 years between seroconversion and ART initiation, and >500 proviruses isolated over a median of 9 years on ART—we evaluated three approaches for masking hypermutation in nucleotide alignments. Our goals were to (i) reconstruct phylogenies that can be used for molecular dating and (ii) phylogenetically infer the integration dates of hypermutated proviruses persisting during ART. Two of the approaches (stripping all positions containing putative APOBEC3 mutations from the alignment or replacing individual putative APOBEC3 mutations in hypermutated sequences with the ambiguous base R) consistently normalized tree topologies, eliminated erroneous clustering of hypermutated proviruses, and brought env-intact and hypermutated proviruses into comparable ranges with respect to multiple tree-based metrics. Importantly, these corrected trees produced integration date estimates for env-intact proviruses that were highly concordant with those from benchmark trees that excluded hypermutated sequences, supporting the use of these corrected trees for molecular dating. Subsequent molecular dating of hypermutated proviruses revealed that these sequences spanned a wide within-host age range, with the oldest ones dating to shortly after infection. This indicates that hypermutated proviruses, like other provirus types, begin to be seeded into the proviral pool immediately following infection and can persist for decades. In two of the six participants, hypermutated proviruses differed from env-intact ones in terms of their age distributions, suggesting that different provirus types decay at heterogeneous rates in some hosts. These simple approaches to reconstruct hypermutated provirus’ evolutionary histories reveal insights into their in vivo origins and longevity toward a more comprehensive understanding of HIV persistence during ART.
Higher-order interactions lead to ‘reluctant’ synchrony breaking
Authors: von der Gracht Sören , Nijholt Eddie , Rink Bob
Published: November 2024

To model dynamical systems on networks with higher-order (non-pairwise) interactions, we recently introduced a new class of ordinary differential equations (ODEs) on hypernetworks. Here, we consider one-parameter synchrony breaking bifurcations in such ODEs. We call a synchrony breaking steady-state branch ‘reluctant’ if it is tangent to a synchrony space, but does not lie inside it. We prove that reluctant synchrony breaking is ubiquitous in hypernetwork systems, by constructing a large class of examples that support it. We also give an explicit formula for the order of tangency to the synchrony space of a reluctant steady-state branch.
Phenylacetic acid metabolism in land plants: novel pathways and metabolites
Authors: Hladík Pavel , Brunoni Federica , Žukauskaitė Asta , Zatloukal Marek , Bělíček Jakub , Kopečný David , Briozzo Pierre , Ferchaud Nathan , Novák Ondřej , Pěnčík Aleš
Published: November 2024

In recent years, substantial progress has been made in exploring auxin conjugation and metabolism, primarily aiming at indole-3-acetic acid (IAA). However, the metabolic regulation of another key auxin, phenylacetic acid (PAA), remains largely uncharacterized. Here, we provide a comprehensive exploration of PAA metabolism in land plants. Through LC-MS screening across multiple plant species and their organs, we identified four previously unreported endogenous PAA metabolites: phenylacetyl-leucine (PAA-Leu), phenylacetyl-phenylalanine (PAA-Phe), phenylacetyl-valine (PAA-Val), and phenylacetyl-glucose (PAA-glc). Enzyme assays, genetic evidence, crystal structures, and docking studies demonstrate that PAA and IAA share core metabolic machinery, revealing a complex regulatory network that maintains auxin homeostasis. Furthermore, our study of PAA conjugation with amino acids and glucose suggests limited compensatory mechanisms within known conjugation pathways, pointing to the existence of alternative metabolic routes in land plants. These insights advance our knowledge of auxin-specific metabolic networks and highlight the unique complexity within plant hormone regulation.
A consensus variant-to-function score to functionally prioritize variants for disease
Authors: Fabiha Tabassum , Evergreen Ivy , Kundu Soumya , Pampari Anusri , Abramov Sergey , Boytsov Alexandr , Strouse Kari , Dura Katherine , Fang Weixiang , Kerner Gaspard , Butts John , Ali Thahmina , Gschwind Andreas , Mualim Kristy S , Moore Jill E , Weng Zhiping , Ulirsch Jacob , Ji Hongkai E , Vierstra Jeff , Reddy Timothy E. , Montgomery Stephen B , Engreitz Jesse , Kundaje Anshul , Tewhey Ryan , Price Alkes , Dey Kushal
Published: November 2024

Identifying and functionally characterizing causal disease variants in genome-wide association studies remains a pressing challenge. Here, we construct a consensus variant-to-function (cV2F) score that assigns a single value to each common single-nucleotide variant in the genome, and helps to predict and characterize causal disease variants. The cV2F score leverages features reflecting variant-level experimentally and computationally predicted function (e.g. allelic imbalance and sequence-based deep learning models) and element-level function (e.g. predicted enhancers), and learns optimal combinations of features by training a gradient boosting model on GWAS fine-mapping results. The cV2F-annotated variants attained an AUPRC of 0.822 at identifying held-out fine-mapped variants. Variants with high cV2F scores are highly enriched for heritability (14.2x, s.e. 0.5) across 66 diseases/traits, are uniquely informative for disease heritability, and are highly predictive of variants implicated by reporter assays; cV2F substantially outperforms previous variant-to-function scores using all of these metrics. GWAS fine-mapping of 110 diseases/traits informed by cV2F identified 14.3% more confidently fine-mapped (PIP > 0.95) variants than non-functionally informed fine-mapping. We further constructed tissue/cell line-specific cV2F scores that prioritize variants based on regulatory potential in specific tissues/cell lines, attaining high heritability enrichment for tissue-related diseases/traits (15.6x, s.e. 2.3) while providing independent information (average correlation of 0.27 with the primary cV2F score). We highlight examples of GWAS loci for which cV2F pinpoints causal variants with high confidence and elucidates their functional role.