bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning emulation of high resolution inundation maps
Authors: Briseid Storrøsten Erlend , Ragu Ramalingam Naveen , Lorito Stefano , Volpe Manuela , Sánchez-Linares Carlos , Løvholt Finn , Gibbons Steven J 
Published: April 2024

SUMMARY
Estimating coastal tsunami impact for early-warning or long-term hazard analysis requires the calculation of inundation metrics such as flow-depth or momentum flux. Both applications require the simulation of large numbers of scenarios to capture both the aleatory variability and the epistemic tsunami uncertainty. A computationally demanding step in simulating inundation is solving the non-linear shallow water (NLSW) equations on meshes with sufficiently high resolution to represent the local elevation accurately enough to capture the physics governing the flow. This computational expense is particularly challenging in the context of Tsunami Early Warning where strict time constraints apply. A machine learning (ML) model that predicts inundation maps from offshore simulation results with acceptable accuracy, trained on an acceptably small training set of full simulations, could replace the computationally expensive NLSW part of the simulations for vast numbers of scenarios and predict inundation rapidly and with reduced computational demands. We consider the application of an encoder–decoder based neural network to predict high-resolution inundation maps based only on more cheaply calculated simulated time-series at a limited number of offshore locations. The network needs to be trained using input offshore time-series and the corresponding inundation maps from previously calculated full simulations. We develop and evaluate the ML model on a comprehensive set of inundation simulations for the coast of eastern Sicily for tens of thousands of subduction earthquake sources in the Mediterranean Sea. We find good performance for this case study even using relatively small training sets (order of hundreds) provided that appropriate choices are made in the specification of model parameters, the specification of the loss function and the selection of training events. The uncertainty in the prediction for any given location decreases with the number of training events that inundate that location, with a good range of flow depths needed for accurate predictions. This means that care is needed to ensure that rarer high-inundation scenarios are well-represented in the training sets. The importance of applying regularization techniques increases as the size of the training sets decreases. The computational gain of the proposed methodology depends on the number of complete simulations needed to train the neural network, ranging between 164 and 4196 scenarios in this study. The cost of training the network is small in comparison with the cost of the numerical simulations and, for an ensemble of around 28 000 scenarios, this represents a 6- to 170-fold reduction in computing costs.
State paid sick leave mandates associated with increased mental health disorder prescriptions among Medicaid enrollees
Authors: Maclean Johanna Catherine , Golberstein Ezra , Stein Bradley 
Published: April 2024

Abstract
The United States does not have a federal paid sick leave policy. As a result, many workers, in particular lower wage workers, cannot take time off work to attend to health and family responsibilities. Fifteen states have adopted or announced paid sick leave mandates that offer employees approximately 7 days of financially protected work time each year. This time can facilitate health care use, including treatment related to mental health disorders, conditions for which treatment is time-consuming. We studied the effect of state paid sick leave mandates on prescription medications dispensed for mental health disorders using the Medicaid State Drug Utilization Database 2011–2022. We found that medications dispensed for mental health disorders increased 6% per year following adoption of a state paid sick leave mandate.
A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A
Authors: Bhattacharya Aniket , Parlanti Paola , Cavallo Luca , Farrow Edward , Spivey Tyler , Renieri Alessandra , Mari Francesca , Manzini M Chiara 
Published: April 2024

Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.
Defensins of the Stable Fly (Stomoxys calcitrans) have Developmental-Specific Regulation and Evolve at Different Rates
Authors: Asgari Danial , Nayduch Dana , Meisel Richard P 
Published: April 2024

Synopsis
Organisms produce antimicrobial peptides (AMPs) either in response to infection (induced) or continuously (constitutively) to combat microbes encountered during normal trophic activities and/or through pathogenic infections. The expression of AMPs is tightly regulated, often with specificity to particular tissues or developmental stages. As a result, AMPs face varying selective pressures based on the microbes the organism’s tissue or developmental stage encounters. Here, we analyzed the evolution and developmental-specific expression of Defensins, which are ancient AMPs in insects, in the stable fly (Stomoxys calcitrans). Stable fly larvae inhibit microbe-rich environments, whereas adult flies, as blood-feeders, experience comparatively fewer encounters with diverse microbial communities. Using existing RNA-seq datasets, we identified six Defensins that were only expressed in larvae (larval Defensins) and five that were not expressed in larvae (non-larval Defensins). Each of the non-larval Defensins was expressed in at least one adult tissue sample. Half of the larval Defensins were induced by mating or feeding in adults, and all three of the induced Defensins were located downstream of canonical binding sites for an Imd transcription factor involved in the highly conserved NF-κB signaling that regulates induction of AMPs. The larval and non-larval Defensins were located in distinct genomic regions, and the amino acid sequences of the larval Defensins formed a monophyletic clade. There were more amino acid substitutions across non-larval Defensins, with multiple genes losing a highly conserved furin cleavage site thought to be required for the removal of the amino terminus from the mature Defensin domain. However, larval Defensins had a higher proportion of radical amino acid substitutions, altering amino acid size and polarity. Our results reveal insights into the developmental stage-specific regulation of AMPs, and they suggest different regulatory regimes impose unique selection pressures on AMPs, possibly as a result of variation in exposure to microbial communities across development.
A pre–post study of pharmacist-led medication reviews within a hospital-based residential aged care support service
Authors: Chan June , Bolitho Richard , Hay Karen , Yong Faith 
Published: April 2024

Abstract

Background
Hospital-based residential aged-care support service teams typically consist of doctors and nurses who provide hospital substitutive care to aged-care residents. There is limited literature evaluating the pharmacist’s role in such aged-care support teams.

Objective
To analyse the effect of residential aged-care support service pharmacist-led medication reviews on polypharmacy, drug burden index, potentially inappropriate medications, and potential prescribing omissions for aged-care residents.

Methods
Residents referred to a residential aged-care support service pharmacist for medication review over a 12-month period were included. The pharmacist communicated medication-related problems and recommendations to the resident’s general practitioner and residential aged-care support service medical practitioner. Residents’ medication histories were obtained at baseline and one-month postintervention. The number of medications and their associated drug burden indices were compared using paired t-tests; potentially inappropriate medications and potential prescribing omissions were compared using Wilcoxon’s signed rank test.

Key findings
Of 175 residents (mean age 84 years) referred for pharmacist-led medication review, 146 had postintervention evaluation after one-month (median 29 days). Mean number of medications reduced from 12.47 at baseline to 11.84 postintervention (mean difference (95% CI): 0.63(0.33–0.93), P &lt; .001). Mean drug burden index score reduced from 1.54 at baseline to 1.37 postintervention (mean difference (95% CI): 0.17(0.10–0.24), P &lt; .001). More residents experienced a decrease in inappropriate medications (median (IQR) pre: 2(1–3), post: 1(0–2), P &lt; .001) and prescribing omissions (median (IQR) pre: 0(0–1), post: 0(0–0), P = .003) compared with those that had an increase.

Conclusions
Medication reviews performed by pharmacists embedded in hospital-based residential aged-care support services may improve medication prescribing. Further research into such preventative health service models is required.
Relative controllability for conformable impulsive delay differential equations
Authors: Luo Danfeng , Huang Jizhao 
Published: April 2024

Abstract
In this paper, we mainly study a class of conformable impulsive delay differential equations (CIDDEs). We first define a conformable impulsive delayed matrix function, and construct an explicit solution for linear CIDDEs by virtue of variation of constants method. Subsequently, based on impulsive delayed Grammian matrix, we study the relative controllability for the addressed linear equations. Moreover, with the help of Krasnoselskii’s fixed point theorem, relative controllability for the considered semilinear equations is proposed. Finally, two examples with numerical simulations are given to illustrate the main results.
Influence of vasoactive intestinal polypeptide on growth performance, nutrient digestibility, nitrogen balance, and digestive enzyme activity in lambs
Authors: Mia Golam K , Hawley Emma , Yusuf Mustapha , Dorsam Glenn , Swanson Kendall C 
Published: April 2024

Abstract
This study evaluated if vasoactive intestinal polypeptide (VIP) influences growth performance, nutrient digestibility, nitrogen balance, and digestive enzyme activity. Sixteen wether lambs (69.6 ± 1.9 kg) were housed in individual pens, adapted to a corn grain-based diet, and randomly assigned to 2 treatment groups. Lambs were injected intraperitoneally every other day for 28 d with saline (0.9% NaCl) containing no VIP (n = 8; control) or containing VIP (n = 8; 1.3 nmol/kg body weight [BW]). All lambs were transferred to individual metabolic crates for the final 7 d of the experiment to measure nitrogen balance and nutrient digestibility. At the end of the treatment period, lambs were slaughtered, and pancreatic tissue, small intestinal tissue, and rumen fluid were collected for protein, digestive enzymes, ruminal pH, and volatile fatty acid (VFA) analyses. Lambs treated with VIP had greater final BW, average daily gain, and gain:feed (P = 0.01, 0.05, 0.03, respectively). No differences between treatment groups were observed (P ≥ 0.25) for nutrient intake, digestibility, nitrogen retention, ruminal pH, and VFA concentrations. Moreover, VIP treatment did not influence (P ≥ 0.19) plasma glucose, urea N, and insulin concentrations. Treatment with VIP increased (P = 0.03) relative cecum weight (g/kg BW) and decreased (P = 0.05) relative brain weight. Pancreatic and intestinal digestive enzyme activities, except for duodenal maltase (P = 0.02), were not influenced (P ≥ 0.09) by VIP treatment. These data suggest that the administration of VIP may have potential to improve average daily gain and gain:feed in lambs fed grain-based diets.
Dopamine signalling in pancreatic islet cells and role in adaptations to metabolic stress
Authors: Sridhar Ananyaa , Flatt Peter R , Draper Matthew , Tarasov Andrei I , Moffett R Charlotte , Irwin Nigel , Khan Dawood 
Published: April 2024

Abstract

Objectives
Dopamine and related receptors are evidenced in pancreatic endocrine tissue, but the impact on islet β-cell stimulus-secretion as well as (patho)physiological role are unclear.

Methods
The present study has evaluated islet cell signalling pathways and biological effects of dopamine, as well as alterations of islet dopamine in rodent models of diabetes of different aetiology.

Key findings
The dopamine precursor l-DOPA partially impaired glucose tolerance in mice and attenuated glucose-, exendin-4, and alanine-induced insulin secretion. The latter effect was echoed by the attenuation of glucose-induced [Ca2+]i dynamics and elevation of ATP levels in individual mouse islet cells. l-DOPA significantly decreased β-cell proliferation rates, acting predominantly via the D2 receptor, which was most abundant at the mRNA level. The administration of streptozotocin (STZ) or high-fat diet (HFD) in mice significantly elevated numbers of dopamine-positive islet cells, with HFD also increasing colocalization of dopamine with insulin. At the same time, colocalization of dopamine with glucagon was increased in STZ-treated and pregnant mice, but unaffected by HFD.

Conclusion
These findings highlight a role for dopamine receptor signalling in islet cell biology adaptations to various forms of metabolic stress.
Sexy ways: approaches to studying plant sex chromosomes
Authors: Hobza Roman , Bačovský Václav , Čegan Radim , Horáková Lucie , Hubinský Marcel , Janíček Tomáš , Janoušek Bohuslav , Jedlička Pavel , Kružlicová Jana , Kubát Zdeněk , Rodríguez Lorenzo José Luis , Novotná Pavla , Hudzieczek Vojtěch 
Published: April 2024

Abstract
Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the specific genetic and epigenetic mechanisms responsible for shaping distinct sexes in plants. While the fundamental methods of molecular biology and genomics are generally employed for the analysis of sex chromosomes, it is often necessary to modify classical procedures not only to simplify and expedite analyses but sometimes to make them possible at all. In this review, we demonstrate how, at the level of structural and functional genetics, cytogenetics, and bioinformatics, it is essential to adapt established procedures for sex chromosome analysis.
Constraining the global composition of D/H and 18O/16O in Martian water using SOFIA/EXES
Authors: Alday J , Aoki S , DeWitt C , Montmessin F , Holmes J A , Patel M R , Mason J P , Encrenaz T , Richter M J , Irwin P G J , Daerden F , Terada N , Nakagawa H 
Published: April 2024

ABSTRACT
Isotopic ratios in water vapour carry important information about the water reservoir on Mars. Localized variations in these ratios can inform us about the water cycle and surface–atmosphere exchanges. On the other hand, the global isotopic composition of the atmosphere carries the imprints of the long-term fractionation, providing crucial information about the early water reservoir and its evolution throughout history. Here, we report the analysis of measurements of the D/H and 18O/16O isotopic ratios in water vapour in different seasons (LS = 15○, 127○, 272○, and 305○) made with the Echelon-Cross-Echelle Spectrograph (EXES) aboard the Stratospheric Observatory for Infrared Astronomy (SOFIA). These measurements, free of telluric absorption, provide a unique tool for constraining the global isotopic composition of Martian water vapour. We find the maximum planetary D/H ratio in our observations during the northern summer (D/H = 5.2 ± 0.2 with respect to the Vienna Standard Mean Ocean Water, VSMOW) and to exhibit relatively small variations throughout the year (D/H = 5.0 ± 0.2 and 4.3 ± 0.4 VSMOW during the northern winter and spring, respectively), which are to first order consistent though noticeably larger than the expectations from condensation-induced fractionation. Our measurements reveal the annually averaged isotopic composition of water vapour to be consistent with D/H = 5.0 ± 0.2 and 18O/16O = 1.09 ± 0.08 VSMOW. In addition, based on a comparison between the SOFIA/EXES measurements and the predictions from a Global Climate Model, we estimate the D/H in the northern polar ice cap to be $\sim\!{5}~{{\ \rm per\ cent}}$ larger than that in the atmospheric reservoir (D/Hice = 5.3 ± 0.3 VSMOW).
The impact of cosmic rays on the interstellar medium and galactic outflows of Milky Way analogues
Authors: Rodríguez Montero Francisco , Martin-Alvarez Sergio , Slyz Adrianne , Devriendt Julien , Dubois Yohan , Sijacki Debora 
Published: April 2024

ABSTRACT
During the last decade, cosmological simulations have managed to reproduce realistic and morphologically diverse galaxies, spanning the Hubble sequence. Central to this success was a phenomenological calibration of the few included feedback processes, while glossing over higher complexity baryonic physics. This approach diminishes the predictive power of such simulations, preventing to further our understanding of galaxy formation. To tackle this fundamental issue, we investigate the impact of cosmic rays (CRs) and magnetic fields on the interstellar medium and the launching of outflows in a cosmological zoom-in simulation of a Milky Way-like galaxy. We find that including CRs decreases the stellar mass of the galaxy by a factor of 10 at high redshift and ∼4 at cosmic noon, leading to a stellar mass to halo mass ratio in good agreement with abundance matching models. Such decrease is caused by two effects: (i) a reduction of cold, high-density, star-forming gas, and (ii) a larger fraction of supernova (SN) events exploding at lower densities, where they have a higher impact. SN-injected CRs produce enhanced, multiphase galactic outflows, which are accelerated by CR pressure gradients in the circumgalactic medium of the galaxy. While the mass budget of these outflows is dominated by the warm ionized gas, warm neutral and cold gas phases contribute significantly at high redshifts. Importantly, our work shows that future JWST observations of galaxies and their multiphase outflows across cosmic time have the ability to constrain the role of CRs in regulating star formation.
Iterative removal of sources to model the turbulent electromotive force
Authors: Bendre Abhijit B , Schober Jennifer , Dhang Prasun , Subramanian Kandaswamy 
Published: April 2024

ABSTRACTWe describe a novel method to compute the components of dynamo tensors from direct magnetohydrodynamic (MHD) simulations. Our method relies upon an extension and generalization of the standard Högbom CLEAN algorithm widely used in radio astronomy to systematically remove the impact of the strongest beams on to the corresponding image. This generalization, called the Iterative Removal of Sources (IROS) method, has been adopted here to model the turbulent electromotive force (EMF) in terms of the mean magnetic fields and currents. Analogous to the CLEAN algorithm, IROS treats the time series of the mean magnetic field and current as beams that convolve with the dynamo coefficients which are treated as (clean) images to produce the EMF time series (the dirty image). We apply this method to MHD simulations of galactic dynamos, to which we have previously employed other methods of computing dynamo coefficients such as the test-field method, the regression method, as well as local and non-local versions of the singular value decomposition (SVD) method. We show that our new method reliably recovers the dynamo coefficients from the MHD simulations. It also allows priors on the dynamo coefficients to be incorporated easily during the inversion, unlike in earlier methods. Moreover, using synthetic data, we demonstrate that it may serve as a viable post-processing tool in determining the dynamo coefficients, even when the power of additive noise to the EMF is twice as much the actual EMF.
Mass reconstruction and noise reduction with cosmic-web environments
Authors: Fang Feng , Cai Yan-Chuan , Li Zhuoyang , Yue Shiyu , Zhu Weishan , Feng Longlong 
Published: April 2024

ABSTRACT
The clustering of galaxies and their connections to their initial conditions is a major means by which we learn about cosmology. However, the stochasticity between galaxies and their underlying matter field is a major limitation for precise measurements of galaxy clustering. Efforts have been made with an optimal weighting scheme to reduce this stochasticity using the mass-dependent clustering of dark matter haloes. Here, we show that this is not optimal. We demonstrate that the cosmic-web environments (voids, sheets, filaments, and knots) of haloes, when combined linearly with the linear bias, provide extra information for reducing stochasticity in terms of two-point statistics. Using the environmental information alone can increase the signal-to-noise of clustering by a factor of 3 better than the white-noise level at the scales of the baryon acoustic oscillations. The information about the environment and halo mass are complementary. Their combination increases the signal-to-noise by another factor of 2-3. The information about the cosmic web correlates with other properties of haloes, including halo concentrations and tidal forces – all are related to the assembly bias of haloes.