bluuebunny/crossref_metadata_2025 huggingface dataset:
Collective movement of schooling fish reduces locomotor cost in turbulence
Authors: Zhang Yangfan , Ko Hungtang , Calicchia Michael , Ni Rui , Lauder George V.
Published: January 2024

The ecological and evolutionary benefits of collective behaviours are rooted in the physical principles and physiological mechanisms underpinning animal locomotion. We propose a turbulence sheltering hypothesis that collective movements of fish schools in turbulent flow can reduce the total energetic cost of locomotion by shielding individuals from the perturbation of chaotic turbulent eddies. We test this hypothesis by quantifying energetics and kinematics in schools of giant danio (Devario aequipinnatus) compared to solitary individuals swimming under control and turbulent conditions over a wide speed range. We discovered that, when swimming at high speeds and high turbulence levels, fish schools reduced their total energy expenditure (TEE, both aerobic and anaerobic energy) by 63–79% compared to solitary fish. Solitary individuals spend ∼25% more kinematic effort (tail beat amplitude*frequency) to swim in turbulence at higher speeds than in control conditions. However, fish schools swimming in turbulence reduced their three-dimensional group volume by 41–68% (at higher speeds) and did not alter their kinematic effort compared to control conditions. This substantial energy saving highlighted a ∼261% higher TEE when fish swimming alone in turbulence are compared to swimming in a school. Schooling behaviour could mitigate turbulent disturbances by sheltering fish within schools from the eddies of sufficient kinetic energy that can disrupt the locomotor gaits. Providing a more desirable internal hydrodynamic environment could be one of the ecological drivers underlying collective behaviours in a dense fluid environment.

One-Sentence Summary

The collective movement of fish schools substantially reduces the energetic cost of locomotion in turbulence compared to that of swimming alone.
Programmable DNA shell scaffolds for directional membrane budding
Authors: Dietz Hendrik , Pinner Michael T
Published: January 2024

In the pursuit of replicating biological processes at the nanoscale, controlling cellular membrane dynamics has emerged as a key area of interest. Here, we report a system mimicking virus assembly to control directional membrane budding. We employ three-dimensional DNA origami techniques to construct cholesterol-modified triangles that self-assemble into polyhedral shells on lipid vesicles, resulting in gradual curvature induction, bud formation and spontaneous neck scission. Strategic positioning of cholesterols on the triangle surface provides control over the directionality of bud growth and yields daughter vesicles with DNA endo- or exoskeletons reminiscent of clathrin-coated vesicles. This process occurs with rapid kinetics and across various lipid compositions. When combined into a two-step process, nested bivesicular objects with DNA shells encapsulated between lipid vesicles could be produced. Our work replicates key aspects of natural endocytic and exocytic pathways, opening new avenues for exploring membrane mechanics and applications in targeted drug delivery and synthetic biology.
Parasite contingency loci and the evolution of host specificity: Simple sequence repeats mediateBartonellaadaptation to a wild rodent host
Authors: Rodríguez-Pastor Ruth , Knossow Nadav , Shahar Naama , Hasik Adam Z. , Deatherage Daniel E. , Gutiérrez Ricardo , Harrus Shimon , Zaman Luis , Lenski Richard E. , Barrick Jeffrey E. , Hawlena Hadas
Published: January 2024

Parasites can adapt to better exploit their hosts on many scales, ranging from within an infection of a single individual to series of infections spanning multiple host species. However, little is known about how the genomes of parasites in natural communities evolve when they face diverse hosts. We investigated howBartonellabacteria that circulate in rodent communities in the dunes of the Negev Desert in Israel adapt to different species of rodent hosts. We propagated 15Bartonellapopulations through infections of either a single host species (Gerbillus andersoniorGerbillus pyramidum) or alternating between the two. After 20 rodent passages, strains withde novomutations replaced the ancestor in most populations. Mutations in two mononucleotide simple sequence repeats (SSRs) that caused frameshifts in the same adhesin gene dominated the evolutionary dynamics. They appeared exclusively in populations that encounteredG. andersoniand altered the dynamics of infections of this host. Similar SSRs in other genes are conserved and exhibit ON/OFF variation inBartonellaisolates from the Negev Desert dunes. Our results suggest that SSR-based contingency loci could be important not only for rapidly and reversibly generating antigenic variation to escape immune responses but that they may also mediate the evolution of host specificity.
M2WISH: an easy and efficient protocol for whole-mount mRNAin situhybridization that allows 3D cell resolution of gene expression inArabidopsis thaliana
Authors: Chelysheva Liudmila , Morin Halima , Biot Eric , Nicolas Antoine , Rech Philippe , da Costa Marco , Barel Lisa , Laufs Patrick , Palauqui Jean-Christophe
Published: January 2024

Gene expression analysis is essential for understanding the mechanisms involved in plant development. Here, we developed M2WISH, a protocol based onMicroWave treatment forWholemount mRNA InSituHybridization in Arabidopsis. By permeabilizing tissues without damaging cellular organisation this protocol results in high and homogeneous hybridization yields that enables systematic analysis of gene expression dynamics. Moreover, when combined with cellular histochemical staining, M2WISH provides a cellular resolution of gene expression on roots, aerial meristems, leaves and embryos in the seed. We applied M2WISH to study the spatial dynamics ofWUSCHEL(WUS) andCLAVATA3(CLV3) expression duringin vitromeristematic conversion of roots into shoot apical meristems. Thus, we showed that shoot apical meristems could arise from two different types of root structures that differed by theirCLV3gene expression patterns. We constructed 3D cellular representations ofWUSandCLV3gene co-expression pattern, and stressed the variability inherent to meristem conversion. Thus, this protocol generates a large amount of data on the localization of gene expression, which can be used to model complex systems.
Geographic variation in resistance of the invasiveDrosophila suzukiito parasitism by the biological control agent,Ganaspis brasiliensis
Authors: Istas Oscar , Szűcs Marianna
Published: January 2024

Host-parasitoid interactions are often tied in coevolutionary arms races where parasitoids continuously have to evolve increased virulence as hosts evolve increased resistance. Invasion theories predict that when a host is introduced to a novel region without its coevolved natural enemies, they will evolve lower defenses. Resistance may also differ geographically and temporally due to abiotic and biotic factors. We investigated spatial, temporal and host plant related differences in resistance of the invasiveD. suzukiiin seven geographically distinct populations in Michigan and of one population from Oregon against a coevolved parasitoid,Ganaspis brasiliensis.Encapsulation rates (resistance) ofG. brasiliensiseggs byD. suzukiireached 39% in August and 48% in September regionally. These relatively high levels of resistance in North America contrast with expectations and may be due to the low levels of competitionD. suzukiiexperiences in the invaded range. Encapsulation rates ofD. suzukiidiffered regionally and temporally but not between fruit types. The northernmost site with the lowest encapsulation rate had the highest rate of parasitism suggesting that parasitoids may be able to detect the defensive capacities of their hosts and adjust attack rates accordingly. The lowest encapsulation rates at the northernmost and thus overall coldest site indicate a negative effect of temperature on resistance. However, temporal differences in resistance from August to September were not consistent among sites. These results indicate that there can be regional and temporal variation in the outcome of host-parasitoid interactions betweenD. suzukiiandG. brasiliensis. This may influence the efficacy and biocontrol potential ofG. brasiliensisthat has been recently approved for field releases againstD. suzukiiin North America.
Patient Subtyping Analysis of Baseline Multi-omic Data Reveals Distinct Pre-immune States Predictive of Vaccination Responses
Authors: Bayrak Cigdem Sevim , Forst Christian , Jones Drew R. , Gresham David , Pushalkar Smruti , Wu Shaohuan , Vogel Christine , Mahal Lara , Ghedin Elodie , Ross Ted , García-Sastre Adolfo , Zhang Bin
Published: January 2024

Understanding the molecular mechanisms that underpin diverse vaccination responses is a critical step toward developing efficient vaccines. Molecular subtyping approaches can offer valuable insights into the heterogeneous nature of responses and aid in the design of more effective vaccines. In order to explore the molecular signatures associated with the vaccine response, we analyzed baseline transcriptomics data from paired samples of whole blood, proteomics and glycomics data from serum, and metabolomics data from urine, obtained from influenza vaccine recipients (2019-2020 season) prior to vaccination. After integrating the data using a network-based model, we performed a subtyping analysis. The integration of multiple data modalities from 62 samples resulted in five baseline molecular subtypes with distinct molecular signatures. These baseline subtypes differed in the expression of pre-existing adaptive or innate immunity signatures, which were linked to significant variation across subtypes in baseline immunoglobulin A (IgA) and hemagglutination inhibition (HAI) titer levels. It is worth noting that these significant differences persisted through day 28 post-vaccination, indicating the effect of initial immune state on vaccination response. These findings highlight the significance of interpersonal variation in baseline immune status as a crucial factor in determining vaccine response and efficacy. Ultimately, incorporating molecular profiling could enable personalized vaccine optimization.
Current limitations in predicting mRNA translation with deep learning models
Authors: Schlusser Niels , González Asier , Pandey Muskan , Zavolan Mihaela
Published: January 2024

Background

The design of nucleotide sequences with defined properties is long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mRNA vaccines. The rate of protein synthesis depends on the 5’ untranslated region (5’UTR) of the mRNAs, and recently, deep learning models were proposed to predict the translation output of mRNAs from the 5’UTR sequence. At the same time, large data sets of endogenous and reporter mRNA translation have become available.

Results

In this study we use complementary data obtained in two different cell types to assess the accuracy and generality of currently available models of translation. We find that while performing well on the data sets on which they were trained, deep learning models do not generalize well to other data sets, in particular of endogenous mRNAs, which differ in many properties from reporter constructs.

Conclusions

These differences limit the ability of deep learning models to uncover mechanisms of translation control and to predict the impact of genetic variation. We suggest directions that combine high-throughput measurements and machine learning to unravel mechanisms of translation control and improve construct design.
Monitoring transcription of miR-15a and miR-124 in mesenchymal stem cells from adipose tissue origin differentiated into pancreatic beta-cells
Authors: Rajabi Hadi
Published: January 2024

MicroRNAs are small noncoding pieces of nucleic acid with the potential to control mRNA translation. These sequences participate in the regulation of cell dynamic growth and differentiation. In this study, the expression of miR-15a and miR-124 was monitored in adipose-derived tissue stem cells committed to pancreatic β cellsin vitroover 28 days. In the current experiment, adipose-derived mesenchymal stem cells were incubated in an induction medium to accelerate differentiation toward endocrine pancreatic lineage for 28 days with a three-stage protocol. To confirm the efficient trans-differentiation of stem cells into pancreatic β cells, we performed a Dithizone staining, a zinc chelating agent, and pancreas-specific hormones (insulin and C peptide) examination via electrochemiluminescence. Real-time PCR analysis was done to assess the expression of miR-15a and miR-124. Dithizone staining confirmed a successful orientation of adipose-derived mesenchymal stem cells into pancreatic β cells indicating with red to strong brown appearance compared to negative control stem cells, indicating insulin positivity in differentiating cells. These effects were prominent by time and reached maximum level at day 28. Concurrently, the expression of both miR-15a and miR-124 was induced and reached a peak expression level at the end stage of the experiment compared to the stem cells (p<0.05).

Conclusion

The dynamic of distinct miRNAs, in particular, miR-15a and miR-124 was induced during pancreatic β cells derivation of adipose-derived mesenchymal stem cells.
Conjugation related costs have reduced impact onin silicoplasmid persistence
Authors: Newbury Arthur
Published: January 2024

Due to the important role they play in the antimicrobial resistance (AMR) crisis and in microbial evolution in general, a great deal of empirical and theoretical work is currently underway, trying to understand plasmid ecology. One of the key questions is how these often costly genetic elements persist in host populations. Here I show that when modelling plasmid population dynamics, it is not sufficient to treat them as always costly (or beneficial). I argue that conjugation related costs may be more important to plasmids in nature than they are in benign laboratory settings. Furthermore, I show that these conjugation related costs can be very severe and still not lead to extinction of a plasmid from a host population.
Blood Cholesterol and Triglycerides Associate with Right Ventricular Function in Pulmonary Hypertension
Authors: Fakhry Battoul , Peterson Laura , Comhair Suzy A.A. , Sharp Jacqueline , Park Margaret M. , Tang W.H. Wilson , Neumann Donald R. , DiFilippo Frank P. , Farha Samar , Erzurum Serpil C. , Mulya Anny
Published: January 2024

Background

Blood lipids are dysregulated in pulmonary hypertension (PH). Lower high-density lipoproteins cholesterol (HDL-C) and low-density lipoproteins cholesterol (LDL-C) are associated with disease severity and death in PH. Right ventricle (RV) dysfunction and failure are the major determinants of morbidity and mortality in PH. This study aims to test the hypothesis that dyslipidemia is associated with RV dysfunction in PH.

Methods

We enrolled healthy control subjects (n=12) and individuals with PH (n=30) (age: 18-65 years old). Clinical characteristics, echocardiogram, 2-[18F] fluoro-2-deoxy-D-glucose positron emission tomography (PET) scan, blood lipids, including total cholesterol (TC), triglycerides (TG), lipoproteins (LDL-C and HDL-C), and N-terminal pro-B type Natriuretic Peptide (NT-proBNP) were determined.

Results

Individuals with PH had lower HDL-C [PH, 41±12; control, 56±16 mg/dL,p<0.01] and higher TG to HDL-C ratio [PH, 3.6±3.1; control, 2.2±2.2, p<0.01] as compared to controls. TC, TG, and LDL-C were similar between PH and controls. Lower TC and TG were associated with worse RV function measured by RV strain (R=–0.43,p=0.02 andR=–0.37,p=0.05 respectively), RV fractional area change (R=0.51,p<0.01 andR=0.48,p<0.01 respectively), RV end-systolic area (R=–0.63,p<0.001 andR=–0.48,p<0.01 respectively), RV end-diastolic area:R=–0.58,p<0.001 andR=–0.41,p=0.03 respectively), and RV glucose uptake by PET (R=–0.46,p=0.01 andR=–0.30,p=0.10 respectively). NT-proBNP was negatively correlated with TC (R=–0.61,p=0.01) and TG (R=–0.62,p<0.02) in PH.

Conclusion

These findings confirm dyslipidemia is associated with worse right ventricular function in PH.
Effect of Paxlovid Treatment During Acute COVID-19 on Long COVID Onset: An EHR-Based Target Trial Emulation from the N3C and RECOVER Consortia
Authors: Preiss Alexander , Bhatia Abhishek , Aragon Leyna V. , Baratta John M. , Baskaran Monika , Blancero Frank , Brannock M. Daniel , Chew Robert F. , Díaz Iván , Fitzgerald Megan , Kelly Elizabeth P. , Zhou Andrea , Carton Thomas W. , Chute Christopher G. , Haendel Melissa , Moffitt Richard , Pfaff Emily
Published: January 2024

Background

Preventing and treating post-acute sequelae of SARS-CoV-2 infection (PASC), commonly known as Long COVID, has become a public health priority. Researchers have begun to explore whether Paxlovid treatment in the acute phase of COVID-19 could help prevent the onset of PASC.

Methods and Findings

We used electronic health records from the National Covid Cohort Collaborative (N3C) to define a cohort of 426,352 patients who had COVID-19 since April 1, 2022, and were eligible for Paxlovid treatment due to risk for progression to severe COVID-19. We used the target trial emulation (TTE) framework to estimate the effect of Paxlovid treatment on PASC incidence. We estimated overall PASC incidence using a computable phenotype. We also measured the onset of novel cognitive, fatigue, and respiratory symptoms in the post-acute period. Paxlovid treatment did not have a significant effect on overall PASC incidence (relative risk [RR] = 0.98, 95% confidence interval [CI] 0.95-1.01). However, it had a protective effect on cognitive (RR = 0.90, 95% CI 0.84-0.96) and fatigue (RR = 0.95, 95% CI 0.91-0.98) symptom clusters.

Conclusions

In this cohort, Paxlovid had a weaker preventative effect on PASC than in prior observational studies. Differing effects by symptom cluster suggest that the etiology of cognitive and fatigue symptoms may be more closely related to viral load than that of respiratory symptoms. Ongoing clinical trials will help clarify Paxlovid’s overall effect on PASC, and future research should explore potential heterogeneous treatment effects across PASC subphenotypes.
Prognostic significance of circulating exosomal PD-L1 in various malignant tumors: A systematic review and meta-analysis
Authors: Li Wentao , Cui Qian , Ge Ting , Wang Shuangcui , Wang Dong , He Guixin , Yu Jianchun
Published: January 2024

Although the prognostic significance of exosomal PD-L1 (exoPD-L1) has been previously reported, its value is still controversial. For the first time, we conducted a meta-analysis to systematically evaluate the prognostic value of exoPD-L1 in various types of cancer. The pooled hazard ratio (HR) and 95% confidence interval (CI) in these studies were used to explore the relationship between these indexes and overall survival (OS), recurrence-free survival (RFS), and progression-free survival (PFS). Utilizing the NewcastleLJOttawa Scale (NOS), the quality of the listed studies was assessed. Heterogeneity was explored by subgroup analyses. Begg’s and Egger’s tests assessed publication bias. This meta-analysis included 11 trials involving 964 cancer cases. The pooled results indicate that high-level pre-treatment exoPD-L1 in circulation was associated with worse OS (HR = 2.10, 95% CI 1.51–2.91, P < 0.001), RFS (HR = 1.67, 95% CI 1.18–2.37, P < 0.01) and PFS (HR = 3.49, 95% CI 2.60–4.68, P < 0.001) compared to those with low-level pre-treatment exoPD-L1. However, high fold changes in circulating exoPD-L1 after receiving immune checkpoint inhibitors (ICIs) were correlated with significantly superior OS (HR = 0.19, 95% CI 0.10–0.38, P < 0.001) and PFS (HR = 0.35, 95% CI 0.23–0.52, P < 0.001). Through this meta-analysis, we found that pre-treatment with high levels of exoPD-L1 is associated with a poor prognosis. However, a high fold change in circulating exoPD-L1 following immunotherapy was correlated with a superior prognosis. ExoPD-L1 may have important clinical significance for assessing the prognosis of cancer patients.
Elucidating the Role of Primary and Secondary Sphere Zn2+Ligands in the Cyanobacterial CO2Uptake Complex NDH-14: The Essentiality of Arginine in Zinc Coordination and Catalysis
Authors: Walker Ross M. , Zhang Minquan , Burnap Robert L.
Published: January 2024

The uptake of inorganic carbon in cyanobacteria is facilitated by an energetically intensive CO2-concentrating mechanism (CCM). Specialized Type-1 NDH complexes function as a part of this mechanism to couple photosynthetic energy generated by redox reactions of the electron transport chain (ETC) to CO2hydration. This active site of CO2hydration incorporates an arginine side chain as a Zn ligand, diverging from the typical histidine and/or cysteine residues found in standard CAs. In this study, we focused on mutating three amino acids in the active site of the constitutively expressed NDH-14CO2hydration complex inSynechococcussp. PCC7942: CupB-R91, which acts as a zinc ligand, and CupB-E95 and CupB-H89, both of which are in close interaction with the arginine ligand. These mutations aimed to explore how they affect the unusual metal ligation by CupB-R91 and potentially influence the unusual catalytic process. The most severe defects in activity among the targeted residues are due to a substitution of CupB-R91 and the ionically interacting E95 since both proved essential for the structural stability of the CupB protein. On the other hand, CupB-H89 mutations show a range of catalytic phenotypes indicating a role of this residue in the catalytic mechanism of CO2-hydration, but no evidence was obtained for aberrant carbonic anhydrase activity that would have indicated uncoupling of the CO2-hydration activity from proton pumping. The results are discussed in terms of possible alternative CO2hydration mechanisms.
Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications
Authors: Ctortecka Claudia , Clark Natalie M. , Boyle Brian , Seth Anjali , Mani D. R. , Udeshi Namrata D. , Carr Steven A.
Published: January 2024

Mass spectrometry (MS)-based single-cell proteomics (SCP) has gained massive attention as a viable complement to other single cell approaches. The rapid technological and computational advances in the field have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell at reasonable proteome depth to characterize biological phenomena remains a challenge. To address some of those limitations we present a combination of fully automated single cell sample preparation utilizing a dedicated chip within the picolitre dispensing robot, the cellenONE. The proteoCHIP EVO 96 can be directly interfaced with the Evosep One chromatographic system for in-line desalting and highly reproducible separation with a throughput of 80 samples per day. This, in combination with the Bruker timsTOF MS instruments, demonstrates double the identifications without manual sample handling. Moreover, relative to standard high-performance liquid chromatography, the Evosep One separation provides further 2-fold improvement in protein identifications. The implementation of the newest generation timsTOF Ultra with our proteoCHIP EVO 96-based sample preparation workflow reproducibly identifies up to 4,000 proteins per single HEK-293T without a carrier or match-between runs. Our current SCP depth spans over 4 orders of magnitude and identifies over 50 biologically relevant ubiquitin ligases. We complement our highly reproducible single-cell proteomics workflow to profile hundreds of lipopolysaccharide (LPS)-perturbed THP-1 cells and identified key regulatory proteins involved in interleukin and interferon signaling. This study demonstrates that the proteoCHIP EVO 96-based SCP sample preparation with the timsTOF Ultra provides sufficient proteome depth to study complex biology beyond cell-type classifications.
Strand asymmetry of DNA damage tolerance mechanisms
Authors: Cañas Juan Carlos , Jurado-Santiago Dolores , Al Mamun Mohammed , Sacristán María P. , Morafraile Esther C. , Zamarreño Javier , Fujiki Katsunori , Shirahige Katsuhiko , Bueno Avelino , Bermejo Rodrigo
Published: January 2024

DNA damage tolerance mechanisms are crucial for timely and accurate chromosomal replication in response to DNA polymerase stalling. Ubiquitylation of the replicative sliding clamp PCNA drives major tolerance pathways, error-free homologous recombination template switching and error-prone translesion synthesis, though their dynamics at forks and pathway choice determinants are poorly understood. Using strand-specific genomics we revealed an asymmetric nature of tolerance pathways, characterized by preferential template switching-driven recombinase engagement of stalled nascent lagging strands and translesion synthesis usage in response to leading strand polymerase stalling. This asymmetry, determined by a strand-dynamic interplay between PCNA-ubiquitin writers and erasers, likely stems from necessities dictated by leading and lagging strand replication mechanisms and has implications for asymmetric mutation inheritance.

One-Sentence Summary

DNA damage tolerance mechanisms respond asymmetrically to leading or lagging strand polymerase blocks.
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
Authors: Dony Leander , Krontira Anthi C. , Kaspar Lea , Ahmad Ruhel , Demirel Ilknur Safak , Grochowicz Malgorzata , Schaefer Tim , Begum Fatema , Sportelli Vincenza , Raimundo Catarina , Koedel Maik , Labeur Marta , Cappello Silvia , Theis Fabian J. , Cruceanu Cristiana , Binder Elisabeth B.
Published: January 2024

Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factors have been less studied at molecular and cellular levels. In this study, we used single-cell and cell-type-specific techniques to investigate the effect of glucocorticoid (GC) exposure, a mediator of antenatal environmental risk, on gene regulation and lineage specification in unguided human neural organoids. We characterized the transcriptional response to chronic GC exposure during neural differentiation and studied the underlying gene regulatory networks by integrating single-cell transcriptomics-with chromatin accessibility data. We found lasting cell type-specific changes that included autism risk genes and several transcription factors associated with neurodevelopment. Chronic GCs influenced lineage specification primarily by priming the inhibitory neuron lineage through key transcription factors like PBX3. We provide evidence for convergence of genetic and environmental risk factors through a common mechanism of altering lineage specification.
Automated stratification of trauma injury severity across multiple body regions using multi-modal, multi-class machine learning models
Authors: Gao Jifan , Chen Guanhua , O’Rourke Ann P. , Caskey John , Carey Kyle , Oguss Madeline , Stey Anne , Dligach Dmitriy , Miller Timothy , Mayampurath Anoop , Churpek Matthew M. , Afshar Majid
Published: January 2024

The timely stratification of trauma injury severity can enhance the quality of trauma care but it requires intense manual annotation from certified trauma coders. There is a need to establish an automated tool to identify the severity of trauma injuries across various body regions. We gather trauma registry data from a Level I Trauma Center at the University of Wisconsin-Madison (UW Health) between 2015 and 2019. Our study utilizes clinical documents and structured electronic health records (EHR) variables linked with the trauma registry data to create two machine learning models with different approaches to representing text. The first one fuses concept unique identifiers (CUIs) extracted from free text with structured EHR variables, while the second one integrates free text with structured EHR variables. Both models demonstrate impressive performance in categorizing leg injuries, achieving high accuracy with macro-F1 scores of around 0.8. Additionally, they show considerable accuracy, with macro- F1 scores exceeding 0.6, in assessing injuries in the areas of the chest and head. Temporal validation is conducted to ensure the models’ temporal generalizability. We show in our variable importance analysis that the most important features in the model have strong face validity in determining clinically relevant trauma injuries.
Multiplicative topological semimetals
Authors: Pal Adipta , Winter Joe H. , Cook Ashley M.
Published: January 2024

Exhaustive study of topological semimetal (TSM) phases of matter in equilibriated electonic systems and myriad extensions has built upon the foundations laid by earlier introduction and study of Weyl semimetals, with broad applications in topologically protected quantum computing, spintronics, and optical devices. We extend recent introduction of multiplicative topological phases to find previously overlooked TSM phases of electronic systems in equilibrium, with minimal symmetry protection. We show these multiplicative TSM (MTSM) phases exhibit rich and distinctive bulk-boundary correspondence and response signatures that greatly expand understanding of consequences of topology in condensed matter settings, such as the limits on Fermi arc connectivity and structure, and transport signatures such as the chiral anomaly. In this paper, we therefore lay the foundation for extensive future study of MTSMs.

Published by the American Physical Society
2024
Three-loop effective potential for softly broken supersymmetry
Authors: Martin Stephen P.
Published: January 2024

The effective potential has been previously calculated through three-loop order, in Landau gauge, for a general renormalizable theory using dimensional regularization. However, dimensional regularization is not appropriate for softly broken supersymmetric gauge theories, because it explicitly violates supersymmetry. In this paper, I obtain the three-loop effective potential using a supersymmetric regulator based on dimensional reduction. Checks follow from the vanishing of the effective potential in examples with supersymmetric vacua, and from renormalization-scale invariance in examples for which supersymmetry is broken, either spontaneously or explicitly by soft terms. As by-products, I obtain the three-loop Landau gauge anomalous dimension for the scalar component of a chiral supermultiplet, and the beta function for the field-independent vacuum energy.

Published by the American Physical Society
2024
Primordial magnetogenesis in the two-Higgs-doublet model
Authors: Olea-Romacho María Olalla
Published: January 2024

γ-ray emission of blazars infer the presence of large-scale magnetic fields in the intergalactic medium, but their origin remains a mystery. Using recent data from MAGIC, H.E.S.S., and Fermi-LAT, we investigate whether the large-scale magnetic fields in the intergalactic medium could have been generated by a first-order electroweak phase transition in the two-Higgs-doublet model (2HDM). We study two representative scenarios where we vary the initial conditions of the magnetic field and the plasma, assuming either a primordial magnetic field with maximal magnetic helicity or a primordial magnetic field with negligible magnetic helicity in a plasma with kinetic helicity. By considering a primordial magnetic field with maximal helicity and applying the conservative constraints derived from MAGIC and Fermi-LAT data, we demonstrate that a first-order electroweak phase transition within the 2HDM may account for the observed intergalactic magnetic fields in the case of the strongest transitions. We show that this parameter space also predicts strong gravitational wave signals in the reach of space-based detectors such as LISA, providing a striking multimessenger signal of the 2HDM.

Published by the American Physical Society
2024
Study of
Bs0→TT(a2(1320), K2*(1430), f2(1270), f2′(1525))
in the perturbative QCD approach
Authors: Dai Jing , Yu Xian-Qiao
Published: January 2024

In the present study, the calculations of two-body decays Bs0→TT [T denotes tensor mesons, a2(1320), K2*(1430), f2(1270), f2′(1525)] in the perturbative QCD approach are presented. The ensuing predictions encompass branching ratios, polarization fractions, and direct CP violations, all elucidated in comprehensive detail. It is discerned that (1) for pure annihilation decay, the longitudinal polarization is around 90.0%, whereas the transverse polarizations manifest comparatively diminutive magnitudes. (2) The direct CP asymmetry is directly proportional to the interference between the tree and penguin contributions. For most of the decays investigated within this discourse, the direct CP asymmetry remains modest in magnitude. (3) There are precisely six distinct categories of Feynman diagrams for Bs0→TT, because the tensor mesons cannot be produced through the (V±A) currents or (S±P) density, thereby prohibiting factorizable emission diagrams. The nonfactorizable and annihilation contributions are ascertained to be pivotal in these decay modes. The calculated branching ratios of our calculation for Bs0→TT are at the order of 10−6 and 10−7, which can be tested in the LHCb and Belle II experiments. (4) Mixing exists for the f2(1270) and f2′(1525), just as the η and η′ mixing, the branching ratios about the mixing angle θ are given in this work. However, it is different from f1(1285)−f1(1420), the mixing angle is notably small, thereby resulting in only marginal alterations in the decay branching ratios.

Published by the American Physical Society
2024
Detectable gravitational waves from preheating probes nonthermal dark matter
Authors: Ghoshal Anish , Saha Pankaj
Published: January 2024

We describe the challenges and pathways when probing inflaton as dark matter with the stochastic gravitational waves (GWs) signal generated during the (p)reheating. Such scenarios are of utmost interest when no other interaction between the visible and dark sectors is present, therefore having no other detectability prospects. We consider the remnant energy in the coherently oscillating inflaton’s zeroth mode to contribute to the observed relic dark matter density in the Universe. To fully capture the nonlinear dynamics and the effects of backreactions during the oscillation, we resort to full nonlinear lattice simulation with pseudospectral methods to eliminate the differencing noises. We investigate for models whose behavior during the reheating era is of mΦ2Φ2 type and find the typical primordial stochastic GWs backgrounds spectrum from scatterings among highly populated inflaton modes behaving like matter. We comment on the challenges of constructing viable inflationary models such that the inflaton will account for the total dark matter of the Universe while the produced GWs are within the future GWs detectors e.g., BBO, DECIGO, PTA, AION-MAGIS, and CE. We also describe the necessary modifications to the standard perturbative reheating scenario to prevent the depletion of residual inflaton energy via perturbative decay.

Published by the American Physical Society
2024
Colloidal gelation induced by ring polymers
Authors: Moghimi Esmaeel , Chubak Iurii , Kaliva Maria , Kiany Parvin , Chang Taihyun , Ahn Junyoung , Patelis Nikolaos , Sakellariou Georgios , Egorov Sergei A. , Vlassopoulos Dimitris , Likos Christos N.
Published: January 2024

We provide unambiguous experimental evidence that ring polymers are stronger depleting agents in colloidal suspensions than their linear counterparts. We use an intermediate volume fraction (ϕc=0.44) colloidal gel based on the classic poly(methyl methacrylate) (PMMA) hard spheres, in which the polystyrene depletant is either linear or ring of the same molar mass or the same size. We systematically increase the depletant concentration from zero (no attraction) to well above the gelation point and find that in the presence of rings, gels are formed at smaller concentrations and possess a larger storage modulus in comparison to those induced by the linear chains. Consequently, the yield stress is enhanced; however, the yield strain (gel deformability) remains concomitantly unaffected. Our experimental findings are in agreement with theoretical calculations based on effective interaction potentials. Hence, polymer architecture is a powerful entropic tool to tailor the strength of colloidal gels.

Published by the American Physical Society
2024
Dehydroxylation and structural transition in α-GaOOH investigated by in situ X-ray diffraction
Authors: Ding Ning , Shi Honglong , Zhang Zeqian , Luo Minting , Hu Zhenfei
Published: January 2024

Ga2O3 is an ultra-wide-bandgap semiconductor that is receiving considerable attention due to its promising applications in high-frequency, high-power and high-temperature settings. It can be prepared by calcinating the α-GaOOH phase at high temperatures. Understanding the significance of hydroxyl groups in α-GaOOH, dehydroxylation and the structural transition at high temperatures has become a key aspect of preparing high-quality α-Ga2O3 crystals, but the underlying mechanism remains unknown. In this research, α-GaOOH nanorods were hydrothermally synthesized and the structural evolution of α-GaOOH investigated at high temperatures by in situ X-ray diffraction. The hydroxyl group in α-GaOOH squeezes Ga3+ from the center of the [GaO6] octahedron, resulting in deformed [GaO6] octahedra and significant microstrain in α-GaOOH. The hydroxyl groups are peeled off from α-GaOOH when the temperature exceeds 200°C, resulting in contraction along the c-axis direction and expansion along the a-axis direction of α-GaOOH. When the temperature exceeds 300°C, the Ga—O bond inside the double chains preferentially breaks to generate square-wave-like octahedron chains, and the neighboring chains repack to form hexagonal-like octahedron layers. The octahedron layers are packed up and down by electrostatic interaction to generate the α-Ga2O3 structure. This work highlights the role of hydroxyl groups in α-GaOOH, dehydroxylation and the structural transition on the atomic scale, providing valuable guidelines for the fabrication of high-quality α-Ga2O3 crystals.
Inclusive leader and job crafting: the role of work engagement and job autonomy in service sector organisations
Authors: Jaleel Aqsa , Sarmad Muhammad
Published: January 2024

Purpose

The ever-demanding role of employees in the hospitality sector stimulates job crafting. This study examines the relationship between inclusive leadership and job-crafting dimensions under the mediating role of work engagement through the lens of conservation of resources (COR) theory. It also aims to analyse the boundary condition of job autonomy between inclusive leadership and work engagement.

Design/methodology/approach

The data were collected in 3-time lags from 319 front-line workers in the hospitality sector. The adopted and adapted questionnaires were executed through a deductive approach and an applied research method. The data were analysed through SmartPLS by applying the structural equation modelling (SEM) technique.

Findings

This study provides evidence for a predictive relationship between inclusive leadership and job-crafting dimensions under the mediating psychological mechanism of work engagement. Additionally, the moderating role of job autonomy is established in the unique context of the hospitality sector of an underdeveloped country, Pakistan.

Practical implications

Services-based organisations need to endure the inclusive leadership style by establishing work engagement practices. Engaged employees result in better job-crafting behaviours through better training and subsequent performance.

Originality/value

This study established that work engagement and job autonomy are imperative forces that impact the relationship between inclusive leadership and job-crafting dimensions. The research study has time-lagged data and conveys meaningful theoretical and practical implications.
More autonomy, more proactive? The (in)congruence effects of autonomy on proactive behaviour
Authors: Yang Chang , Bao Yuanjie , Zhang Zixu
Published: January 2024

Purpose

Based on person-job fit and self-determination theory, this paper examined the effects of (in)congruence between autonomy expectation and perceived autonomy on proactive behaviour, and the moderating role of humble leadership in this relationship among Chinese public employees.

Design/methodology/approach

Data were collected from a two-wave survey, and the research model was tested using polynomial regression and response surface methodology.

Findings

Results suggested that employees' proactive behaviour will be highest when autonomy congruence was achieved, while autonomy incongruence led to different levels of proactive behaviour based on the specific situations. Furthermore, the moderating effect of humble leadership was proved such that it accentuated the positive influence of autonomy congruence on proactive behaviour.

Practical implications

Managers should be fully aware of the benefits and importance of person-job fit and strive to reduce autonomy incongruence. Meanwhile, humble leadership should be considered in the context of granting autonomy to boost proactivity.

Originality/value

This paper re-emphasises the importance of autonomy by utilising a congruence perspective to understand the effects of autonomy on proactive behaviour. Meanwhile, it incorporates an important boundary condition, humble leadership, on the effects of autonomy congruence and thus offers a more nuanced understanding. Further, this paper not only highlights the significance of underexplored concepts among public employees, but also extends autonomy (in)congruence study to a new context and culture.
Fish gill surface area can keep pace with metabolic oxygen requirements across body mass and temperature
Authors: Skeeles M. R. , Clark T. D.
Published: January 2024

Climate warming is driving the maximum attainable size of many fish species to decrease, yet the mechanisms underlying this ‘shrinking’ phenomenon are not well understood. The gill oxygen limitation (GOL) hypothesis is perhaps the most prominent mechanistic proposition, asserting that, as fish grow, the two‐dimensional gill surface area (GSA) progressively fails to supply enough oxygen to support the continued growth of the three‐dimensional body—a process exacerbated by increased metabolism associated with warming. However, these ideas have been hotly debated owing to limited empirical understanding of how GSA develops with respect to a fish's body mass and oxygen requirements.

For the first time, we addressed this knowledge gap by rearing Galaxias maculatus for 5 months at normal (15°C) and elevated (20°C) summer temperatures, with (hyperoxia) or without (normoxia) supplementary oxygen. Quantifying individual metabolic rate and GSA traits across body sizes encompassing most of the species' ontogeny, we found little evidence for a change in the proportion of GSA available per unit of metabolic rate (termed the S metric) and no improvements under hyperoxia.

Importantly, at the elevated temperature where gill oxygen limitation should be most pronounced, the S metric did not change across body mass in either oxygen treatment (allometric exponents were no different from 0).

These results indicate that the gills can grow in ways that support an individual's oxygen requirements, contrasting with the suggestion that size reductions of fish in response to climate warming are driven by an insurmountable geometric constraint at the gills.

Read the free Plain Language Summary for this article on the Journal blog.
Putting space into trait ecology: Trait, environment and biodiversity relationships at multiple spatial scales
Authors: Biswas Shekhar R. , He Dong , Li Jialin , Gong Li , Biswas Prity L. , Zhuo Ziqing , Xu Mingshan , Yang Xiao‐Dong , Yan En‐Rong
Published: January 2024

Ecological processes such as environmental filtering and biotic interactions that shape species' traits and community diversity often vary with geographic distance, potentially generating spatial structures in trait variation, covariation and biodiversity data. Understanding spatial structures of trait, environment and biodiversity, or the spatial link between those factors, is fundamental to identifying spatially explicit assembly processes or biodiversity distributions in spatially heterogeneous landscapes but remains unclear.

To address the issue, we gathered individual‐level leaf and diameter traits data paired with environmental data from a 4.8 ha subtropical Chinese forest and divided the forest into 25, 100, 400 and 1936 m2 grids representing contrasting spatial grains. Using Moran's correlograms, we quantified the spatial structures of trait variation and covariation, environmental conditions and biodiversity. We assessed the links between those variables using path analyses.

Most variables were spatially positively autocorrelated. However, trait mean was more autocorrelated than trait variation or covariation, and intraspecific trait variation was more autocorrelated than interspecific variation. Autocorrelations in those community properties were generally weak at the large grain.

Path analyses indicated positive associations between interspecific trait variation and species diversity at a very small to medium scale and a positive association between intraspecific variation and small‐scale functional diversity. Trait covariation constrained biodiversity, and multi‐trait means were negatively linked to very small‐ to medium‐scale species diversity but positively to medium‐ and large‐scale functional diversity. Patterns regarding multi‐trait community structure–environment–biodiversity associations were generally held for individual traits. However, depending on the trait, spatial scale and plant ontogenic stage, the pattern's strength changed, or occasionally, their sign reversed.

We attribute spatial patterns in multi‐trait mean and covariation to scale‐dependent variation in environmental heterogeneity and trait variation to scale‐dependent competition.

Synthesis. Our study provides novel insights into spatial and scale‐dependent variability in functional community structure, environment and biodiversity, and their relationships. Our results demonstrate the usefulness of spatial trait analyses in identifying scale‐dependent assembly processes or finding the importance of processes to biodiversity distributions in spatially heterogeneous landscapes. A spatially explicit perspective is thus helpful for the progress of trait ecology.
Squaring the Circle? Regional Airport Expansion, Climate Change and the Planning Regime
Authors: Bogojević Sanja
Published: January 2024

Airports are contested infrastructures. They are regarded both as icons of modernity and as a threat to a climate‐neutral future. Judicial review is increasingly relied upon to determine the legality of planning permissions for further airport development in light of climate obligations. Focusing on regional airport development and the review of planning approvals for expansion at Bristol, Southampton and Stansted airports, this article shows how the relevant policies and legislation, as well as the courts in applying these, find cohesion between airport expansion and climate action. These efforts, nonetheless, are tantamount to an attempt at squaring the circle: the fundamental disconnect between climate commitments and the increase in greenhouse gas emissions from regional airport expansion remains unsettled.