bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysing the dynamic structure of warm dense matter in the imaginary-time domain: theoretical models and simulations
Authors: Dornheim Tobias , Vorberger Jan , Moldabekov Zhandos A. , Böhme Maximilian 
Published: July 2023

Rigorous diagnostics of experiments with warm dense matter are notoriously difficult. A key method is X-ray Thomson scattering (XRTS), but the interpretation of XRTS measurements is usually based on theoretical models that entail various approximations. Recently, Dornheimet al.[Nat. Commun.13, 7911 (2022)] introduced a new framework for temperature diagnostics of XRTS experiments that is based on imaginary-time correlation functions. On the one hand, switching from the frequency to the imaginary-time domain gives one direct access to a number of physical properties, which facilitates the extraction of the temperature of arbitrarily complex materials without relying on any models or approximations. On the other hand, the bulk of theoretical work in dynamic quantum many-body theory is devoted to the frequency domain, and, to the best of our knowledge, the manifestation of physics properties within the imaginary-time density–density correlation function (ITCF) remains poorly understood. In the present work, we aim to fill this gap by introducing a simple, semi-analytical model for the imaginary-time dependence of two-body correlations within the framework of imaginary-time path integrals. As a practical example, we compare our new model to extensiveab initiopath integral Monte Carlo results for the ITCF of a uniform electron gas, and find excellent agreement over a broad range of wavenumbers, densities and temperatures.This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
Dynamic and transient processes in warm dense matter
Authors: White Thomas G. , Dai Jiayu , Riley David 
Published: July 2023

In this paper, we discuss some of the key challenges in the study of time-dependent processes and non-equilibrium behaviour in warm dense matter. We outline some of the basic physics concepts that have underpinned the definition of warm dense matter as a subject area in its own right and then cover, in a selective, non-comprehensive manner, some of the current challenges, pointing along the way to topics covered by the papers presented in this volume.This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
Development of a new quantum trajectory molecular dynamics framework
Authors: Svensson Pontus , Campbell Thomas , Graziani Frank , Moldabekov Zhandos , Lyu Ningyi , Batista Victor S. , Richardson Scott , Vinko Sam M. , Gregori Gianluca 
Published: July 2023

An extension to the wave packet description of quantum plasmas is presented, where the wave packet can be elongated in arbitrary directions. A generalized Ewald summation is constructed for the wave packet models accounting for long-range Coulomb interactions and fermionic effects are approximated by purpose-built Pauli potentials, self-consistent with the wave packets used. We demonstrate its numerical implementation with good parallel support and close to linear scaling in particle number, used for comparisons with the more common wave packet employing isotropic states. Ground state and thermal properties are compared between the models with differences occurring primarily in the electronic subsystem. Especially, the electrical conductivity of dense hydrogen is investigated where a 15% increase in DC conductivity can be seen in our wave packet model compared with other models.
This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
Disentangling the effects of non-adiabatic interactions upon ion self-diffusion within warm dense hydrogen
Authors: Angermeier William A. , Scheiner Brett S. , Shaffer Nathaniel R. , White Thomas G. 
Published: July 2023

Warm dense matter is a material state in the region of parameter space connecting condensed matter to classical plasma physics. In this intermediate regime, we investigate the significance of non-adiabatic electron-ion interactions upon ion dynamics. To disentangle non-adiabatic from adiabatic electron-ion interactions, we compare the ion self-diffusion coefficient from the non-adiabatic electron force field computational model with an adiabatic, classical molecular dynamics simulation. A classical pair potential developed through a force-matching algorithm ensures the only difference between the models is due to the electronic inertia. We implement this new method to characterize non-adiabatic effects on the self-diffusion of warm dense hydrogen over a wide range of temperatures and densities. Ultimately we show that the impact of non-adiabatic effects is negligible for equilibrium ion dynamics in warm dense hydrogen.This article is part of the theme issue ‘Dynamic and transient processes in warm dense matter’.
Children develop Immunity to cryptosporidiosis in a high transmission intensity area
Authors: Petri William A. O. , Hossain Biplop , Kabir Mamun , So Hannah H , Moreau G. Brett , Nayak Uma , Ma Jennie Z , Noor Zannthan , Faruque ASG , Alum Masud , Haque Rashidul , Petri William A , Gilchrist Carol A 
Published: July 2023

AbstractBackgroundCryptosporidiumis one of the top causes of diarrhea in Bangladesh infants.Cryptosporidiuminfections lead to the production of antibody immune responses, which were associated with a decrease in parasite burden and decreased disease severity in subsequent infections.MethodsWe conducted a longitudinal study of cryptosporidiosis from birth to five years of age in an urban slum of Dhaka Bangladesh. We then retrospectively tested the concentration of anti-Cryptosporidium Cp17 or Cp23 IgA in surveillance stool samples collected from 54 children during their first 3 years of life by enzyme-linked immunosorbent assay (ELISA). We also assessed the concentration of both IgA and IgG antibodies specific to Cryptosporidium Cp17 and Cp23 in the concentration of anti-Cryptosporidium Cp17 or Cp23 IgA and IgG antibodies in the children’s plasma (1-5 years).ResultsThe seroprevalence of both anti-Cp23 and Cp17 antibodies was high at ≤ one year of age and reflected the exposure of these children in this community to cryptosporidiosis. In Bangladesh, the prevalence of cryptosporidiosis is high during the rainy season (June to October) but decreases during the dry season. In younger infants’ plasma anti-Cp17 and Cp23 IgG and anti-Cp17 IgA levels were markedly increased during the rainy season in line with the higher initial exposure to the parasite at this time. Both anti-Cp17, anti-Cp23 fecal IgA and the parasite burden declined during repeat infections.ConclusionsWe found that anti-Cryptosporidium plasma and fecal antibody levels in children could contribute to the decrease in new infections in this study population.
Plasma-treatment with the virucidal beta-propiolactone does not preclude analysis by large panel affinity proteomics, including the discovery of biomarker candidates
Authors: Beutgen Vanessa M. , Bhagwat Aditya M. , Reinartz Silke , Müller Rolf , Graumann Johannes 
Published: July 2023

AbstractVirus inactivation is a prerequisite for safe handling of high-risk infectious samples. Beta-propiolactone (BPL) is an established and commonly used reagent with proven virucidal efficacy. BPL primarily reacts with DNA and RNA, but also amino acids. The latter may yield modified antigenic protein epitopes and thus interfere with the binding properties of affinity reagents such as antibodies and aptamers, including panels of such reagents used in affinity proteomic screens. We investigated the impact of BPL-treatment on the analysis of protein levels in plasma samples using the commercial aptamer-based affinity proteomic platform SomaScan. Heparin-plasma samples from patients with ovarian cancer (n = 12) and benign tumors (n = 12) were analyzed using the SomaScan v4.1 platform, which led to the identification of COL10A1 as a novel ovarian cancer biomarker, a protein strongly associated with poor clinical outcome. BPL-related changes in protein detection were evaluated comparing native and BPL-treated state, simulating virus inactivation, and impact on measurable group differences was assessed. While approximately one third of protein measurements were significantly changed by the BPL treatment, a majority of antigen/aptamer interactions remained unaffected. Interaction effects of BPL treatment and disease state, potentially altering detectability of group differences, were observable for less than one percent of targets (0.6%). Accordingly, noticeable global effects of BPL treatment did not interfere with detectability of differential protein expression between benign and ovarian cancer samples, as measurements are altered in both groups to the same extent. Global effect sizes (Cohen’s d) between benign and cancer in BPL-treated samples and the number of significantly altered protein abundance observed in limma-based linear modeling appeared minimally increased, slightly enhancing the probability of false positive hits. Taken together, the results indicate the SomaScan platform as well suited for the analysis of high biosafety risk samples inactivated using BPL and the identification of novel biomarkers.
The relative effects of staying in school and attending university on smoking, BMI and systolic blood pressure: evidence from multivariable Mendelian randomization
Authors: Sanderson Eleanor , Davies Neil M. 
Published: July 2023

AbstractObjectivesTo investigate which levels of educational attainment affect health.DesignMultivariable Mendelian randomization study (MVMR).SettingUK Biobank.ParticipantsEuropean ancestry participants born in England.Exposure Educationalattainment was defined as leaving school before age 18, leaving school after 18, or getting a university degree. Randomly allocated genetic variants were used as instruments for these traits.Main outcome measuresBody mass index (BMI), smoking initiation, and systolic blood pressure.ResultsThe MVMR estimates provided little evidence that remaining in school to age 18 affected BMI (mean difference=0.04, 95% CI: -0.42, 0.50), but evidence getting a degree reduced BMI by 0.47 standard deviation 95% CI: (0.01 to 0.97). The MVMR estimates provided evidence that remaining in school to age 18 reduced the odds of initiating smoking (odds ratio (OR): 0.48, 95% CI: 0.30 to 0.76), whereas it provided little evidence of effects of getting a degree (OR: 1.14, 95% CI: 0.69 to 1.88). MVMR suggested that both remaining in school to age 18 and getting a degree had similar effects on systolic blood pressure (mean difference=-2.60 95% CI: -3.73 to -1.46 and mean difference=-3.63 95% CI: -4.92 to -2.34, respectively).ConclusionsMultivariable Mendelian randomization can be used to estimate the effects of complex longitudinal exposures such as educational attainment. This approach can help elucidate how and when factors such as educational attainment affect health outcomes.Key messagesPrevious studies have estimated the average effect an additional year of education has on health, irrespective of educational level.However, this assumes that each educational level has the same effect, e.g., an additional year of education in primary school has the same effect as an additional year at university; this assumption is implausible.Multivariable Mendelian randomization can be used to relax this assumption and estimate the independent effects of educational levels.Previously reported effects of education on smoking initiation appear to be due to remaining in school until age 18. In contrast, effects on BMI are due to attending university, and effects on systolic blood pressure are similar across education levels.
Joint models reveal genetic architecture of transitions between pubertal stages and their association with BMI in a Latino population
Authors: Vicuña Lucas , Barrientos Esteban , Leiva-Yamaguchi Valeria , Alvares Danilo , Mericq Veronica , Pereira Ana , Eyheramendy Susana 
Published: July 2023

AbstractEarly or late pubertal onset can lead to disease in adulthood, including cancer, obesity, type 2 diabetes, metabolic disorders, bone fractures and psychopathologies. Thus, knowing the age at which puberty is attained is crucial as it can serve as a risk factor for future diseases. Pubertal development is divided into five stages of sexual maturation in boys and girls according to the standardized Tanner scale. We performed genome-wide association studies (GWAS) on the GOCS cohort composed of admixed children with European and Native American ancestry. Using joint models that integrate time-to-event survival parameters and longitudinal trajectories of body-mass index (BMI), we identified genetic variants associated with phenotypic transitions between pairs of Tanner stages. We identified 43 novel significant associations, most of them in boys. The GWAS on Tanner 3→4 transition in boys captured an association peak around the growth-related genesLARS2andLIMD1genes, the former of which causes ovarian dysfunction when mutated. The associated variants are expression– and splicing Quantitative Trait Loci regulating gene expression and alternative splicing in multiple tissues. Further, higher individual Native American genetic ancestry proportions predicted a significantly earlier arrival to Tanner 2 stage in boys but not in girls. Finally, the joint models identified longitudinal BMI parameters significantly associated in several Tanner stages’ transitions, confirming the association of BMI on pubertal timing.
Patterns in Repeat Reinfections: Pre and Post Omicron Emergence
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Tang Patrick , Coyle Peter , Yassine Hadi M. , Al Thani Asmaa A. , Hasan Mohammad R. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar H. , Latif Ali N. , Shaik Riyazuddin M. , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed G. , Butt Adeel A. , Al-Romaihi Hamad E. , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J. 
Published: July 2023

AbstractOur understanding of SARS-CoV-2 reinfection patterns remains limited. We conducted a longitudinal study using Qatar’s national SARS-CoV-2 data from February 28, 2020 to June 11, 2023 to investigate incidence of reinfections both prior to and after omicron emergence. The latter analysis excluded individuals with pre-omicron infections. Before omicron introduction, the proportion of incident infections classified as reinfections gradually increased but remained minimal, reaching 1.8% just before omicron emerged. During the first omicron wave, this proportion reached 9.0%, a 5-fold increase. After the conclusion of the first omicron wave, the proportion of incident infections identified as reinfections rapidly increased, reaching 43.3% towards the end of the study. In the pre-omicron era, a total of 3,131 reinfections were documented, of which 99.6% were first reinfections and 0.4% were second reinfections. Meanwhile, a total of 20,962 reinfections were documented after an omicron primary infection of which 99.0% were first reinfections, 1.0% were second reinfections, and 0.01% were third reinfections. Reinfections were rare before omicron’s emergence but became widespread during the omicron era, including among individuals previously infected with omicron. Our findings may indicate accelerated viral evolution in the omicron era aimed at evading population immunity, but with minimal impact on COVID-19 severity, or potentially suggest immune imprinting effects that require further investigation.
Environmental predictors of malaria infection in Sussundenga, Mozambique
Authors: Steiber Alexa , Ferrão João L. , Francisco Albino B. , Muhiro Valy , Novela Anísio , Earland Dominique E. , Searle Kelly M. 
Published: July 2023

AbstractMalaria is highly sensitive to environmental conditions, including climate variability and land use practices. Ecologically, Sussundenga district has a significantly lower elevation compared to the Zimbabwe border and a more tropical climate compared to southern and northern Mozambique due to high seasonal rainfall. We aimed to evaluate the effects of climate and environmental factors at the household level on rapid diagnostic test results for Malaria in Sussundenga, Mozambique. To understand this association, we collected publicly available United States Geological Survey satellite data on elevation, vegetation, and land use cover. Additionally, we collected satellite data on day and night land surface temperatures and evapotranspiration which we assessed at 1- and 2-week lags. We spatially and temporally joined these data with malaria infection data at the household level. Using this database, we assessed whether these environmental factors were good predictors for having a positive rapid diagnostic test result using spatio-temporal models that accounted for the underlying correlation structure. Risk factor surveillance is an important tool for controlling the spread of infectious diseases. The results from modeling of the ecological predictors of malaria infection and spatial maps provided in this study could aid in developing frameworks to mitigate malaria transmission and predict future malaria transmission in this region. Understanding how environmental changes impacts malaria transmission and infection at the household level may have important implications for vector control and disease surveillance strategies utilized by the district.
Phylogenomics of the ecdysteroid kinase-like (EcKL) gene family in insects highlights roles in both steroid hormone metabolism and detoxification
Authors: Scanlan Jack L. , Robin Charles 
Published: July 2023

AbstractThe evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid moulting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We also provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. This work provides a robust framework for future functional studies into the EcKL gene family and opens promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied co-evolution of butterflies with their host plants.Significance statementThe ecdysteroid kinase-like (EcKL) gene family has been linked to both steroid inactivation and detoxification in insects, but the functions of most of its members are unknown. Here, we study the evolutionary history of the EcKLs and showcase how phylogenetics can inform the functional characterisation of enzyme families. EcKL family size varies over an order of magnitude and is associated with chemically complex diets, implicating numerous genes in detoxification. We also find a surprising link between a steroid-metabolising clade and host plant diversity in butterflies and moths, suggesting new detoxification functions may evolve through an insect-plant ‘chemical arms-race’. This work advances numerous functional hypotheses for multiple EcKL clades and proposes a new classification system for this poorly characterised gene family.
Competitive Amplification Networks enable molecular pattern recognition with PCR
Authors: Goertz John P , Sedgwick Ruby , Smith Francesca , Kaforou Myrsini , Wright Victoria J , Herberg Jethro A. , Kote-Jarai Zsofia , Eeles Ros , Levin Mike , Misener Ruth , van der Wilk Mark , Stevens Molly M 
Published: July 2023

AbstractGene expression has great potential to be used as a clinical diagnostic tool. However, despite the progress in identifying these gene expression signatures, clinical translation has been hampered by a lack of purpose-built. readily deployable testing platforms. We have developed Competitive Amplification Networks. CANs to enable analysis of an entire gene expression signature in a single PCR reaction. CANs consist of natural and synthetic amplicons that compete for shared primers during amplification, forming a reaction network that leverages the molecular machinery of PCR. These reaction components are tuned such that the final fluorescent signal from the assay is exactly calibrated to the conclusion of a statistical model. In essence, the reaction acts as a biological computer, simultaneously detecting the RNA targets, interpreting their level in the context of the gene expression signature, and aggregating their contributions to the final diagnosis. We illustrate the clinical validity of this technique, demonstrating perfect diagnostic agreement with the gold-standard approach of measuring each gene independently. Crucially, CAN assays are compatible with existing qPCR instruments and workflows. CANs hold the potential to enable rapid deployment and massive scalability of gene expression analysis to clinical laboratories around the world, in highly developed and low-resource J settings alike.Abstract Figure
Geometric Epitope and Paratope Prediction
Authors: Pegoraro Marco , Dominé Clémentine , Rodolà Emanuele , Veličković Petar , Deac Andreea 
Published: July 2023

AbstractAntibody-antigen interactions play a crucial role in identifying and neutralizing harmful foreign molecules. In this paper, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the importance of geometric information. Specifically, we compare different geometric deep learning methods applied to proteins’ inner (I-GEP) and outer (O-GEP) structures. We incorporate 3D coordinates and spectral geometric descriptors as input features to fully leverage the geometric information. Our research suggests that surface-based models are more efficient than other methods, and our O-GEP experiments have achieved state-of-the-art results with significant performance improvements.
Revisiting the role of mean annual precipitation in shaping functional trait distributions at a continental scale
Authors: Towers Isaac R. , Vesk Peter A. , Wenk Elizabeth H. , Gallagher Rachael V. , Windecker Saras M. , Wright Ian J. , Falster Daniel S. 
Published: July 2023

1AbstractMean annual precipitation (MAP) plays an undisputed role in determining the spatial distribution of the vegetative ecosystems on Earth. Nevertheless, the relationship between MAP and plant functional traits remains unclear. Here, we test the relationship between eight key functional traits and MAP. Our analysis reveals a strong, coordinated response of several plant traits including leaf mass per area, leaf nitrogen, the leaf carbon isotope ratio and plant height from resource-conservative to resource-acquisitive values as MAP increased. These results establish an important role for MAP in driving trait selection across space and, therefore, a need for these effects to be included in future theoretical frameworks.