bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on mechanical properties of unsaturated silt in the Yellow River flood area
Authors: Song Da , Sun Yun , Sun Shuxuan , Zhou Pengyuan
Published: August 2024

The alluvial deposits of the Yellow River led to the formation of less clay content, loose soil particles, and low compactness of the unsaturated silt, which makes it complicated to determine the mechanical properties of the Yellow River flood area soil. To investigate the mechanical characteristics of unsaturated silt, the relationship between unsaturated silt saturation and matric suction is analyzed through the soil-water characteristic test, and the soil-water characteristic curve is fitted by the Van-Genuchten model. A series of consolidated undrained shear tests were conducted on silt in Kaifeng using the GDS triaxial apparatus, the influence of moisture content, matric suction (u
a-u
w), and net confining pressure (σ
3-u
a) on the strength characteristics of unsaturated silt was discussed. The results indicated that the net confining pressure, moisture content, and matric suction significantly influenced the shear characteristics of unsaturated silt. The shear strength of unsaturated silt increased with increasing net confining pressure at the same moisture content. The strain-hardening state of silt at high confining pressure was more obvious, while the silt at low confining pressure showed a weak strain-hardening state. Under a constant net confining pressure, the deviatoric stress versus deviatoric strain curves of silt with low moisture content exhibited a strain-softening state, while other moisture content showed a weak strain-hardening state. At the same matric suction, the shear strength increased with increasing normal stress. The cohesion increased and then decreased while the internal friction angle decreased and then increased with the increasing moisture content and matric suction.
Development of a system that changes the speed of the motor for a given radius of curvature of an autonomous car while taking turn
Authors: Chandramouli R , Ghosh Rajesh , T Mahitha , K Siva Gangadhar , K Uday , B Hymavathi , G Sai Rakesh
Published: August 2024

This work endeavors to create a system capable of autonomously regulating a car’s speed while navigating turns, based on the curvature of the road. The primary objective is to bolster the safety and stability of autonomous vehicles by curbing excessive speeds during turns, thereby mitigating the risk of accidents such as loss of control or rollovers. The approach blends theoretical analysis with practical application, involving computations to ascertain the ideal speed for a given curve radius. Factors such as vehicle mass, wheel specifications, and centrifugal and gyroscopic forces are considered in these calculations. Subsequently, an algorithm is devised and implemented using Arduino Uno and programmed within the Arduino IDE software environment. The system employs sensors to monitor the motor’s speed and adjust the motor’s speed accordingly. Both simulated scenarios and real-world experiments validate the system’s efficacy in maintaining safe speeds during turns. The study concludes by underlining the potential of this system to heighten the safety and dependability of autonomous vehicles, while also proposing future avenues for research, such as integration with broader autonomous driving frameworks and field testing across diverse environmental conditions.
Accelerating scientific discovery with generative knowledge extraction, graph-based representation, and multimodal intelligent graph reasoning
Authors: Buehler Markus J
Published: August 2024

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1000 scientific papers focused on biological materials into a comprehensive ontological knowledge graph. Through an in-depth structural analysis of this graph, we have calculated node degrees, identified communities along with their connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. We find that the graph has an inherently scale-free nature, shows a high level of connectedness, and can be used as a rich source for downstream graph reasoning by taking advantage of transitive and isomorphic properties to reveal insights into unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. Using a large language embedding model we compute deep node representations and use combinatorial node similarity ranking to develop a path sampling strategy that allows us to link dissimilar concepts that have previously not been related. One comparison revealed detailed structural parallels between biological materials and Beethoven’s 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed an innovative hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky’s ‘Composition VII’ painting. The resulting material integrates an innovative set of concepts that include a balance of chaos and order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Because our method transcends established disciplinary boundaries through diverse data modalities (graphs, images, text, numerical data, etc), graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.
Improving model robustness to weight noise via consistency regularization
Authors: Hou Yaoqi , Zhang Qingtian , Wang Namin , Wu Huaqiang
Published: August 2024

As an emerging computing architecture, the computing-in-memory (CIM) exhibits significant potential for energy efficiency and computing power in artificial intelligence applications. However, the intrinsic non-idealities of CIM devices, manifesting as random interference on the weights of neural network, may significantly impact the inference accuracy. In this paper, we propose a novel training algorithm designed to mitigate the impact of weight noise. The algorithm strategically minimizes cross-entropy loss while concurrently refining the feature representations in intermediate layers to emulate those of an ideal, noise-free network. This dual-objective approach not only preserves the accuracy of the neural network but also enhances its robustness against noise-induced degradation. Empirical validation across several benchmark datasets confirms that our algorithm sets a new benchmark for accuracy in CIM-enabled neural network applications. Compared to the most commonly used forward noise training methods, our approach yields approximately a 2% accuracy boost on the ResNet32 model with the CIFAR-10 dataset and a weight noise scale of 0.2, and achieves a minimum performance gain of 1% on ResNet18 with the ImageNet dataset under the same noise quantization conditions.
From ‘follow the leader’ to autonomous swarming: physical reservoir computing in two dimensions
Authors: E Heywood Zachary , B Mallinson Joshua , J Bones Philip , A Brown Simon
Published: August 2024

Percolating networks of nanoparticles (PNNs) are self-assembled nanoscale systems that possess brain-like characteristics that are useful for information processing, particularly within a reservoir computing (RC) framework. Previous work has successfully demonstrated one-dimensional RC tasks, such as chaotic time-series prediction and nonlinear transformation. We focus here on the challenge of two-dimensional (2D) tasks and introduce novel ‘follow the leader’ and ‘swarming’ tasks. In the first task a ‘follower’ is required to accurately track a ‘leader’ in two dimensions. The task is performed successfully for a range of trajectories and parameters, for both position-based tracking and velocity-based tracking incorporating inertia. In both cases, the task is successful even for trajectories unseen in training. We then successfully demonstrate a 2D implementation of swarming behavior. Each agent is represented by a PNN which is trained to react to the behavior of the other members of the swarm, such that the future trajectory of all agents is generated autonomously. As well as demonstrating that the computational capabilities of PNNs can be extended into two dimensions, this work presents a first step in the emulation of complex emergent biological behaviors such as swarming, and opens a new route to the solution of complex optimization problems.
Hip fracture has profound psychosocial impacts: a systematic review of qualitative studies
Authors: Taylor Nicholas F , Rimayanti Made U , Peiris Casey L , Snowdon David A , Harding Katherine E , Semciw Adam I , O’Halloran Paul D , Wintle Elizabeth , Williams Scott , Shields Nora
Published: August 2024

Background

Hip fracture is a common and serious traumatic injury for older adults characterised by poor outcomes.

Objective

This systematic review aimed to synthesise qualitative evidence about the psychosocial impact of hip fracture on the people who sustain these injuries.

Methods

Five databases were searched for qualitative studies reporting on the psychosocial impact of hip fracture, supplemented by reference list checking and citation tracking. Data were synthesised inductively and confidence in findings reported using the Confidence in the Evidence from Reviews of Qualitative research approach, taking account of methodological quality, coherence, relevance and adequacy.

Results

Fifty-seven studies were included. Data were collected during the peri-operative period to >12 months post fracture from 919 participants with hip fracture (median age > 70 years in all but 3 studies), 130 carers and 297 clinicians. Hip fracture is a life altering event characterised by a sense of loss, prolonged negative emotions and fear of the future, exacerbated by negative attitudes of family, friends and clinicians. For some people after hip fracture there is, with time, acceptance of a new reality of not being able to do all the things they used to do. There was moderate to high confidence in these findings.

Conclusions

Hip fracture is a life altering event. Many people experience profound and prolonged psychosocial distress following a hip fracture, within a context of negative societal attitudes. Assessment and management of psychosocial distress during rehabilitation may improve outcomes for people after hip fracture.
Multi-Omic Graph Diagnosis (MOGDx): a data integration tool to perform classification tasks for heterogeneous diseases
Authors: Ryan Barry , Marioni Riccardo E , Simpson T Ian
Published: August 2024

Motivation

Heterogeneity in human diseases presents challenges in diagnosis and treatments due to the broad range of manifestations and symptoms. With the rapid development of labelled multi-omic data, integrative machine learning methods have achieved breakthroughs in treatments by redefining these diseases at a more granular level. These approaches often have limitations in scalability, oversimplification, and handling of missing data.

Results

In this study, we introduce Multi-Omic Graph Diagnosis (MOGDx), a flexible command line tool for the integration of multi-omic data to perform classification tasks for heterogeneous diseases. MOGDx has a network taxonomy. It fuses patient similarity networks, augments this integrated network with a reduced vector representation of genomic data and performs classification using a graph convolutional network. MOGDx was evaluated on three datasets from the cancer genome atlas for breast invasive carcinoma, kidney cancer, and low grade glioma. MOGDx demonstrated state-of-the-art performance and an ability to identify relevant multi-omic markers in each task. It integrated more genomic measures with greater patient coverage compared to other network integrative methods. Overall, MOGDx is a promising tool for integrating multi-omic data, classifying heterogeneous diseases, and aiding interpretation of genomic marker data.

Availability and implementation

MOGDx source code is available from https://github.com/biomedicalinformaticsgroup/MOGDx.
Comparison of adaptive imaging receiver coil and traditional coil for multiplexed sensitivity encoding diffusion-weighted imaging of the liver
Authors: Peng Lingrong , Chen Qilong , Meng Zhanao , Zhang Yao , Wang Jin , Wen Huiquan
Published: August 2024

Objectives

To compare the image quality and efficacy of the adaptive imaging receiver (AIR) coil (GE Healthcare) and the traditional coil for multiplexed sensitivity encoding diffusion-weighted imaging (MUSE-DWI) in the detection of focal liver lesions (FLLs).

Methods

Two groups of MUSE-DWI were obtained. Image quality was qualitatively evaluated by 3 independent blinded radiologists on a 5-point scale, and quantitative parameters were calculated by measurements of the region of interest in the liver and FLLs. McNemar’s test were used to compare the characteristics and detectability.

Results

Less image noise, sharper contours, milder susceptibility artefacts, and better liver lesion conspicuity were found by all radiologists in 60 livers with 140 FLLs with the AIR coil than with the traditional coil (reader average mean, 4.3-4.4 vs. 3.7-4.0, P < .001). The signal-to-noise ratio (SNR) of the liver was significantly higher with the AIR coil than with the traditional coil (right lobe: mean, 8.89 vs.7.76, P < .05; left lobe: mean, 7.14 vs.6.19, P < .001), and the SNR of FLLs (mean, 24.62 vs. 21.01, P < .001) and lesion-to-liver CNR (mean, 16.61 vs. 14.02, P < .001) exhibited significant differences between the AIR coil and the traditional coil. Besides, superior detection of FLLs was observed with the AIR coil compared to the traditional coil (95.7% [134/140] vs. 85.7% [120/140], P < .001).

Conclusions

The AIR coil yields less noise, fewer distortions, better lesion detectability, higher SNR of the liver and FLLs, and improved lesion-to-liver CNR during liver MUSE-DWI. Thus, it is a feasible and effective scanning scheme in liver MRI.

Advances in knowledge

The AIR coil improves SNR and the quality of liver MR imaging compared with the traditional coil.
Multi-peptide characterization of plasma neurofilament light chain in preclinical and mild Alzheimer’s disease
Authors: Coulton John B , He Yingxin , Barthélemy Nicolas R , Jiang Hong , Holtzman David M , Bateman Randall J
Published: August 2024

Although neurofilament light chain is a well-known marker of neuronal damage, its characterization at the proteoform level is underdeveloped. Here, we describe a new method to profile and quantify neurofilament light chain in plasma at the peptide level, using three in-house monoclonal antibodies targeting distinct protein domains and nano–liquid chromatography coupled to high-resolution tandem mass spectrometry. This study profiled and compared plasma neurofilament light chain to CSF in 102 older individuals (73.9 ± 6.3 years old), 37 of which had a clinical dementia rating greater than 0. We observed elevated neurofilament light chain in preclinical Alzheimer’s disease plasma for two measures (NfL101 and NfL324) and CSF for seven measures (NfL92, NfL101, NfL117, NfL137, NfL148, NfL165 and NfL530). We found five plasma peptides (NfL92, NfL101, NfL117, NfL324 and NfL530) significantly associated with age and two (NfL148 and NfL324) with body mass index.
Location-specific prognostic significance of plaque burden, stenosis, and plaque morphology in coronary artery disease
Authors: Jukema Ruurt A , Maaniitty Teemu , Nurmohamed Nick S , Raijmakers Pieter G , Planken R Nils , Twisk Jos , van der Harst Pim , Cramer Maarten J , Min James K , Earls James P , Knaapen Paul , Saraste Antti , Knuuti Juhani , Danad Ibrahim
Published: August 2024

Aims

To investigate the location-specific prognostic significance of plaque burden, diameter stenosis, and plaque morphology.

Methods and results

Patients without a documented cardiac history that underwent coronary computed tomography angiography (CCTA) for suspected coronary artery disease were included. Percentage atheroma volume (PAV), maximum diameter stenosis, and plaque morphology were assessed and classified into proximal, mid, or distal segments of the coronary tree. Major adverse cardiac events (MACE) were defined as death or non-fatal myocardial infarction. Among 2819 patients 267 events (9.5%) occurred during a median follow-up of 6.9 years. When adjusted for traditional risk factors and the presence of PAV in other locations, only proximal PAV was independently associated with MACE. However, PAV of the proximal segments was strongly correlated to PAV localized at the mid (R = 0.76) and distal segments (R = 0.74, P < 0.01 for both). When only adjusted for cardiovascular risk factors, the area under the curve (AUC) to predict MACE for proximal PAV was 0.73 (95% CI 0.69–0.76), which was similar compared with mid PAV (AUC 0.72, 95% CI 0.68–0.76) and distal PAV (AUC 0.72, 95% CI 0.68–0.76). Similar results were obtained using diameter stenosis instead of PAV. The presence of proximal low-attenuation plaque had borderline additional prognostic value.

Conclusion

Proximal PAV was the strongest predictor of MACE when adjusted for cardiovascular risk factors and plaque at other locations. However, when the presence of plaque was only adjusted for cardiovascular risk factors, proximal, mid, and distal plaque localization showed a similar predictive ability for MACE.
A rare giant atrial septal cardiac blood cyst in an adult: a case report
Authors: Ong Wei Sheng Jonathan , Keh Yann Shan , Lai Siang Hui , Chang Huan Ying , Amanullah Mohammed Rizwan
Published: August 2024

Background

Cardiac blood cysts are exceedingly rare cardiac tumours usually found on cardiac valves in infants. We report and discuss a rare unique case wherein a giant atrial septal cardiac blood cyst was found in an adult.

Case summary

A 59-year-old Chinese lady with history of hypertension, hyperlipidemia and transient ischaemic attack presented with atypical chest pain. Her ECG suggested right ventricular strain. Echocardiography revealed a large right atrial intracardiac mass attached to the interatrial septum which prolapsed into the right ventricle during each cardiac cycle with associated dilatation of the right atrium and right ventricle. Computed tomography scans showed no evidence of malignancy or metastasis. Considering our patient’s profile and the characteristics of the mass, it was opined to likely be a cardiac myxoma. After consultation with our cardiothoracic surgeons, she underwent surgical resection of the intracardiac mass. Histology revealed that the intracardiac mass was a cardiac blood cyst.

Discussion

First described by Elsasser in 1844, cardiac blood cysts are extremely rare benign cardiac tumours very rarely seen in adults. Though benign, they have been associated with outflow tract obstruction, valvular regurgitation and embolization. Symptomatic patients do well with surgical resection, while long-term outcomes in asymptomatic patients followed up with serial echocardiograms are mixed. Due to its rarity, existing literature is limited to case reports and small case series, with a lack of guidelines on management till recently. Our case report serves to highlight this unique presentation of an exceedingly rare intracardiac tumour.
Quality of life is an independent predictor of mortality in patients with heart failure: a prospective cohort study from the Colombian heart failure registry (RECOLFACA)
Authors: Gómez-Mesa Juan Esteban , Luna-Bonilla Paula , Echeverría Luis Eduardo , Rivera-Toquica Alex , Jurado-Arenales Adriana Milena , Orozco María Johanna , Buitrago-Malaver Lilia Andrea , Rivera Edilma L , González Diana Verónica , Coronado-Villa Estefanny , Toro-Cardona Olga Cristina , López-Montes Cristian Alexander , Vargas-Márquez Ludy Yanet , Martínez-Camargo Silvia , Agudelo-Pérez Adriana , Vivas-Mayor Marcela , Niño Lina María , Mejía-Cadavid Luz Aida , Aponte-Romero Luisa Fernanda , Erazo María José , García-Barrera María , Meza-Roque Julio Armando , Ríos-Sánchez Viviana , Torres-Moreno Fabián , Castañeda-M Jenny , Gallego Cesar A , Martínez Fanny Esther , Blandón-Córdoba Carmen Jineth , Silva-Carmona Mónica , Saldarriaga Clara
Published: August 2024

Aims

Patients with heart failure (HF) commonly have poor quality of life (QoL), secondary to the persistence and severity of HF symptoms. We aimed to evaluate the prognostic value of QoL measures on all-cause mortality in patients with HF from the Colombian registry of heart failure (RECOLFACA).

Methods and results

We analysed data from patients registered in RECOLFACA during 2017–19. QoL was measured using the EuroQol-5D questionnaire (EQ-5D). From the questionnaire, two independent predictors of mortality were obtained, the visual analogue scale (VAS) and the utility score (US). The primary outcome was all-cause mortality, and secondary variables evaluated were demographic factors, comorbidities, NYHA classification, medications used, and laboratory test results. To analyse survival among patients, the Kaplan–Meier method and the hierarchical Cox proportional hazards regression model were used. This study included 2514 patients from RECOLFACA. Most patients were male (57.6%), and the mean age was 67.8 years. The mean value and standard deviation (SD) of the VAS score was 78.8 ± 20.1 points, while the mean and SD of the US score was 0.81 ± 0.20. As the Kaplan–Meier curve illustrated, patients in the lower quartiles of both VAS and US scores had a significantly higher probability of mortality (log-rank test: P < 0.001 for both scores).

Conclusion

QoL, as calculated by the EQ-5D questionnaire, served as an independent predictor of mortality in patients from RECOLFACA. Further studies may be needed to evaluate whether the provision of optimizing therapies and follow-up care based on patients’ perceived QoL reduces short- and long-term mortality rates in this population.
Adaptive shell-morphological differences and differential fitness in two morphospecies of Lanistes (Gastropoda: Ampullariidae) from the northern region of the Malawi Basin
Authors: Van Bocxlaer Bert , Dollion Alexis Y , Ortiz-Sepulveda Claudia M , Calarnou Christophe , Habert Rémi , Pawindo Grant , Vekemans Xavier
Published: August 2024

Environment–phenotype correlations are a central pattern of adaptive radiations, but such correlations and the expected associated reciprocal differences in fitness of divergent phenotypes in their respective niches are rarely demonstrated. Ecophenotypic plasticity may result in environment–phenotype correlations too, however, so that certain observed morphological differences, even in adaptive radiations, may result from plasticity instead of differential adaptation. Here, we examine the nature of observed morphological differences in two morphospecies of Lanistes gastropods from the northern region of the Malawi Basin that are part of an ongoing adaptive radiation. We subjected experimental populations of each of these two morphospecies, i.e. L. sp. (solidus-like), which occupies intralacustrine habitats with comparatively stable environmental conditions, and L. sp. (ovum-like), which occurs in satellite waterbodies with fluctuating environmental conditions, to a common garden experiment in the laboratory. Our experimental conditions approximated those of stable, intralacustrine habitats. We monitored fecundity and subjected wild-caught parents and intraspecific F1 offspring to semilandmark geometric morphometrics. L. sp. (solidus-like) exhibited higher fecundity than L. sp. (ovum-like). Whereas wild-caught parents of both morphospecies had similar shell sizes, 9-month-old F1 offspring of L. sp. (solidus-like) were significantly smaller than those of L. sp. (ovum-like), indicating slower growth. Substantial shell-morphological differences were observed between the two morphospecies in the wild-caught parents as well as in F1 offspring, indicating that shell-morphological differences are genetically inherited. Our results also indicate differential fitness but fully reciprocal transplant experiments would be required to demonstrate local adaptation.
Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii
Authors: McTaggart Lisa R , Braukmann Thomas W A , Kus Julianne V
Published: August 2024

Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single-nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25–75.4 Mb) were ∼8 Mb larger than the B. dermatitidis genomes (64.88–66.61 Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the 2 species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04–39.26 Mb) than in B. dermatitidis (30.85–32.40 Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation, and speciation, highlighting the role of transposable elements in fungal evolution.
Routine Hearing Screening for Older Adults in Primary Care: Insights of Patients and Clinic Personnel
Authors: Silberberg Mina , Singh Anisha , Prvu Bettger Janet , Smith Sherri L , Francis Howard W , Dubno Judy R , Schulz Kristine A , Dolor Rowena J , Walker Amy R , Tucci Debara L
Published: August 2024

Background and Objectives

Hearing loss frequently goes undiagnosed and untreated, with serious sequelae. Hearing screening facilitates diagnosis and treatment but is not routinely conducted in primary care. This study addresses the attitudes and insights of patients and primary care clinic personnel relative to the routinization of hearing screening in primary care for older adults.

Research Design and Methods

Data presented are from the qualitative portion of a larger study. The main study compared screening completion for 3 approaches to coordinating telephone-based hearing screening with primary care—1 offering hearing screening within the primary care encounter and 2 providing information for at-home screening ( 1 with and 1 without provider encouragement). Focus groups/interviews were conducted with personnel (n = 38) at the 6 participating clinics, patients who completed screening and were referred for diagnosis (n = 14), and patients who did not complete screening (n = 10). Analysis used the general inductive approach.

Results

Most patients had unaddressed hearing concerns prior to the study. Negative attitudes toward hearing loss/treatment were common, and experiences of family and friends influenced attitudes, but lack of urgency was the primary barrier to screening completion. Respondents favored routine primary care-based hearing screening for older adults, but clinic personnel noted challenges of time, space, workflow, and reimbursement.

Discussion and Implications

Findings favor greater routinization of hearing screening in primary care. Routinization will be enhanced by improved reimbursement for screening and follow-up; specialist engagement with primary care and the public (including leveraging older adults’ social networks); and further research on specific integration options.
Analytical and numerical models of viscous anisotropy: a toolset to constrain the role of mechanical anisotropy for regional tectonics and fault loading
Authors: Liu Dunyu , Puel Simone , Becker Thorsten W , Moresi Louis
Published: August 2024

To what extent mechanical anisotropy is required to explain the dynamics of the lithosphere is an important yet unresolved question. If anisotropy affects stress and deformation, and hence processes such as fault loading, how can we quantify its role from observations? Here, we derive analytical solutions and build a theoretical framework to explore how a shear zone with linear anisotropic viscosity can lead to deviatoric stress heterogeneity, strain-rate enhancement, as well as non-coaxial principal stress and strain rate. We develop an open-source finite-element software based on FEniCS for more complicated scenarios in both 2-D and 3-D. Mechanics of shear zones with transversely isotropic and orthorhombic anisotropy subjected to misoriented shortening and simple shearing are explored. A simple regional example for potential non-coaxiality for the Leech River Schist above the Cascadia subduction zone is presented. Our findings and these tools may help to better understand, detect and evaluate mechanical anisotropy in natural settings, with potential implications including the transfer of lithospheric stress and deformation through fault loading.
Deep learning models for regional phase detection on seismic stations in Northern Europe and the European Arctic
Authors: Myklebust Erik B , Köhler Andreas
Published: August 2024

Seismic phase detection and classification using deep learning is so far poorly investigated for regional events since most studies focus on local events and short time windows as the input to the detection models. To evaluate deep learning on regional seismic records, we create a data set of events in Northern Europe and the European Arctic. This data set consists of about 151 000 three component event waveforms and corresponding phase arrival picks at stations in mainland Norway, Finland and Svalbard. We train several state-of-the-art and one newly developed deep learning model on this data set to pick P- and S-wave arrivals. The new method modifies the popular PhaseNet model with new convolutional blocks including transformers. This yields more accurate predictions on the long input time windows associated with regional events. Evaluated on event records not used for training, our new method improves the performance of the current state-of-the-art methods when it comes to recall, precision and pick time residuals. Finally, we test our new model for continuous mode processing on 4 d of single-station data from the ARCES array. Results show that our new method outperforms the existing array detector at ARCES. This opens up new opportunities to improve automatic array processing with deep learning detectors.
Enhanced gravity-geologic method to predict bathymetry by considering non-linear effects of surrounding seafloor topography
Authors: Jiang Xiao , Guo Jinyun , Lin Miao , Sun Heping , Jiang Tao
Published: August 2024

The gravity-geological method (GGM) is an approach that utilizes marine gravity anomalies (GAs) and shipborne bathymetric data to invert seafloor topography by resolving short-wavelength GAs through the Bouguer Plate approximation. Such an approximation ignores the non-linear effects caused by surrounding seafloor topographical undulations that actually exist in short-wavelength GAs, and thus leaving the space for further modification of GGM. This study thoroughly derives the relationship between seafloor topography and GA, as well as the formula of GGM. Then, we propose a self-adaptive method to improve the accuracy of the inversion significantly: the enhanced GGM (EGGM). The method uses the equivalent mass line method to approximate the non-linear gravitational effects of the surrounding seafloor topography to correct the short-wavelength GAs. By introducing two optimal density contrast parameters, EGGM has been designed to effectively integrate the combined effects of various non-linear factors to a certain extent. The accuracy of the seafloor topography models, produced with a spatial resolution of 1′ × 1′, was evaluated over the study area (132°E–136°E, 36°N–40°N) located in the Sea of Japan. The results indicate that the accuracy of EGGM has a relative improvement of 13.73 per cent compared to that of GGM in the overall study area, while the accuracy of both models is higher than that of the SIO_unadjusted model. The study further investigated the feasibility and stability of EGGM by examining the accuracy of both GGM and EGGM in various water depth ranges and areas with diverse terrain characteristics.
Personalized nutrition: aligning science, regulation, and marketing
Authors: Rogus Stephanie , Lurie Peter
Published: August 2024

Interest in personalized nutrition among researchers and industry has grown rapidly in recent years and shows no signs of abating. In this paper, we discuss the growth of the personalized nutrition market, the evidence for the approach, and the regulatory landscape for personalized nutrition products. We found that regulatory gaps have led to market growth of products with unknown efficacy that are making bold, and possibly unsubstantiated, claims. As personalized nutrition products and related treatments continue to enter the market without regulation, unreliable products may cause consumers financial, psychological, and physical harm. Stronger regulation will help engender trust in these products among consumers and ensure their safety and effectiveness.
Diabetes in Liberia: a policy brief
Authors: Bleah Paulina , Almost Joan , Wilson Rosemary , Macdonald Danielle , Camargo-Plazas Pilar
Published: August 2024

There is increasing awareness that diabetes is a growing public health threat in Liberia. The high mortality and morbidity associated with diabetes have significant implications for individuals, families and communities. The current response to diabetes in Liberia is limited to the management of acute complications. Long-term strategies for the prevention and control of diabetes are almost entirely absent from national health agendas. This brief provides policy options that Liberian policymakers can adopt to prevent diabetes, improve treatment and enhance the quality of life for people living with diabetes in Liberia.
Spatial transcriptome analysis reveals de novo regeneration of poplar roots
Authors: Lv Kaiwen , Liu Naixu , Niu Yani , Song Xiehai , Liu Yongqi , Yue Zhiliang , Ali Muhammad , Guo Qiuyue , Lv Chunyu , Lu Dongdong , Zhang Shaoman , Zhou Yangyan , Li Bosheng
Published: August 2024

Propagation through cuttings is a well-established and effective technique for plant multiplication. This study explores the regeneration of poplar roots using spatial transcriptomics to map a detailed developmental trajectory. Mapping of the time-series transcriptome data revealed notable alterations in gene expression during root development, particularly in the activation of cytokinin-responsive genes. Our analysis identified six distinct clusters during the second and third stages, each corresponding to specific anatomical regions with unique gene expression profiles. Auxin response cis-elements (AuxREs) were prevalent in the promoters of these cytokinin-responsive genes, indicating a regulatory interplay between auxin and cytokinin. Pseudo-temporal trajectory analysis mapped the differentiation from cambium cells to root primordium cells, revealing a complex pattern of cell differentiation. SAC56 and LOS1 emerged as potential novel biomarkers for enhancing root regeneration, with distinct spatial expression patterns confirmed by in situ hybridization. This comprehensive spatial analysis enhances our understanding of the molecular interactions driving root regeneration and provides insights for improving plant propagation techniques.
Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes
Authors: Li Lijuan , Chen Songcan , Xue Ximei , Chen Jieyin , Tian Jian , Huo Lijuan , Zhang Tuo , Zeng Xibai , Su Shiming
Published: August 2024

Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe–arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.
P18 Uncovering the role of secondary messenger signalling in Acinetobacter baumannii virulence
Authors: Harkova Lyuboslava G , de Dios Rubén , McCarthy Ronan R
Published: August 2024

Backgrounds

Secondary messenger signalling systems play a crucial role in bacterial capability to respond to environmental changes by mediating alternations in transcription, translation and enzyme activity. Secondary messengers are central regulators of various aspects of bacterial life including metabolism, pathogenicity, sessility and cell morphology. Indeed, these molecules are widely recognized mediators of virulence and antibiotic tolerance in well studied pathogens such as Pseudomonas aeruginosa, where over 40 enzymes contain domains with the predicted potential to influence secondary messenger levels. The MDR nosocomial pathogen Acinetobacter baumannii has become increasingly prevalent over the last 20 years with carbapenem-resistant strains surpassing P. aeruginosa to become the WHO top priority pathogen. Despite this, relatively little is known about the role of secondary messengers in A. baumannii pathogenicity.

Methods

In this work, we used high-throughput screening of the A. baumannii AB5075 transposon mutant library to identify novel regulators of biofilm formation. Amongst the hits were genes predicted to influence secondary messenger levels. We further characterized the candidate with the strongest biofilm phenotype and uncovered a range of other phenotypes such as motility, exopolysaccharide production, virulence, antibiotic resistance and link with other signalling systems.

Results

RNA-Seq analysis of a clean deletion mutant compared with a complemented strain showed that operons and genes linked to the observed phenotypes such as pgaABCD, csuA/BABCDE and type IV pili genes were differentially expressed. Moreover, antibiotic resistance and virulence in an in vivo model were directly affected too.

Conclusions

Overall, we demonstrate the important role of secondary messenger signalling in A. baumannii and confirm that it modulates key phenotypes linked to virulence and antimicrobials resistance.
P24 Antimicrobial susceptibility profiles of hypervirulent strains of Clostridioides difficile of pig and human origin
Authors: Doyle Aoife , McElroy Máire , Rogers Thomas
Published: August 2024

Background

Clostridioides difficile places an increasing burden on healthcare because of emerging hypervirulent strains such as RT078/ST11 that may be resistant to commonly prescribed antibiotics e.g. fluoroquinolones. Pigs are often colonized by RT078/ST11 and act as potential reservoir for human C. difficile infection (CDI). They are the highest consumers of veterinary antimicrobials in many countries.1 We investigated the susceptibility of C. difficile to antibiotics that are commonly prescribed and/or used to treat CDI.

Methods

Sequenced C. difficile (humans=50, pigs=40), collected as part of a One Health investigation into the epidemiology of pig and human C. difficile, were chosen for phenotypic antimicrobial susceptibility testing (AST). Strains included ST11 (n=70), ST44 (n=9), ST16 (n=6), ST8 (n=5). Susceptibility to a panel of antibiotics were determined using ANAERO3 Sensititre™ plates and Etest®, according to the manufacturer’s instructions. Selected C. difficile ST11 isolates (n=30) were tested for ciprofloxacin and delafloxacin susceptibility using Etest®. Breakpoints were interpreted as per EUCAST, CLSI and Freeman.2C. difficile genomes (n=90) were screened for AMR markers using NCBI AMRFinderPlus.

Results

Phenotypic testing found all isolates were susceptible to vancomycin and metronidazole, and to penicillin, amoxicillin, amoxiclav, piperacillin/tazobactam, piperacillin, imipenem and chloramphenicol. Resistance was found to cefoxitin (100%), ceftriaxone (100%), erythromycin (48.94%), clindamycin (28.72%), moxifloxacin (48.94%), tetracycline (31.91%) and rifampicin (2.13%). All 30 ST11 isolates were resistant to ciprofloxacin, while the mean MIC for delafloxacin was 0.47 mg/L. There was no difference between resistance rate and C. difficile host. Bioinformatic analysis of 90 C. difficile genomes revealed resistance determinants for quinolones (87%) and tetracyclines (69%).

Conclusions

No resistance to vancomycin and metronidazole in these C. difficile isolates is reassuring, although larger datasets for surveillance should be investigated. Finding resistance determinants in the isolates in this study demonstrates that WGS is a valuable tool for detecting AMR. Quinolone and tetracycline resistance may be linked with use of these antibiotics on Irish pig farms (64.1% and 85.1% of farms, respectively).1
P31 An observational prospective audit on the use of vancomycin and ciprofloxacin in the treatment of severe community-acquired pneumonia in penicillin-allergic patients in NHS Lothian
Authors: Blair Zsofia , Palenzuela Esperanza , Dewar Simon
Published: August 2024

Objectives

To assess the current standard of care in NHS Lothian compared with guidelines for patients prescribed vancomycin and ciprofloxacin in severe community-acquired pneumonia (CAP) with penicillin allergies.

Methods

In total, 182 patients were analysed over 8 weeks. Data were collected from online prescribing records and clinical notes. A total of 18 patients met the criteria of correct antibiotic combination and clinical indication. Data were collated and analysed using Microsoft Excel.

Results

Vancomycin: Levels were taken in 11 out of 18 patients, of which 8 reached therapeutic levels in a median duration of 2 days. First therapeutic levels: median 8.5 mg/L, range <4–15.8 mg/L. Ciprofloxacin: 83% of patients received ciprofloxacin orally; 72% of patients were aged >65 years and 39% were co-prescribed oral steroids. No patients had documented fluoroquinolone counselling. Antibiotics: 33% of patients were stepped down to oral doxycycline. The total mean duration of antibiotic therapy was 7.3 days. Allergies: One documented as ‘anaphylaxis’. Eight unsure of reaction/unspecified in medical notes. Three received penicillin recently with no adverse effect. One penicillin delabelled during admission.

Conclusions

Patients on average received longer than recommended total antimicrobial treatment. Only one third received the recommended IVOS option, however this may have been influenced by other factors such as positive microbiology. In the majority of patients, in which vancomycin levels were taken/required, therapeutic levels were achieved in 2 days. Most patients received ciprofloxacin orally, suggesting that patients were well enough to not necessitate IV route. This opens the possibility of recommending other oral antibiotics with high oral bioavailability as alternatives (e.g. levofloxacin, doxycycline). Additionally, patients were not counselled on the potential adverse effects of ciprofloxacin as recommended by MHRA guidance, despite almost three quarters of patients having factors (i.e. elderly, on steroids) placing them at greater risk of adverse effects. However, the benefits of giving treatment in severe CAP may outweigh these risks. This audit highlights that practice varies from the NHS Lothian guidelines. It raises the question of whether alternative antibiotic therapies should be considered for first line in penicillin allergic patients, such as levofloxacin used in the rest of Scotland. However, given the new MHRA guidance on limitation of fluoroquinolones, it may be that other health boards also consider changes to their guidelines. Education regarding fluoroquinolone use should be provided for clinicians and patients to ensure that the risks are included in decision-making. Focus should be put on reducing the number of patients with inappropriate penicillin allergy labels.
Automatic locally stationary time series forecasting with application to predicting UK gross value added time series
Authors: Killick Rebecca , Knight Marina I , Nason Guy P , Nunes Matthew A , Eckley Idris A
Published: August 2024

Accurate forecasting of the UK gross value added (GVA) is fundamental for measuring the growth of the UK economy. A common nonstationarity in GVA data, such as the ABML series, is its increase in variance over time due to inflation. Transformed or inflation-adjusted series can still be challenging for classical stationarity-assuming forecasters. We adopt a different approach that works directly with the GVA series by advancing recent forecasting methods for locally stationary time series. Our approach results in more accurate and reliable forecasts, and continues to work well even when the ABML series becomes highly variable during the COVID pandemic.