bluuebunny/crossref_metadata_2025 huggingface dataset:
Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph
Authors: Huang Kexin , Zeng Tony , Koc Soner , Pettet Alexandra , Zhou Jingtian , Jain Mika , Sun Dongbo , Ruiz Camilo , Ren Hongyu , Howe Laurence , Richardson Tom G. , Cortes Adrian , Aiello Katie , Branson Kim , Pfenning Andreas , Engreitz Jesse M. , Zhang Martin Jinye , Leskovec Jure
Published: December 2024

Genome-wide association studies (GWASs) have identified tens of thousands of disease associated variants and provided critical insights into developing effective treatments. However, limited sample sizes have hindered the discovery of variants for uncommon and rare diseases. Here, we introduce KGWAS, a novel geometric deep learning method that leverages a massive functional knowledge graph across variants and genes to improve detection power in small-cohort GWASs significantly. KGWAS assesses the strength of a variant’s association to disease based on the aggregate GWAS evidence across molecular elements interacting with the variant within the knowledge graph. Comprehensive simulations and replication experiments showed that, for small sample sizes (N=1-10K), KGWAS identified up to 100% more statistically significant associations than state-of-the-art GWAS methods and achieved the same statistical power with up to 2.67× fewer samples. We applied KGWAS to 554 uncommon UK Biobank diseases (Ncase<5K) and identified 183 more associations (46.9% improvement) than the original GWAS, where the gain further increases to 79.8% for 141 rare diseases (Ncase<300). The KGWAS-only discoveries are supported by abundant functional evidence, such as rs2155219 (on 11q13) associated with ulcerative colitis potentially via regulatingLRRC32expression in CD4+ regulatory T cells, and rs7312765 (on 12q12) associated with the rare disease myasthenia gravis potentially via regulatingPPHLN1expression in neuron-related cell types. Furthermore, KGWAS consistently improves downstream analyses such as identifying disease-specific network links for interpreting GWAS variants, identifying disease-associated genes, and identifying disease-relevant cell populations. Overall, KGWAS is a flexible and powerful AI model that integrates growing functional genomics data to discover novel variants, genes, cells, and networks, especially valuable for small cohort diseases.
Potential health and cost impacts of a point-of-care test for neonatal sepsis and possible serious bacterial infections in infants: a modeling analysis in two settings
Authors: Chevalier Joshua M , Hansen Megan A , Grantz Kyra H , Gleeson Birgitta , Blumel Benjamin , Chuchu Veronicah , Khan Shaukat , Sigwebela Ntombi , Chimhini Gwendoline , Fitzgerald Felicity , Ferreyra Cecilia , Nichols Brooke E
Published: December 2024

Introduction

Sepsis accounts for up to 50% of neonatal deaths in resource-limited countries. Accurate and timely diagnosis could improve clinical outcomes, reduce inappropriate antibiotic use, and provide healthcare cost savings. We aimed to identify the minimum technical specifications and cost required of a point-of-care test (POCT) for neonatal sepsis to be clinically useful in hospital and community levels in low-resource settings.

Methods

We modeled the diagnosis and treatment of two cohorts: hospitalized neonates and infants presenting to primary health care facilities with suspected sepsis. We compared health outcomes, including mortality, length of hospital stays, and acquisition of healthcare-associated infections (HAIs), under a POCT compared to empiric treatment and blood culture across varying test performance, prevalence of bacterial infection and discharge eligibility. A threshold health economic analysis was performed to determine the allowable POCT price to remain cost neutral to the healthcare system.

Results

A POCT could lead to a net reduction in neonatal deaths at both the hospital level (up to 19% of deaths averted compared to baseline) and community level (up to 76% deaths averted) through faster initiation of appropriate therapy and reducing unnecessary hospitalizations and HAIs. Healthcare costs could be reduced substantially with implementation of a POCT (17%–43% of baseline costs saved in hospital and 48%–81% saved in primary healthcare settings across the range of analyzed scenarios), suggesting a POCT costing up to $21 in hospitals and $3 in community settings could be cost neutral.

Conclusions

A POCT for neonatal sepsis, even with imperfect accuracy, could substantially improve clinical outcomes by improving time to diagnosis, while also supporting antibiotic de-escalation and stewardship and lowering healthcare costs. However, high clinical sensitivity is required to avoid causing deaths through missed diagnoses due to false negative results and delayed antibiotic initiation.

Key Questions

What is already known on this topic?

It is known that neonatal sepsis and possible serious bacterial infections in infants are a serious cause of mortality; however, diagnosis to provide proper treatment and care remains difficult.

What does this study add?

This study generates evidence on what the technical specifications and costs are required of a novel point-of-care test through mathematical modeling.

How might this study affect research, practice, or policy?

These results can be used as criteria to guide the development of a novel point-of-care test for neonatal sepsis and bacterial infection in infants.
Assessing the mental health literacy of young adults from rural and urban communities in Malawi
Authors: Chitalah Beatrice Cynthia , Nanda Ishani , Nyali Joel , Chirwa Gloria , Jumbe Sandra
Published: December 2024

Mental health literacy is the ability to recognise mental disorders, have knowledge of professional help available, effective self-help strategies, prevention strategies, and skills to support others. Mental health literacy is linked to better help-seeking behaviours and the management of mental illness. The prevalence of mental illness in Malawi is increasing. Assessing mental health literacy in communities crucially helps identify knowledge gaps, informing the development of evidence-based interventions. This study assessed the mental health literacy levels of young adults (16-to-30 years old) in rural and urban communities in Malawi. A cross-sectional national survey was administered to 682 people across 13 districts in Malawi using a self-reporting Mental Health Literacy questionnaire (MHLq) that assessed knowledge of mental health problems, erroneous beliefs/stereotypes, first-aid skills, help-seeking behaviour, and self-help strategies. Most respondents were either unemployed (36%) or enrolled in school (43%). 73% had completed primary or secondary education, 48% knew someone with a mental illness but only 14.1% of this group could specify the illness. The mean mental health literacy score was 111.8 [Standard Deviation (SD) = 13.9]. Individuals with primary and secondary school qualifications had significantly lower scores in Factor 2 (erroneous beliefs/stereotypes) and Factor 3 (First-aid skills and assistance-seeking behaviour) of the MHLq than those with higher education. This research highlights persisting mental health misconceptions, limited knowledge about specific mental illnesses, and low help-seeking behaviour among young adult Malawians. Higher education is linked to a better understanding of mental health. Prioritising community education on causes, signs, treatments, and prognosis of mental illness is crucial for increased mental health literacy.
CancerSpot: A multi-cancer early detection test developed and validated on a retrospective cohort
Authors: Basu Swaraj , Hiremath M Prakash , Rathod Nihesh , Chatterjee Aditi , Vishwanath Divya , Ghosh Arunima , Sanguri Sweta , Chakraborty Sampuran , Tripathi Aastha , Preetha RT , Nair Arya , Kumar Goutham , Sekar Kannadhasan , Yete Subuhi , Bhanumathy G , Bahadur Urvashi , Radhakrishnan Aneesha , Khan Ankita , Kannan S Yasodha , Bollipalli Lavanya , Ghana Pallavi , Ramanathan Aparnaa , Saha Puja , Phalke Sameer , Cantor Charles , Limaye Sewanti , Chandru Vijay , Veeramachaneni Vamsi , Hariharan Ramesh
Published: December 2024

Next-generation sequencing (NGS) technologies have transformed biomarker discovery, enabling the detection of disease-associated markers at the earliest stages of illness. In this study, we introduce a blood-based, non-invasive test for multi-cancer detection using cell-free DNA (cfDNA) methylation sequencing. The test employs a novel methylation scoring system derived from sequencing data and integrates machine learning to analyze a retrospective cohort of newly diagnosed cancer cases and controls recruited from multiple centers across India. To enhance robustness, the study includes a substantial proportion of controls with habitual tobacco and alcohol use, ensuring the test’s resilience against confounding factors. The test’s accuracy was further validated through synthetic data augmentation, demonstrating reliability under conditions of random signal perturbation. At an approximate specificity of 97%, the assay achieves sensitivities of 79.3% for Stage I, 78.4% for Stage II, 78.4% for Stage III, and 86.8% for Stage IV cancers in an independent validation cohort. Additionally, the test demonstrates Top 2 Tissue of Origin (TOO) accuracies of 78.3% for Stage I, 79.3% for Stage II, 82.8% for Stage III, and 69.7% for Stage IV cancers. This blood-based test holds considerable promise for early cancer detection, offering a precise test for cancer screening.
Neural Network-Based Assessment of Coronary Angiogram Flow
Authors: Resnick Jesse M. , Assi Ismael Z. , Pastapur Aishwarya , Sankardas Ajit Mullasari , Figueroa C. Alberto , Nallamothu Brahmajee K.
Published: December 2024

Adequate blood flow through the coronary tree is critical for maintaining cardiac perfusion. Coronary angiography has the potential to provide rich and dynamic hemodynamic information, however, current strategies to assess flow through the coronary vessels depend on either subjective expert opinion (TIMI flow grade) or laborious frame-by-frame anatomical analysis (TIMI frame count and quantitative flow ratio). Here we present a strategy for automated characterization of bulk flow through the coronary tree using the right coronary artery as an example. We leverage the AngioNet neural network to generate sequential segmentations of angiograms, create time series of the summed segmentation intensities (i.e., a contrast intensity profile), and quantitatively characterize the filling and washout phases of these intensity profiles. We demonstrate that AngioNet-derived frame counts and normalized mean filling slopes of contrast intensity profiles correlate well with manual frame counts and flow grades in both our derivation and validation datasets. Furthermore, the generated washout dynamics appear to provide different information to the traditional frame count and flow grade metrics, which only deal with the initial filling phase, suggesting that washout dynamics of the contrast intensity profiles may capture novel information about the coronary microcirculation.
An accelerating, decreasing phylogenetic trend in SARS-CoV-2 genome compositional heterogeneity during the pandemic
Authors: Oliver Jose L , Bernaola Galvan Pedro , Carpena Pedro , Perfectti Francisco , Gomez Martin Cristina , Castiglione Silvia , Raia Pasquale , Verdu Miguel , Moya Andres
Published: December 2024

The rapid evolution of SARS-CoV-2 during the pandemic, driven by a plethora of mutations, many of which enable the virus to evade host resistance, has likely altered its genome's compositional structure (i.e. the arrangement of compositional domains of varying lengths and nucleotide frequencies within the genome). To explore this hypothesis, we summarize the evolutionary effects of these mutations by computing the Sequence Compositional Complexity (SCC) in random datasets of fully sequenced genomes. Phylogenetic ridge regression of SCC against time reveals a striking downward evolutionary trend, as well as an increasing rate of change, suggesting the ongoing adaptation of the virus's genome structure to the human host. Other genomic features, such as strand asymmetry, the effective number of K-mers, and the depletion of CpG dinucleotides, each linked to the virus's adaptation to its human host, also exhibit decreasing phylogenetic trends over the course of the pandemic, along with strong phylogenetic correlations to SCC. Overall, our findings suggest an accelerated, genome-wide evolutionary trend toward a more symmetric and homogeneous genome compositional structure in SARS-CoV-2.
Platelet bioenergetics correlate with skeletal muscle metabolism in C57BL/6J mice
Authors: Wilkinson Mia S , Ferguson Emily J , Bureau Justin , Veeneman Jennifer LMH , Lima Patricia DA , McGlory Chris , Dunham-Snary Kimberly J
Published: December 2024

Skeletal muscle insulin resistance is a key step in progression of cardiometabolic disease, and impaired mitochondrial bioenergetics has been implicated. However, mitochondrial bioenergetic research in skeletal muscle is limited by the need for muscle biopsies. We sought to determine if platelet bioenergetics could be used as a minimally invasive surrogate for skeletal muscle bioenergetics. Multiple parameters of mitochondrial respiration, measured by high resolution respirometry, correlated between platelets and gastrocnemius muscle in mice. We propose the coupling state of platelet mitochondria reflects that of skeletal muscle in mice, providing a foundation for future research on using platelets as a liquid biopsy for muscle mitochondrial health in cardiometabolic disease, offering early insights into muscle metabolism to enhance clinical biomarker implementation.

Graphical Abstract
Identification of colorectal malignancies enabled by phasor-based autofluorescence lifetime macroimaging and ensemble learning
Authors: Lagarto João L. , Herrando Alberto I. , Rego Rafaela , Fernández Laura , Azevedo José , Domingos Hugo , Vieira Pedro , Parvaiz Amjad , Shcheslavskiy Vladislav I. , Silva Pedro G. , Castillo-Martin Mireia
Published: December 2024

Significance

Colorectal cancer (CRC) remains one of the most frequent cancers and a leading contributor to cancer-associated mortality globally. CRCs are often diagnosed at an advanced stage, which leads to high mortality and morbidity. This outcome is exacerbated by high rates of recurrence and postoperative complications that contribute substantially to poor prognosis. Advancements in endoscopic assessment have improved CRC prevention, early detection, and surveillance over the years. Yet, CRC remains one of the most significant health challenges of the 21st century. Label-free optical spectroscopy methods have long been explored as potential partners to endoscopy, not only to enhance diagnostic accuracy but also to confer predictive capabilities to endoscopic evaluations.

Aim

We investigated the potential of time-resolved autofluorescence measurements excited at 375 nm and 445 nm to correctly classify benign and malignant tissues in CRC surgical specimens from 117 patients.

Approach

Multiparametric autofluorescence lifetime data were collected in two distinct datasets, which were used for training (n = 73) and testing (n = 44) a supervised ensemble learning classification model, with standard histopathology assessment serving as ground truth.

Results

Using 5-fold cross-validation, we achieved 82.6 ± 0.02% sensitivity, 90.4 ± 0.01% specificity, 87.4 ± 0.01% accuracy, and 0.941 ± 0.004 area under the curve (AUC) for training data. Evaluation on unseen test data yielded similar results, with 85.2% sensitivity, 84.5% specificity, 84.8% accuracy, and 0.915 AUC.

Conclusions

While preliminary, our findings underscore the potential impact of AI-assisted autofluorescence lifetime measurements in advancing CRC prevention, early detection, and surveillance efforts.
Glucagon-like peptide-1 receptor agonists (GLP-1RA) for neuroprotection following aneurysmal subarachnoid haemorrhage (aSAH): a scoping review protocol
Authors: Thomas Matt , Mastitskaya Svetlana , Parker Sam , Cookson Ruth , Holmes Lucy , Marsh Aidan , Ramesh Aravind , Rudd Sarah , Teo Mario , Mortimer Alex
Published: December 2024

Objective

The objective of this scoping review is to understand the extent and type of evidence in relation to the use of glucagon-like peptide-1 receptor agonists (GLP1-RA) for neuroprotection in aneurysmal subarachnoid haemorrhage (aSAH).

Introduction

The individual and societal costs of aSAH remain high. Effective neuroprotection would reduce morbidity and mortality but there are uncertainties around both established and emerging therapies. GLP1-RA show promise as neuroprotective drugs in other forms of acute and chronic brain injury and could be repurposed for aSAH.

Inclusion criteria

Animal and human studies of the use of GLP1-RA for aSAH will be included. Key exclusions are traumatic or non-aneurysmal subarachnoid haemorrhage, or the use of multi-agonist drugs.

Methods

Searches will conducted in Embase (Ovid), Medline (Ovid), Cochrane Central Register of Controlled Trials (Wiley) and the World Health Organisation’s International Clinical Trials Registry Platform with no limits applied. Studies for data extraction will be identified by two independent reviewers after screening of titles and abstracts then full text review of potentially relevant articles against inclusion criteria. Data will be extracted by two independent reviewers using a charting tool based on the Joanna Briggs Institute template. A narrative review and summary of findings will be presented.
Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024
Authors: Lambisia Arnold W. , Morobe John Mwita , Moraa Edidah , Mwarumba Salim , Korir Fredrick K.N. , Athman Raila Seif , Kiptui Rebecca , Mbee Micheal , Mugo Nelly , Amoth Patrick , Muange Penny , Houldcroft Charlotte J. , Barasa Edwine , Mwangangi Joseph , Githinji George , Holmes Edward C. , Ochola-Oyier Lynette Isabella , Agoti Charles N.
Published: December 2024

Background

In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as “red eye” disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.

Methods

Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.

Results

Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative.

Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CA24v detections were confirmed by both CA24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CA24v genotype IV.

Conclusion

The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.
AER-270 and TGN-020 are not aquaporin-4 water channel blockers
Authors: Unger Lucas , Wagner Kim , Steffen Jonas H , Wind Malene Lykke , Al-Jubair Tamim , Zou Hongjun , Clarke-Bland Charlotte , Murray Rebecca , Qureshi Bareerah , Lundström Susanna , Gaetani Massimiliano , Poyner David , Ayub Hoor , Wheatley Mark , Gourdon Pontus , Yool Andrea J , Törnroth-Horsefield Susanna , Bill Roslyn M , Salman Mootaz M. , Kitchen Philip
Published: December 2024

Aquaporin-4 (AQP4) is the most abundant water channel protein in the brain. It controls water homeostasis, facilitates glymphatic function and is a drug target for brain edema following injury or stroke. Dysregulation of brain water homeostasis affects millions of people every year leading to death, disability and cognitive decline, for which no medicines are available. Two compounds, AER-270 and TGN-020, are sold as AQP4 inhibitors and a prodrug of AER-270 is currently in a phase I human trial. However, the direct effect of these compounds on AQP4 function has not been unequivocally demonstrated. Our data across multiple cellular and molecular assay systems demonstrate, unexpectedly, that AER-270 and TGN-020 do not inhibit AQP4. Although we observed an apparent inhibitory effect of AER-270 and TGN-020 in theXenopus laevisoocyte assay, there was no effect in assays using reconstituted recombinant AQP4 or mammalian cells expressing exogenous or endogenous AQP4. We identify alternative mechanisms of action for both molecules that may explain previously reportedin vivoresults that were interpreted in the context of AQP4 inhibition. Overall, we conclude that AER-270 and TGN-020 should not be used to investigate the AQP4-dependence of biological processes in the brain.
A novel SUN1-ALLAN complex coordinates segregation of the bipartite MTOC across the nuclear envelope during rapid closed mitosis in Plasmodium
Authors: Zeeshan Mohammad , Blatov Igor , Yanase Ryuji , Ferguson David J. P. , Pashley Sarah L. , Chahine Zeinab , Botté Yoshiki Yamaryo , Mishra Akancha , Marché Baptiste , Bhanvadia Suhani , Hair Molly , Batra Sagar , Markus Robert , Brady Declan , Bottrill Andrew , Vaughan Sue , Botté Cyrille Y. , Le Roch Karine , Holder Anthony A. , Tromer Eelco C. , Tewari Rita
Published: December 2024

Mitosis in eukaryotes involves reorganization of the nuclear envelope (NE) and microtubule-organizing centres (MTOCs). During male gametogenesis in Plasmodium, the causative agent of malaria, mitosis is exceptionally rapid and highly divergent. Within 8 min, the haploid male gametocyte genome undergoes three replication cycles (1N to 8N), while maintaining an intact NE. Axonemes assemble in the cytoplasm and connect to a bipartite MTOC-containing nuclear pole (NP) and cytoplasmic basal body, producing eight flagellated gametes. The mechanisms coordinating NE remodelling, MTOC dynamics, and flagellum assembly remain poorly understood.

We identify the SUN1-ALLAN complex as a novel mediator of NE remodelling and bipartite MTOC coordination duringPlasmodiummale gametogenesis. SUN1, a conserved NE protein, localizes to dynamic loops and focal points at the nucleoplasmic face of the spindle poles. ALLAN, a divergent allantoicase, has a location like that of SUN1, and these proteins form a unique complex, detected by live-cell imaging, ultrastructural expansion microscopy, and interactomics. Deletion of either SUN1 or ALLAN genes disrupts nuclear MTOC organization, leading to basal body mis-segregation, defective spindle assembly, and impaired spindle microtubule-kinetochore attachment, but axoneme formation remains intact. Ultrastructural analysis revealed nuclear and cytoplasmic MTOC miscoordination, producing aberrant flagellated gametes lacking nuclear material. These defects block development in the mosquito and parasite transmission, highlighting the essential functions of this complex.
Cholinergic interneurons of the dorsomedial striatum mediate winner-loser effects on social hierarchy dynamics in male mice
Authors: Hsu Mao-Ting , Akamine Yumiko , Kurima Kiyoto , Tanaka Kazumasa Z. , Wickens Jeffery R.
Published: December 2024

Cholinergic interneurons of the dorsomedial striatum may play a role in social hierarchy dynamics. A social hierarchy is an organization of individuals by rank that occurs in social animals. Establishing a new social hierarchy involves flexible behavior in deciding whether to be a winner or loser, experience of winning or losing, and stabilization of rank. The neural circuits underlying such flexible behavior have yet to be fully understood, but previous research indicates that cholinergic interneurons in the dorsomedial striatum play a role in behavioral flexibility. We used the dominance tube test to measure ranking within group housed mice, before and after between-cage competitions using the same test. We found that the experience of winning or losing against mice from different cages not only contributes to new social hierarchies among the competitors, but also causally influences the subsequent social hierarchy among their cage mates in the home cage – supporting the hypothesis of winner-loser effects on later social ranking. To test the hypothesis that cholinergic interneurons contribute to social hierarchy dynamics, we made a selective lesion of cholinergic interneurons in the dorsomedial striatum. The lesion did not prevent social hierarchy formation among pairs of similarly ranked individuals from different cages. However, it reduced the loser effect of external competition on the subsequent home-cage rankings in dominant mice. In light of these results we suggest that cholinergic interneurons in dorsomedial striatum increase the flexibility of social hierarchy dynamics.

Significance statement

The effect of winning or losing a competition on subsequent ranking in mouse home cage social hierarchies was examined using the dominance tube test. We found that losing, when dominant mice were defeated by equally ranked mice from another cage, led to decreased social rank in their home cage. Conversely, winning by initially subordinate mice led to increased rank in the home cage social hierarchy. The loser effect on subsequent behavior in dominant mice was reduced after selective lesions of the cholinergic interneurons of the dorsomedial striatum. We suggest that losing might produce these effects by altering the activity of cholinergic interneurons, and thus modulating synaptic plasticity in neural circuits involved in flexible decision making and positive reinforcement.
The RNA-binding protein PRRC2B preserves 5’ TOP mRNA during starvation to maintain ribosome biogenesis during nutrient recovery
Authors: Goldberg Nadav , Bril Doron , Eisenstein Miriam , Olender Tsviya , Savidor Alon , Bialik Shani , Pietrokovski Shmuel , Kimchi Adi
Published: December 2024

PRRC2B is an intrinsically disordered RNA-binding protein that is part of the cell’s translation machinery. Here we show that PRRC2B has two alternatively spliced mRNA transcripts producing major long and minor short isoforms. Mass spectrometry-based interaction studies indicated that both isoforms associate with the 40S ribosomal subunit and translation initiation factors. Importantly, the long isoform also interacted with additional RNA-binding proteins through its unique Arg/Gly-rich region. Among these is LARP1, a regulator of 5’ terminal oligopyrimidine (TOP) mRNAs under conditions of mTOR inhibition. We discovered that like LARP1, PRRC2B is necessary for preservation of 5’ TOP mRNA levels, particularly those encoding ribosomal proteins, during amino acid starvation. In its absence, the rapidde novotranslation of ribosomal proteins that takes place upon nutrient recovery is impeded. Overall, our study elucidates a newly discovered function for PRRC2B as an RNA-binding protein that regulates ribosomal biogenesis upon metabolic shift, in addition to its established function in initiating translation of specific mRNA targets.
Avian telencephalon and cerebellum volumes can be accurately estimated from digital brain endocasts
Authors: Keirnan Aubrey R. , Cunha Felipe , Citron Sara , Prideaux Gavin , Iwaniuk Andrew N. , Weisbecker Vera
Published: December 2024

For studies of the evolution of vertebrate brain anatomy and potentially associated behaviours, reconstructions of digital brain endocasts from computed tomography scans have revolutionised our capacity to collect neuroanatomical data. However, measurements from digital endocasts must be validated as reflecting actual brain anatomy, which is difficult because the collection of soft tissue information through histology is laborious and time consuming. In birds, the reliability of digital endocast measurements as volume proxies for the two largest brain regions – the telencephalon and cerebellum - remains to be validated despite their use as proxies e.g. of cognitive performance or flight ability. We here use the largest dataset of histology and digital endocasts to date, including 136 species from 25 avian orders, to compare digital endocast surface area measurements with actual brain volumes of the telencephalon, cerebellum, and whole-brain endocast. Using linear and phylogenetically informed regression analyses, we demonstrate that endocast surfaces are strongly correlated with their brain volume counterparts for both absolute and relative size. This provides empirical support for using endocast-derived cerebellar and telencephalic surface areas in existing and future studies of living and extinct birds, with potential to expand to the dinosaur-bird transition in the future.
Extended Quality (eQual): Radial threshold clustering based on n-ary similarity
Authors: Chen Lexin , Smith Micah , Roe Daniel R. , Miranda-Quintana Ramón Alain
Published: December 2024

We are transforming Radial Threshold Clustering (RTC), anO(N2) algorithm, into Extended Quality Clustering, anO(N)algorithm with several novel features. Daura et al’s RTC algorithm is a partitioning clustering algorithm that groups similar frames together based on their similarity to the seed configuration. Two current issues with RTC is that it scales asO(N2) making it inefficient at high frame counts, and the clustering results are dependent on the order of the input frames. To address the first issue, we have increased the speed of the seed selection by usingk-means++ to select the seeds of the available frames. To address the second issue and make the results invariant with respect to frame ordering, whenever there is a tie in the most populated cluster, the densest and most compact cluster is chosen using the extended similarity indices. The new algorithm is able to cluster in linear time and produce more compact and separate clusters.
Enhanced dark matter abundance in first-order phase transitions
Authors: Allahverdi Rouzbeh , Hauptmann Cash , Huang Peisi
Published: December 2024

We propose a novel scenario to obtain the correct relic abundance for thermally underproduced dark matter. This scenario utilizes a strongly first-order phase transition at temperature TPT that gives rise to dark matter mass m. Freeze-out in the broken phase can yield the desired abundance in the entire region currently allowed by observational bounds and theoretical constraints for 102TPT≲m≲104TPT. We show that the accompanying gravitational waves are strong enough to be detected by many upcoming and proposed experiments. This, in tandem with dark matter indirect searches, provides a multimessenger probe of such models. Positive signals in the future can help reconstruct the potential governing the phase transition and shed light on an underlying particle physics realization.

Published by the American Physical Society
2024
Leptogenesis with dynamical couplings
Authors: Huang Peisi , Xu Tao
Published: December 2024

We propose a novel leptogenesis mechanism with a temperature-dependent coupling between the right-handed neutrino and Standard Model particles. This coupling experiences suppression at high temperatures and becomes sizable when the lepton asymmetry washout processes are Boltzmann-suppressed. Such a feature ensures that the washout rates remain consistently below the Hubble expansion rate, preserving all lepton asymmetry generated in the decay of right-handed neutrinos. We illustrate the feasibility of this mechanism with two example models and show that the observed baryon asymmetry of the Universe can be successfully obtained for right-handed neutrino masses larger than 109  GeV as well as for smaller violation of charge-parity symmetry.

Published by the American Physical Society
2024
Scalar field with a time-independent classical source is not trivial after all: From vacuum decay to scattering
Authors: Tinti Leonardo , Vereijken Arthur , Jafarzade Shahriyar , Giacosa Francesco
Published: December 2024

Historically it has been believed that a time-independent classical source has no effect on the scattering of relativistic uncharged fields, in contrast with single particle quantum mechanics. In this work we show that the dynamics is not trivial. We solve exactly for the scattering amplitudes and find that a key ingredient is the production of particles from the unstable vacuum, conceptually similar to the Schwinger mechanism. We compute exactly the probabilities for the vacuum to decay in n particles. The time dependence of such probabilities displays interesting properties such as the quantum Zeno effect and, in particular, has no regime where the exponential decay law is a good approximation. We show that the trivial scattering found in the past is the by-product of the adiabatic switching of the interaction. In fact, it is not possible to switch off the interaction (adiabatically or otherwise) at distant times and recover the exact results. Finally, this nontrivial vacuum behavior is a source of particle production. We argue that such nonperturbative calculations can be phenomenologically relevant for the production processes that are suppressed at the lower orders in perturbation theory, for instance dilaton production in a medium.

Published by the American Physical Society
2024
Circularly polarized photon emission from magnetized chiral plasmas
Authors: Wang Xinyang , Shovkovy Igor A.
Published: December 2024

We investigate the emission of circularly polarized photons from a magnetized quark-gluon plasma with nonzero quark-number and chiral charge chemical potentials. These chemical potentials qualitatively influence the differential emission rates of circularly polarized photons. A nonzero net electric charge density, induced by quark-number chemical potentials, enhances the overall emission of one circular polarization over the other, while a nonzero chiral charge density introduces a spatial asymmetry in the emission with respect to reflection in the transverse plane. The signs of the electrical and chiral charge densities determine which circular polarization dominates overall and whether the emission preferentially aligns with or opposes the magnetic field. Based on these findings, we propose that polarized photon emission is a promising observable for characterizing the quark-gluon plasma produced in heavy-ion collisions.

Published by the American Physical Society
2024
Singular-value statistics of directed random graphs
Authors: Méndez-Bermúdez J. A. , Aguilar-Sánchez R.
Published: December 2024

Singular-value statistics (SVS) has been recently presented as a random matrix theory tool able to properly characterize non-Hermitian random matrix ensembles []. Here, we perform a numerical study of the SVS of the non-Hermitian adjacency matrices A of directed random graphs, where A are members of diluted real Ginibre ensembles. We consider two models of directed random graphs: Erdös-Rényi graphs and random geometric graphs. Specifically, we focus on the singular-value-spacing ratio r and the minimum singular value λmin. We show that 〈r〉 (where 〈·〉 represents ensemble average) can effectively characterize the crossover between mostly isolated vertices to almost complete graphs, while the probability density function of λmin can clearly distinguish between different graph models.

Published by the American Physical Society
2024
Improving student understanding of the number of distinct many-particle states for a system of identical particles with a fixed number of available single-particle states
Authors: Keebaugh Christof , Marshman Emily , Singh Chandralekha
Published: December 2024

We examine students’ challenges in determining the number of distinct many-particle stationary states for a system of noninteracting identical particles, focusing on how these insights guided the design, validation, and evaluation of a quantum interactive learning tutorial (QuILT) to aid students’ understanding. Specifically, we focus on systems with a fixed number of available single-particle states and particles, where the total energy is not fixed. The QuILT is designed to provide scaffolding support to help students learn these complex concepts more effectively. This study was conducted in advanced quantum mechanics courses, where written questions were administered to students in class following traditional instruction on the relevant concepts. Additionally, individual interviews were conducted with students to gain deeper insights. Our findings reveal that both upper-level undergraduate and graduate students face similar challenges in understanding these concepts. Additionally, difficulty with basic concepts in combinatorics that are necessary to answer the questions correctly was also found. The QuILT offers scaffolding support to help undergraduate and graduate students systematically reason through these concepts.

Published by the American Physical Society
2024
Counting statistics of ultrabroadband microwave photons
Authors: Bolduc Beaudoin Simon , Pinsolle Edouard , Reulet Bertrand
Published: December 2024

We report measurements of counting statistics, average and variance, of microwave photons of ill-defined frequency: bichromatic photons, i.e., photons involving two well separated frequencies, and “white” broadband photons. Our setup allows for the analysis of single photonic modes of arbitrary waveform over the 1–10 GHz frequency range. The photon statistics are obtained by on-the-fly numerical calculation from the sampled time-dependent voltage. Using an ac+dc biased tunnel junction as a source of quantum microwave, we report an ultrawide squeezing spectrum representing a competitive source for entanglement generation (up to 0.9 billion measured entangled bits per second) easily achievable experimentally. We also report the observation of quantum steering by the tunnel junction, and show how the presence of squeezing of a broadband mode implies the existence of entanglement between two modes it encompasses.

Published by the American Physical Society
2024
Ideal Chern bands with strong short-range repulsion: Applications to correlated metals, superconductivity, and topological order
Authors: Wilhelm Patrick H. , Läuchli Andreas M. , Scheurer Mathias S.
Published: December 2024

Motivated by recent experiments on correlated van der Waals materials, including twisted and rhombohedral graphene and twisted WSe2, we perform an analytical and numerical study of the effects of strong on-site and short-range interactions in fractionally filled ideal Chern bands. We uncover an extensive nontrivial ground state manifold within the band filling range 0<ν<1 and introduce a general principle, the “three-rule,” for combining flat band wave functions, which governs their zero-energy property on the torus geometry. Based on the structure of these wave functions, we develop a variational approach that reveals distinct phases under different perturbations: metallic behavior emerges from a finite dispersion, and superconductivity is induced by attractive Cooper channel interactions. Our approach, not reliant on the commonly applied mean-field approximations, provides an analytical expression for the macroscopic wave function of the off-diagonal long-range order correlator, attributing pairing susceptibility to the set of nontrivial zero-energy ground state wave functions. Extending to finite screening lengths and beyond the ideal limit using exact diagonalization simulations, we demonstrate the peculiar structure in the many-body wave function's coefficients to be imprinted in the low-energy spectrum of the topologically ordered Halperin spin-singlet state. Our findings also make connections to frustration-free models of noncommuting projector Hamiltonians, potentially aiding the future construction of exact ground states for various fractional fillings.

Published by the American Physical Society
2024
Probing the exciton spin-valley depolarization with spin-momentum-valley locked unbound states using tr-ARPES
Authors: Arfaoui Mehdi , Ferreira Robson , Jaziri Sihem
Published: December 2024

Time-resolved, angle-resolved photoemission spectroscopy (tr-ARPES) is a powerful technique to access the ultrafast dynamics of intervalley couplings and population exchanges. In monolayer transition metal dichalcogenides, this is advantageous due to the fact that excitons have a large binding energy, allowing them to be resonantly excited by a short-pulse pump without also putting into play a large set of dissociated electron-hole pairs, while at the same time remaining relatively localized in momentum space so that the outgoing currents related to different local valleys can be safely distinguished in the energy-momentum resolved tr-ARPES signal. In this work, we present a detailed theoretical description of the high-energy states that form the escape continuum for photoejected electrons in a tr-ARPES experiment, paying particular attention to their momentum dispersions, time-reversal symmetries, and spin characteristics. The analysis of the various symmetries fulfilled by such unbound states reveals the existence of a momentum-valley locking for the unbound final electron states, sharing various features with the valley Hall effect. Moreover, the photoextracted current under a circularly polarized pump ideally presents a robust triple locking of momentum direction, valley origin, and spin orientation, which permits envisioning an on-demand source of highly spin-polarized electrons on vacuum. We also present a study of the robustness of such findings against intervalley processes that tend to mitigate the valley-spin polarization of the intermediate exciton states. To further investigate this aspect, we consider in detail the role of Coulomb-exchange driven intervalley coupling. That allows us to quantify the dependence of the tr-ARPES measurements upon various setup parameters, such as the incident angle and light helicity. Finally, we present a critical discussion about the role of a few intervalley couplings and/or scattering processes. Our findings have broad implications and are anticipated to be applicable to other two-dimensional structures and intervalley scattering events.

Published by the American Physical Society
2024
Mechanisms of Chromosome Positioning During Mitosis
Authors: Sigmund Ivan , Božan Domagoj , Šarić Ivana , Pavin Nenad
Published: December 2024

The mitotic spindle, a micromachine composed of microtubules and associated proteins, plays a pivotal role in ensuring the accurate segregation of chromosomes. During spindle assembly, initially randomly distributed chromosomes are transported toward the equatorial plate and experiments suggest that several competing mechanisms can contribute to this process of chromosome congression. However, a systematic theoretical study of forces relevant to chromosome congression is still lacking. Here we show, by introducing a physical model, that length-dependent forces generated by motor proteins transport chromosomes toward the spindle equator. Passive cross-linkers, on the other hand, can generate off-centering forces that impair chromosome congression. Our mean-field approach also reveals that stable points can exist in the vicinity of spindle poles, in addition to the one in the center, and thus provides an explanation for erroneous spindles with polar chromosomes. Taking all these processes into account, our study provides a comprehensive approach to understanding how different spindle components interact with each other and generate forces that drive chromosome congression.

Published by the American Physical Society
2024
Identifying the determinants of biorefineries location in a core-periphery polarised Europe
Authors: Celi Giuseppe , Sica Edgardo
Published: December 2024

Purpose

The challenge posed by the new European bioeconomy strategy in support of green transition goals is significant and raises serious questions regarding its sustainability, from socio-economic, territorial and ecological perspectives. Such a strategy is indeed being implemented in a Europe divided between economically strong and weak areas and where regional divergences within countries have increased nearly everywhere. Considering this polarised context, the present paper investigates the determinants of biorefinery presence in Europe, adopting a core-periphery perspective.

Design/methodology/approach

Spatial analysis is employed to identify core and periphery regions at the NUTS2 level, and econometric estimates show that the factors determining biorefinery implementation differ between these regions.

Findings

In the core regions, socio-economic factors (e.g. higher income, education and social acceptability) are most significant, while in the periphery, agricultural and territorial determinants play a more prominent role. However, the differences between regions are mitigated when the sample is narrowed to focus on biorefineries with the greatest technological readiness.

Originality/value

To the best of our knowledge, the determinants of biorefineries' presence in a territory is an under-explored topic. Moreover, the existence of core-periphery dynamics even within bio-based activities raises important questions and policy implications in ecological transition processes in Europe.
Text mining in tourism and hospitality research: a bibliometric perspective
Authors: Lekmiti Amine , Stolk Paul John , Taylor Alex , Ramachandran Sridar , Yap Ng Keng
Published: December 2024

Purpose

The purpose of this study is to assess the current level of knowledge on the application of text mining in tourism and hospitality (T&H) research and provide a novel comprehensive framework for the field. This study also identifies gaps and proposes future research directions.

Design/methodology/approach

This bibliometric study analyzes 814 journal articles, sourced from Scopus between 2004 and 2024, and uses performance analysis and science mapping using Biblioshiny and VOSviewer software.

Findings

Over 50% of the articles were published between 2022 and 2024, reflecting a surge in text-mining applications in T&H research. These studies primarily focus on topics such as customer satisfaction, sustainability, destination image and COVID-19 effects, with sentiment analysis and topic modeling being the predominant techniques. The primary data sources are online reviews and microblogs. The review also highlights recent research trends (e.g. long–short-term memory, support vector machines and crisis) and classifies them into four conceptual categories concerning the application of text mining in T&H research: How? Where? Why? When?

Originality/value

This study comprehensively explores the evolution of T&H, contributions from research constituents and the intellectual structure of the field, providing a novel comprehensive framework while also assessing the field and highlighting its challenges.