bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic inverse design of metasurfaces using mixture density neural networks
Authors: Torfeh Mahsa , Hsu Chia Wei 
Published: December 2024

Abstract
Metasurfaces are planar sub-micron structures that can outperform traditional optical elements and miniaturize optical devices. Optimization-based inverse designs of metasurfaces often get trapped in a local minimum, and the inherent non-uniqueness property of the inverse problem plagues approaches based on conventional neural networks. Here, we use mixture density neural networks to overcome the non-uniqueness issue for the design of metasurfaces. Once trained, the mixture density network (MDN) can predict a probability distribution of different optimal structures given any desired property as the input, without resorting to an iterative local optimization. As an example, we use the MDN to design metasurfaces that project structured light patterns with varying fields of view. This approach enables an efficient and reliable inverse design of fabrication-ready metasurfaces with complex functionalities without getting trapped in local optima.
Enhancing image quality in circular-view photoacoustic tomography using randomized detection points
Authors: Hakakzadeh Soheil , Rajendran Praveenbalaji , Kavehvash Zahra , Pramanik Manojit 
Published: December 2024

Abstract
Circular-view (circular scan) photoacoustic computed tomography (PACT) with low-density detection points (DPs) is an efficient, high-speed, and inexpensive modality with numerous (pre-) clinical applications. However, as the number of DPs decreases (decrease in A-lines), some unwanted streak artifacts appear in the reconstructed PACT image. Here, we present an approach to address the mentioned challenge and enhance image contrast. In this method, several low-resolution-images (LRIs) are reconstructed by employing a few DPs’ data with randomized locations. These LRIs are used in computing an artifact score matrix (ASM) to identify the location of artifacts. Three numerical (two vasculatures and human brain), two experimental (triangle and complex leaf), and an in vivo (a rat brain) studies were conducted to evaluate the efficacy of the proposed method (applying the computed ASM to the final reconstructed PA image). Our findings show that the proposed method outperforms conventional methods and offers better image quality. The signal-to-noise ratio and structural similarity index values of the proposed method are quantitatively 20 dB and 25% better than the conventional method, respectively. Furthermore, compared to the conventional method, the proposed method has an artifact standard deviation that is 50 times lower.
Diversity in Naturally Acquired Immunity to Group B Streptococcus: A Comparative Study of Women From Bangladesh, Malawi, and the United Kingdom
Authors: Khandaker Shadia , Sharma Shilpee , Hall Tom , Lim Suzanna , Lehtonen Janne , Leung Stephanie , Ahmed Zabed Bin , Gorringe Andrew , Saha Samir K , Marchant Arnaud , Le Doare Kirsty , Kadioglu Aras , French Neil 
Published: December 2024

Abstract

Background
Significant disparities in group B Streptococcus (GBS) colonization and neonatal disease rates have been documented across different geographic regions. For example, Bangladesh reports notably lower rates as compared with the United Kingdom and Malawi. This study investigates whether this epidemiologic variability correlates with the immune response to GBS in these regions.

Methods
Qualitative and quantitative analyses of naturally acquired immunoglobulin G (IgG) antibodies against GBS capsular polysaccharide and the Alp protein family were conducted in serum samples from women of childbearing age in the United Kingdom, Bangladesh, and Malawi. The efficacy of these antibodies in clearing vaginal colonization or protecting newborns from GBS infection was assessed with humanized mouse models.

Results
Bangladeshi women displayed the highest diversity in serotype distribution, with elevated IgG levels in the serum against GBS capsular polysaccharides Ia, Ib, II, III, IV, and V, as well as Alp family proteins. In contrast, Malawian sera demonstrated the weakest antibody response. Bangladeshi sera also showed heightened IgG-mediated complement deposition, opsonophagocytic killing, and neonatal Fc receptor binding while tested against capsular polysaccharide Ib. In a humanized neonatal Fc receptor mouse model, Bangladeshi sera led to faster clearance of GBS virulent serotype Ib vaginal colonization. Additionally, offspring from dams passively immunized with Bangladeshi sera demonstrated notably increased survival rates.

Conclusions
This study demonstrates significant variability in the immune response to GBS across different geographic regions. These findings underscore the importance of understanding GBS-induced immune response in diverse populations, which may significantly affect vaccine efficacy in these regions.
Arguing against the Brahmanical tradition: Dr B. R. Ambedkar’s engagement with the Manusmṛti
Authors: Khiamniungan Chiangmong 
Published: December 2024

Abstract
This essay attempts to provide an overview of Dr B. R. Ambedkar’s intense, extensive, and sustained examination and critique of what he took to be the ‘bible’ or ‘gospel’ of Brahmanism, the Manusmṛti. It will outline Ambedkar’s views concerning the significance of the text; undertake a survey of the primary and secondary sources Ambedkar relied on; present his arguments for the authorship and date of the text; indicate his argument about the sectarian and ideologically charged origin of the text; and, finally, elaborate his critique of the inegalitarian scheme that the text institutes. The singularity of Ambedkar’s perspective on, the uncompromisingly critical stance he adopts towards, and the sheer extent and earnestness of his engagement with, the Manusmṛti lends his treatment of this most authoritative of texts a topic worthy of closer attention not just from the burgeoning legion of scholars studying him but even from specialists of dharmaśāstra, especially in the light of recent interest in the political and social aspects of the origin and nature of this genre.
Symbolic and Non-Symbolic numbers differently affect center identification in a number-line bisection task
Authors: Porru Annamaria , Ronconi Lucia , Lucangeli Daniela , Regolin Lucia , Benavides-Varela Silvia , Rugani Rosa 
Published: December 2024

AbstractNumerical and spatial representations are intertwined as in the Mental Number Line, where smaller numbers are on the left and larger numbers on the right. This relationship has been repeatedly demonstrated with various experimental approaches, such as the line bisection task.Spatial accuracy appears to be systematically distorted leftward for smaller digits by elaboration of spatial codes during number processing. Other studies have investigated perceptual and visuo-spatial attention bias using the digit line bisection task, suggesting that these effects may be related to a cognitive illusion in which the reference numbers project their values onto the straight line, creating an illusory lateral disparity. On the other hand, both dot arrays (non-symbolic stimuli) and arabic numbers (symbolic stimuli) demonstrate a privileged relation between spatial and numerical elaboration. The bias toward the larger numerosity flanker was attributed to a length illusion. There is, however, no consensus regarding whether physical features and symbolic and non-symbolic numerical representations exert the same influence over spatial ones.In the present study, we carried out a series of 4 Experiments to provide further evidence for a better understanding of the nature of this differential influence. All experiments presented the numbers in both symbolic and non-symbolic formats. In Experiment 1, the numbers “2-8” were presented in a variety of left-right orientations. In Experiment 2, the flankers were identical, “2-2” or “8-8”, and symmetrically displaced with respect to the line. In Experiment 3, we employed asymmetrically distributed eight dots, or font sizes in “8-8” numerals, to create a perceptual imbalance. In Experiment 4, we replicated the manipulation used in Experiment 3, but with two dots and “2-2” numerals.The Non-Symbolic format induced stronger leftward biases, particularly when the larger numerosity (Experiment 1) or the denser stimuli near the line (Experiments 3 and 4) were on the left, while no bias emerged when flankers were numerically equivalent and symmetrical (Experiment 2). The left bias may result from a tendency to estimate the influence of stimulus perception associated with participant’ scanning direction, similar to the direction of pseudoneglect. Conversely, the Symbolic format induced mostly right bias, possibly due to left-lateralized processing and a tendency to use a common strategy involving scanning from left to right.Altogether our data support the view that abstract numbers and non-symbolic magnitude affect perceptual and attentional biases, yet in distinctive ways.
Vibratory stimulation and not action observation or mirror therapy reduces paralyzed hand spasticity in chronic stroke survivors
Authors: Nakano Hideki , Nakagawa Kotaro , Ikuno Tatsuya , Nagashima Munenori , Naito Eiichi 
Published: December 2024

ObjectivePost-stroke spasticity prevalence increases with time from stroke onset, and negatively impacts the patient’s quality of life. Vibratory stimulation (VS) to the spastic muscles can reduce spasticity, whereas action observation (AO) and mirror therapy (MT) are reported to be less effective for spasticity reduction. However, these effects have not been compared within the same individuals. Therefore, this study compared the spasticity-reducing effects of VS, AO, and MT.MethodsIndependent groups of 13 patients with chronic stroke participated in the study. In Experiment 1, the participants underwent VS, AO, and combined VS+AO on separate days. In Experiment 2, different participants received VS, MT, and VS+MT. Spasticity was assessed using the Modified Ashworth Scale (MAS) before and after the interventions.ResultsIn Experiment 1, VS significantly reduced MAS scores but not AO, and AO did not enhance the VS effect in combined therapy. In Experiment 2, VS significantly reduced the MAS scores, but not MT, and MT did not enhance the VS effect in combined therapy.ConclusionSpastic muscle VS reduced spasticity in chronically paralyzed hands; however, AO and MT did not enhance the VS effect. VS alone may be a more effective treatment for spasticity in patients with chronic stroke.
Willingness to pay for COVID-19 vaccine and its correlates: A cross-sectional survey in Bangladesh
Authors: Hossain Mohammad Bellal , Alam Md. Zakiul , Islam Md. Syful , Sultan Shafayat , Faysal Md. Mahir , Rima Sharmin , Hossain Md. Anwer , Mamun Abdullah Al , Mamun Abdullah-Al- 
Published: December 2024

AbstractThe Government of Bangladesh has offered COVID-19 vaccines at no cost; however, sustaining this free vaccination program for a large population poses significant challenges. Assessing willingness to pay (WTP) is essential for understanding potential pricing strategies, subsidy requirements, and vaccine demand. This study aimed to estimate the prevalence of WTP for COVID-19 vaccines and identify its influencing factors to support program sustainability. Using a cross-sectional design, data were collected from 1,497 respondents through online, and face-to-face interviews and multiple logistic regression was employed to analyze the correlates of WTP. Results showed that 50.9% of participants were willing to pay, with an average WTP of 754.55 BDT (US$8.93) and a median of 300 BDT (US$3.55). WTP was significantly higher among individuals with graduate (aOR=2.2, P=0.007) or Masters & MPhil/PhD education (aOR=2, P=0.030), higher family income (aOR=1, P=0.039), and those with more excellent knowledge about the vaccine (aOR=1.1, P=0.003), positive behavioral practices (aOR=1.1, P<0.001), stronger subjective norms (aOR=1.2, P=0.009), higher anticipated regret (aOR=1.2, P=0.005), and perceived benefits (aOR=1.1, P=0.029). Conversely, WTP was lower among participants with negative attitudes toward vaccines (aOR=0.9, P<0.001) and high behavioral control (aOR=0.9, P=0.006). With nearly half of respondents unwilling to pay, the study highlights the need to improve vaccine-related knowledge, promote positive behaviors, reduce vaccine hesitancy, and enhance income-based affordability to increase WTP. Health promotion efforts should focus on disseminating vaccine knowledge and addressing negative perceptions. Additionally, a subsidized program for low-income groups could help mitigate financial barriers and promote equitable vaccine access.
High-efficiency genomic mapping of chromatin-associated targets with CUT&RUN
Authors: Firestone Tessa M. , Venters Bryan J. , Novitzky Katherine , Albertorio-Sáez Liz Marie , Barnes Courtney A. , Fedder-Semmes Karlie N. , Hall Nathan W. , Hickman Allison R. , Kaderli Mark , Windham Carolina Lin , Marunde Matthew R. , Maryanski Danielle N. , Noll Kelsey , Shannon Leslie , Spengler Jennifer , Cowles Martis W. , Sun Zu-Wen , Keogh Michael-Christopher , Johnstone Andrea L. , Weinzapfel Ellen N. , Sun Lu 
Published: December 2024

ABSTRACTThe precise regulation of chromatin composition is critical to gene expression and cellular identity, and thus a key component in development and disease. Robust assays to study chromatin features, including histone post-translational modifications (PTMs) and chromatin-associated proteins (e.g., transcription factors or PTM readers), are essential to understand their function and identify novel therapeutic strategies. To this end, Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has emerged as a powerful tool for high-resolution epigenomic profiling. The approach has been successfully applied to numerous cell and tissue types, informing on target genomic distribution with unprecedented sensitivity and throughput. Here, we provide a detailed CUT&RUN protocol from sample collection through data analysis, including best practices and defined controls to ensure specific, efficient, and robust target profiling.
Neural Dynamics of Tonic Cold Pain: A Novel Investigation of an In-Scanner Alternative to the Cold Pressor Test in Healthy Individuals
Authors: Medina Sonia , Hughes Sam W. 
Published: December 2024

AbstractThe cold pressor task (CPT) is widely used to study tonic pain during acute and chronic conditions and is often as used as a conditioning stimulus to activate descending pain control systems. However, logistical challenges in magnetic resonance imaging (MRI) limit its application, hindering the understanding of CPT’s neural dynamics. To address this, we acquired resting-state functional MRI data from 30 healthy participants before, during, and after immersion in gelled-cold water, the closest in-scanner alternative to date to CPT for prolonged stimulation. Participants provided subjective pain intensity ratings after each scan, as well as average pain perceived during noxious stimulation, using a numeric rating scale (NRS). Following fMRI, participants rated their pain continuously during identical tonic noxious stimulation of the contralateral hand using a visual analogue scale (VAS). We employed three complementary methods to examine changes in brain function across fMRI conditions: a data-driven approach via independent component analysis (ICA), seed-to-whole-brain connectivity analysis with the periaqueductal grey (PAG) as seed, and spectral dynamic causal modelling (spDCM) to explore effective connectivity changes across the dorsal anterior cingulate cortex (dACC), anterior insulae (AI), thalamus, and PAG. NRS scores were significantly higher following tonic cold compared to baseline and recovery conditions. Continuous VAS reflected sustained mild-to-moderate pain over six minutes, with average VAS scores not significantly differing from NRS ratings recorded in the scanner. ICA identified engagement of descending pain control and sensorimotor networks during pain, with the latter persisting during recovery. Seed-based analysis revealed a disengagement between the PAG and cortical/subcortical regions involved in pain processing, such as the dACC, midcingulate cortex, AI, intraparietal sulcus, and precuneus. Finally, spDCM revealed tonic pain neural signature was most likely characterised by top-down inhibitory and bottom-up excitatory connections. This study establishes the cold gelled-water paradigm as a robust in-scanner alternative to CPT. By uncovering key neural dynamics of CPT, we provide new insights into the brain and brainstem mechanisms of tonic cold pain paradigms routinely used in psychophysical pain studies.Key pointsImmersion in gelled-cold water is a reliable in-scanner substitute for the cold pressor task, enabling prolonged tonic cold pain research in MRI.Key neural dynamics, such as PAG-driven excitatory inputs and AI-mediated inhibitory control, were identified, providing new insights into cold pain modulation.By taking a multi-method approach, including ICA, seed-based connectivity, and DCM, we offer a comprehensive view of the neural networks involved in tonic cold pain, bridging neuroimaging and behavioural research.
Spatial and feature-selective attention interact to drive selective coding in frontoparietal cortex
Authors: Dermody Nadene , Lorenz Romy , Goddard Erin , Villringer Arno , Woolgar Alexandra 
Published: December 2024

AbstractAttention enables the selective processing of relevant information. Two types of selective attention, spatial and feature attention, have separable neural effects but in real life are often used together. Here, we asked how these types of attention interact to affect information coding in a frontoparietal ‘multiple-demand’ (MD) network, essential for attentional control. Using functional magnetic resonance imaging (fMRI) with multivariate pattern analysis, we examined how covert attention to object features (colour or shape) and spatial locations (left or right) influences coding of task-related stimulus information. We found that spatial and feature attention interacted multiplicatively on information coding in MD and visual regions, such that there was above-chance decoding of the attended feature of the attended object and no detectable coding of visually equivalent but behaviourally irrelevant aspects of the visual display. The attended information had a multidimensional neural representation, with stimulus information (e.g., colour) and discrimination difficulty (distance from the categorical decision boundary) reflected in separate dimensions. Rather than boosting processing of whole objects or relevant features across space, our results suggest neural activity reflects precise tuning to relevant information, indicating a highly selective control process that codes behaviourally relevant information across multiple dimensions.
Developmental programmes drive cellular plasticity, disease progression and therapy resistance in lung adenocarcinoma
Authors: Bienkowska Kamila J , Gallardo Y Stephany , Zainal Nur S , Ellis Matthew , Lopez Maria-Antoinette , Austine Judith , Pittla Sai , Chee Serena J , Alzetani Aiman , Shaw Emily C , Ottensmeier Christian H , Thomas Gareth J , Hanley Christopher J 
Published: December 2024

AbstractBackgroundCellular plasticity, involving loss of lineage determination and emergence of hybrid cell states, plays a pivotal role in non-small cell lung cancer (NSCLC) disease progression and therapy resistance. However, the full spectrum of atypical states generated in human NSCLC and the pathways that regulate them are yet to be fully elucidated. Here we examine the role of developmental programmes, alveogenesis and branching morphogenesis (BM), in regulating phenotypic diversity in NSCLC.MethodsTranscriptomic analysis of epithelial cells isolated from murine lungs at different stages of organogenesis were used to derive gene signatures for developmental programmes. Bulk tissue transcriptomic datasets from human NSCLC and non-neoplastic control samples were used to identify whether developmental programmes were associated with molecular, morphological, and clinical parameters. Single-cell RNA-sequencing was used to identify malignant cell states in human NSCLC (n = 16,621 epithelial cells from 72 samples) and protein level validation of these states was carried out using multiplexed immunohistochemistry (n = 40).ResultsMutually antagonistic regulation of alveogenesis and BM was found to account for a significant proportion of transcriptomic variance in human NSCLC bulk tissue datasets. BM activation was associated with poor overall survival rates in five independent lung adenocarcinoma (LUAD) cohorts (p=2.04e-13); and was significantly prognostic for resistance to tyrosine kinase inhibitors (TKIs; p=0.003) and immune checkpoint blockade (ICBs; p=0.014), in pre-treatment biopsies. Single-cell RNA-sequencing analysis revealed that malignant LUAD cells with loss of alveolar lineage fidelity predominantly acquired inflamed or basal-like cellular states, which were variably persistent in samples from TKI and ICB recurrence.ConclusionsOur results show LUAD tumours undergo reversion from an alveogenic to branching morphogenic phenotype during disease progression, generating inflamed or basal-like cell states that are variably persistent following TKI or ICB treatments. These findings identify prognostic biomarkers for therapy response and underscore the role of different cell states in resistance to multiple treatment modalities.
Stranded short nascent strand sequencing reveals the topology of eukaryotic DNA replication origins inTrypanosoma brucei
Authors: Stanojcic Slavica , Barckmann Bridlin , Monsieurs Pieter , Crobu Lucien , George Simon , Sterkers Yvon 
Published: December 2024

ABSTRACTThe structure of eukaryotic origins is a long-standing question in the DNA replication field, and the universal features that define the genomic regions acting as replication starting sites remain unclear. In this study, we employed the stranded SNS-seq methodology, a high-throughput sequencing method that preserves the directionality of short nascent strands, to map a set of origins inTrypanosoma brucei. This approach enhanced the specificity and resolution of origin mapping. Our findings indicated that replication predominantly initiates in intergenic regions, situated between poly(dA) and poly(dT) enriched sequences. Experimentally detected G4 structures were observed in the vicinity of some origins. These structures were observed to be embedded within poly(dA) enriched sequences in a strand-specific manner, with the G4s on the plus strand located upstream and the G4s on the minus strand located downstream of the centre. The centre of origin was mainly characterised by low nucleosome occupancy, with flanking regions displaying high nucleosome occupancy. Additionally, our findings revealed that 90% of origins overlapped with previously reported R-loops. To gain further insight, DNA combing analysis was employed to compare replication at the single-cell level with that observed at the entire cell population level. Finally, a model of eukaryotic origin has been proposed.GRAPHICAL ABSTRACT