bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathological insights derived from neuroimaging in amyotrophic lateral sclerosis: emerging clinical applications
Authors: Tu Sicong , Vucic Steve , Kiernan Matthew C. 
Published: July 2024

Purpose of review
Neuroimaging has been instrumental in shaping current understanding of the pathoanatomical signature of amyotrophic lateral sclerosis (ALS) across clinically well defined patient cohorts. The potential utility of imaging as an objective disease marker, however, remains poorly defined.

Recent findings
Increasingly advanced quantitative and computational imaging studies have highlighted emerging clinical applications for neuroimaging as a complementary clinical modality for diagnosis, monitoring, and modelling disease propagation. Multimodal neuroimaging has demonstrated novel approaches for capturing primary motor disease. Extra-motor subcortical dysfunction is increasingly recognized as key modulators of disease propagation.

Summary
The neural signature of cortical and subcortical dysfunction in ALS has been well defined at the population level. Objective metrics of focal primary motor dysfunction are increasingly sensitive and translatable to the individual patient level. Integrity of extra-motor subcortical abnormalities are recognized to represent critical pathways of the ALS disease ‘connectome’, predicting pathological spread. Neuroimaging plays a pivotal role in capturing upper motor neuron pathology in ALS. Their potential clinical role as objective disease markers for disease classification, longitudinal monitoring, and prognosis in ALS have become increasingly well defined.
Genomic and single-cell characterization of patient-derived tumor organoid models of head and neck squamous cell carcinoma
Authors: Um Jung Hyun , Zheng Yueyuan , Mao Qiong , Nam Chehyun , Zhao Hua , Koh Yoon Woo , Shin Su-Jin , Park Young Min , Lin De-Chen 
Published: July 2024

AbstractHead and Neck Squamous Cell Carcinoma (HNSCC) remains a significant health burden due to tumor heterogeneity and treatment resistance, emphasizing the need for improved biological understanding and tailored therapies. This study enrolled 31 HNSCC patients for the establishment of patient-derived tumor organoids (PDOs), which faithfully maintained genomic features and histopathological traits of primary tumors. Long-term culture preserved key characteristics, affirming PDOs as robust representative models. PDOs demonstrated predictive capability for cisplatin treatment responses, correlatingex vivodrug sensitivity with patient outcomes. Bulk and single-cell RNA sequencing unveiled molecular subtypes and intratumor heterogeneity (ITH) in PDOs, paralleling patient tumors. Notably, a hybrid epithelial-mesenchymal transition (hEMT)-like ITH program is associated with cisplatin resistance and poor patient survival. Functional analyses identified amphiregulin (AREG) as a potential regulator of the hybrid epithelial/mesenchymal state. Moreover, AREG contributes to cisplatin resistance via EGFR pathway activation, corroborated by clinical samples. In summary, HNSCC PDOs serve as reliable and versatile models, offer predictive insights into ITH programs and treatment responses, and uncover potential therapeutic targets for personalized medicine.One Sentence SummaryThis study establishes patient-derived tumor organoids (PDOs) from 31 Head and Neck Squamous Cell Carcinoma (HNSCC) patients, faithfully recapitulating characteristics of primary tumors and accurately predicting clinical responses to cisplatin treatment. We reveal intertumoral heterogeneity within PDOs and a hybrid epithelial-mesenchymal transition (hEMT) program conferring cisplatin resistance, highlighting amphiregulin (AREG) as a regulator of cellular plasticity and potential therapeutic target for HNSCC treatment.
Network architecture of transcriptomic stress responses in zebrafish embryos
Authors: Beine Kaylee , Feugere Lauric , Turner Alexander P. , Valero Katharina C. Wollenberg 
Published: July 2024

AbstractProtein-protein interaction (PPI) network topology can contribute to explain fundamental properties of genes, from expression levels to evolutionary constraints. Genes central to a network are more likely to be both conserved and highly expressed, whereas genes that are able to evolve in response to selective pressures but expressed at lower levels are located on the periphery of the network. The stress response is likewise thought to be conserved, however, experimental evidence for these patterns is limited. We examined whether the transcriptomic response to two environmental stressors (heat, UV, and their combination) is related to PPI architecture in zebrafish (Danio rerio)embryos. We show that stress response genes are situated more centrally in the PPI network. The transcriptomic response to heat was located in both central and peripheral positions, whereas UV response occupied central to intermediate positions. Across treatments, differentially expressed genes in different parts of the network affected identical phenotypes. Our results indicate that the zebrafish stress response has mostly conserved but also some stressor-specific aspects. These properties can aid in better understanding the organismal response to diverse and co-occurring stressors. Network position was further linked to the magnitude of fold changes of genes and types and number of linked phenotype components. Given the speed of contemporary changes in aquatic ecosystems, our approach can aid in identifying novel key regulators of the systemic response to specific stressors.
Devonian stromatoporoid historical collections in the Natural History Museum, London (UK): redescription, taxonomic revision and implications for stromatoporoid global paleobiogeography
Authors: Huang Jiayuan , Sendino Consuelo , Kershaw Stephen 
Published: July 2024

AbstractDevonian stromatoporoid collections in the Natural History Museum, London (UK) have been deposited for over 100 years. The characteristics and systematic position of these specimens, however, have received little attention. In this study, a total of 307 Devonian stromatoporoid specimens comprising material documented by Nicholson (1886–1892) from the UK, Germany, United States, and Canada, plus specimens described by Ripper (1933, 1937a, b, c) from Australia, were re-examined. Overall, 50 species belonging to 29 genera were systematically redescribed based on recent progress, mainly includingActinostroma,Petridiostroma,Stictostroma,Pseudotrupetostroma,Parallelopora. Three-dimensional reconstructions of the type genus are illustrated following the earlier works of Stearn (1966) and Cockbain (1984). The reconstructed skeletons reveal stromatoporoid architectural patterns, crucial for enhancing understanding and revision of stromatoporoid identification. This study underscores the significance of three-dimensional reconstruction in taxonomic research on stromatoporoid. The NHMUK material is combined with data from publications and the Paleobiology Database (PBDB) to perform a network analysis of the global occurrence of Devonian stromatoporoids at the generic level; this reveals a close relationship of global stromatoporoid fauna during the Early Devonian, indicating a widespread distribution, despite this interval being regarded as a time of global stromatoporoid contraction. The Middle Devonian assemblage shows a much higher cosmopolitan occurrence in the context of the subsequent Eifelian-Givetian global stromatoporoid proliferation, consistent with the known pattern from other studies of Middle Devonian stromatoporoids. Overall, the NHMUK collections are a valuable resource to help understand the global occurrence of Devonian stromatoporoids.
The evolutionary modifications of a GoLoco motif in the AGS protein facilitate micromere formation in the sea urchin embryo
Authors: Emura Natsuko , Wavreil Florence D.M. , Fries Annaliese , Yajima Mamiko 
Published: July 2024

AbstractThe evolutionary introduction of asymmetric cell division (ACD) into the developmental program facilitates the formation of a new cell type, contributing to developmental diversity and, eventually, to species diversification. The micromere of the sea urchin embryo may serve as one of those examples: An ACD at the 16-cell stage forms micromeres unique to echinoids among echinoderms. We previously reported that a polarity factor, Activator of G-protein Signaling (AGS), plays a crucial role in micromere formation. However, AGS and its associated ACD factors are present in all echinoderms and across most metazoans. This raises the question of what evolutionary modifications of AGS protein or its surrounding molecular environment contributed to the evolutionary acquisition of micromeres only in echinoids. In this study, we learned that the GoLoco motifs at the AGS C-terminus play critical roles in regulating micromere formation in sea urchin embryos. Further, other echinoderms’ AGS or chimeric AGS that contain the C-terminus of AGS orthologs from various organisms showed varied localization and function in micromere formation. In contrast, the sea star or the pencil urchin orthologs of other ACD factors were consistently localized at the vegetal cortex in the sea urchin embryo, suggesting that AGS may be a unique variable factor that facilitates ACD diversity among echinoderms. Consistently, sea urchin AGS appears to facilitate micromere-like cell formation and accelerate the enrichment timing of the germline factor Vasa during early embryogenesis of the pencil urchin, an ancestral type of sea urchin. Based on these observations, we propose that the molecular evolution of a single polarity factor facilitates ACD diversity while preserving the core ACD machinery among echinoderms and beyond during evolution.HighlightsEvolutionary modifications of GoLoco motifs are critical for AGS function in micromere formation in the sea urchin embryo.The chimeric AGS, which contains the C-terminus of AGS orthologs from various organisms, suggests that human LGN, pencil urchin AGS, andDrosophilaPins compensate for the activity of sea urchin AGS.Sea urchin AGS (SpAGS) regulates the localization of the conserved asymmetric cell division (ACD) machinery members at the vegetal cortex.SpAGS is a variable factor facilitating ACD diversity during species diversification.
A Pipeline for the Automatic Identification of Randomized Controlled Oncology Trials and Assignment of Tumor Entities Using Natural Language Processing
Authors: Windisch Paul , Dennstädt Fabio , Koechli Carole , Förster Robert , Schröder Christina , Aebersold Daniel M. , Zwahlen Daniel R. 
Published: July 2024

AbstractBackgroundMost tools trying to automatically extract information from medical publications are domain agnostic and process publications from any field. However, only retrieving trials from dedicated fields could have advantages for further processing of the data.MethodsWe trained a transformer model to classify trials into randomized controlled trials (RCTs) vs. non-RCTs and oncology publications vs. non-oncology publications. We assessed the performance and then developed a simple set of rules to extract the tumor entity from the retrieved oncology RCTs.ResultsOn the unseen test set consisting of 100 publications, the model achieved an F1 score of 0.96 (95% CI: 0.92 - 1.00) with a precision of 1.00 and a recall of 0.92 for predicting whether a publication was an RCT. For predicting whether a publication covered an oncology topic the F1 score was 0.84 (0.77 - 0.91) with a precision of 0.75 and a recall of 0.95. The rule-based system was able to correctly assign every oncology RCT in the test set to a tumor entity.ConclusionIn conclusion, classifying publications depending on whether they were randomized controlled oncology trials or not was feasible and enabled further processing using more specialized tools such as rule-based systems and potentially dedicated machine learning models.
Preventive dental visits and health literacy in patients with diabetes: a nationwide cross-sectional study
Authors: Saito Kyoko , Kawai Yuki , Ishikawa Hirono , Tabuchi Takahiro , Kuwahara Keisuke 
Published: July 2024

AbstractAimThis cross-sectional study examined the association between health literacy and preventive dental visits in patients with diabetes.MethodsWe used cross-sectional data from the Japan COVID-19 and Society Internet Survey (JACSIS), a web-based nationwide survey. The participants were 1,441 patients reporting to have diabetes in 2020. Health literacy was measured using the validated scales for health literacy. Preventive dental visits in the past 12 months were self-reported. We estimated the multivariable-adjusted prevalence ratio (PR) for preventive dental visits.ResultsOver 50% of the patients had preventive dental visits in the past 12 months, and approximately one-third had high health literacy. Compared with the low health literacy group, the high health literacy group was more likely to engage in preventive dental visits (the multivariable-adjusted PR associated with high health literacy: 1.12 [95% confidence interval: 1.01 to 1.23]). Similar results were obtained when health literacy was treated as a continuous variable.ConclusionsThe present data from the JACSIS showed that health literacy was positively associated with preventive dental visits among patients with diabetes.
Diffusion model enables quantitative CBF analysis of Alzheimer’s Disease
Authors: Shou Qinyang , Cen Steven , Chen Nan-kuei , Ringman John M , Wen Junhao , Kim Hosung , Wang Danny JJ ,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2024

ABSTRACTObjectivesCerebral blood flow (CBF) measured by arterial spin labeling (ASL) is a promising biomarker for Alzheimer’s Disease (AD). ASL data from multiple vendors were included in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. However, the M0 images were missing in Siemens ASL data, prohibiting CBF quantification. Here, we utilized a generative diffusion model to impute the missing M0 and validated generated CBF data with acquired data from GE.MethodsA conditional latent diffusion model was trained to generate the M0 image and validate it on an in-house dataset (N=55) based on image similarity metrics, accuracy of CBF quantification, and consistency with the physical model. This model was then applied to the ADNI dataset (Siemens:N=211) to impute the missing M0 for CBF calculation. We further compared the imputed data (Siemens) and acquired data (GE) regarding regional CBF differences by AD stages, their classification accuracy for AD prediction, and CBF trajectory slopes estimated by a mixed effect model.ResultsThe trained diffusion model generated the M0 image with high fidelity (Structural similarity index, SSIM=0.924±0.019; peak signal-to-noise ratio, PSNR=33.348±1.831) and caused minimal bias in CBF values (mean difference in whole brain is 1.07±2.12ml/100g/min). Both generated and acquired CBF data showed similar differentiation patterns by AD stages, similar classification performance, and decreasing slopes with AD progression in specific AD-related regions. Generated CBF data also improved accuracy in classifying AD stages compared to qualitative perfusion data.Interpretation/ConclusionThis study shows the potential of diffusion models for imputing missing modalities for large-scale studies of CBF variation with AD.
Effect of Shenfu Injection on Myocardial Injury After Primary PCI for STEMI: The RESTORE Trial
Authors: Wang Xiao , Fan Zeyuan , Jiang Jianjun , Guo Jincheng , Wang Zhifang , Ma Likun , He Ruili , Su Guohai , Liu Hongtao , Yin Delu , Zhao Guoan , Guo Yingying , Shang Meixia , Ma Xinliang , Nie Shaoping 
Published: July 2024

ABSTRACTBACKGROUNDShenfu injection, as a traditional Chinese medicine, can alleviate reperfusion injury after ST-segment elevation myocardial infarction (STEMI) through multiple pharmacologic effects. This trial aimed to evaluate the effect of Shenfu injection on myocardial injury in STEMI patients undergoing primary percutaneous coronary intervention (PCI).METHODSThis was a multicenter, randomized, double-blind, parallel-group, placebo-controlled trial. First-time anterior STEMI patients undergoing primary PCI within 12 hours of symptom onset due to a proximal or mid left anterior descending artery occlusion were randomized 1:1 to receive either intravenous Shenfu injection or placebo before reperfusion and followed by once a day until 5 days after primary PCI. The primary endpoint was infarct size by cardiac magnetic resonance (CMR) at 5 days after randomization.RESULTSA total of 295 patients were randomized with evaluable CMR in 273 patients. Infarct size (37.4±14.1% vs 37.5±14.5%; effect size −0.04%, 95% confidence interval: −3.45, 3.37; P=0.982) did not differ between the Shenfu injection and placebo groups. This was true for other CMR parameters. The area under curve for creatine kinase-myocardial band did not differ between groups. The incidences of thrombolysis in myocardial infarction (TIMI) flow grade 3 (94.8% vs 97.1%, P=0.324), TIMI myocardial perfusion grade 3 (91.7% vs 92.1%, P=0.914), and ST-segment resolution ≥70% (25.4% vs 26.1%, P=0.906), were also similar between groups. Adverse events were evenly distributed across groups.CONCLUSIONSFor patients with anterior STEMI undergoing primary PCI, administration of Shenfu injection was safe but did not reduce infarct size by CMR.REGISTRATIONURL:https://www.clinicaltrials.gov; Unique identifier:NCT04493840.Clinical PerspectiveWhat Is New?Among 295 anterior ST-segment elevation myocardial infarction patients randomized to intravenous Shenfu injection or placebo, the primary analysis demonstrated that the infarct size revealed by cardiac magnetic resonance was 37.4 % in the Shenfu injection group and 37.5% in the placebo group, a difference that was not statistically significant.For patients with anterior ST-segment elevation myocardial infarction patients undergoing primary percutaneous coronary intervention, administration of Shenfu injection was safe and well tolerated.What Are the Clinical Implications?Cardiovascular clinicians need to realize that successful cardioprotective therapies may require synergistic multitarget approaches.Future clinical trials are required to investigate the use of additive cardioprotective strategies in patients with large infarcts or severe hemodynamic alterations (eg. concomitant heart failure or cardiogenic shock).
New soft tissue data of pterosaur tail vane reveals sophisticated, dynamic tensioning usage and expands its evolutionary origins
Authors: Jagielska Natalia , Kaye Thomas G. , Habib Michael B. , Hirasawa Tatsuya , Pittman Michael 
Published: July 2024

AbstractPterosaurs were the first vertebrates to achieve powered flight. Early pterosaurs had long stiff tails with a mobile base that could shift their center of mass, potentially benefiting flight control. These tails ended in a tall, thin soft tissue vane that would compromise aerodynamic control and efficiency if it fluttered excessively during flight. Maintaining stiffness in the vane would have been crucial in early pterosaur flight, but how this was achieved has been unclear, especially since vanes were lost in later pterosaurs and are absent in birds and bats. Here we use Laser-Stimulated Fluorescence imaging to reveal a cross-linking lattice within the tail vanes of early pterosaurs. The lattice supported a sophisticated dynamic tensioning system used to maintain vane stiffness, allowing the whole tail to augment flight control and the vane to function as a display structure.
Social disparities in flood exposure and associations with the urban environment in 44,698 neighborhoods in 276 cities in eight Latin American countries
Authors: Kephart Josiah L. , Bilal Usama , Gouveia Nelson , Sarmiento Olga Lucia , Shingara Emily , Moreno Karla Rangel , Bakhtsiyarava Maryia , Rodriguez Juan Pablo , Ayala Salvador , Carrasco-Escobar Gabriel , Roux Ana V Diez ,   SALURBAL-Climate Project
Published: July 2024

AbstractBackgroundClimate change is expected to greatly increase exposure to flooding, particularly in urban populations in low- and middle-income countries. We examined within-city social disparities in exposure to flooding in 276 Latin American cities and associated features of the neighborhood urban environment.MethodsWe used a spatially granular dataset of historical flood events from 2000 to 2018 to describe neighborhood flooding within cities across eight Latin American countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Guatemala, Mexico, and Panama). We estimated the percentage of the population living in flooded neighborhoods, described social disparities in flooding based on neighborhood educational attainment, and compared the magnitude of disparities across and within cities. We used multilevel models to examine how city- and neighborhood-level factors are related to neighborhood flooding.ResultsWe examined 44,698 neighborhoods in 276 cities from eight countries with a total of 223 million residents and 117 distinct flood events from 2000-2018. One in four residents in neighborhoods in the lowest education quintile lived in neighborhoods with flooding, compared to one in 20 residents of the highest neighborhood education quintile. Greater neighborhood flooding was associated with lower neighborhood-level educational attainment and with neighborhoods that were coastal, less dense (population or intersection), further from the city center, greener, and had steeper slopes. There was no association between city-level educational attainment and flooding.ConclusionThere are large social disparities in neighborhood flooding within Latin American cities. Residents of areas with lower education attainment face substantially higher risks of flooding. Policymakers must prioritize flood adaptation and recovery efforts in neighborhoods with lower socioeconomic position.
Unequal Benefits: The Effects of Health Insurance Integration on Consumption Inequality in Rural China
Authors: Han Linlin , Yang Feng , Yu Jinxiang 
Published: July 2024

AbstractReleasing the consumption potential of rural residents and narrowing the consumption gap is crucial for expanding domestic demand and enhancing social equity. This study leverages data from the China Family Panel Studies (CFPS) spanning the years 2012 to 2018 to analyze the impact of the rural-urban health insurance integration policy on consumption inequality in rural areas and its underlying mechanisms. Employing a staggered difference-in-differences (DID) approach, the analysis reveals that the policy significantly raises consumption levels among middle and high-income groups while concurrently reducing expenditures for the lowest-income bracket, thereby exacerbating consumption inequality. Heterogeneity analysis indicates that the impact of rural-urban health insurance integration on rural consumption inequality is manifested in both consumption structure and life-cycle effects, with the most significant disparities observed in subsistence and enjoyment consumption, particularly among middle-aged and older age groups. Mechanism analysis identifies increased utilization of medical services, the release of precautionary savings among middle and high-income cohorts, and variations in health insurance funding modalities as key drivers of the widening consumption inequality gap. The study concludes with recommendations to progressively advance the establishment of parity in rural-urban integrated health insurance and to prioritize policy support for vulnerable groups, especially the elderly and impoverished households.