bluuebunny/crossref_metadata_2025_split huggingface dataset:
A worldwide study of subcortical shape as a marker for clinical staging in Parkinson’s disease
Authors: Laansma Max A. , Zhao Yuji , van Heese Eva M. , Bright Joanna K. , Owens-Walton Conor , Al-Bachari Sarah , Anderson Tim J. , Assogna Francesca , van Balkom Tim D. , Berendse Henk W. , Cendes Fernando , Dalrymple-Alford John C. , Debove Ines , Dirkx Michiel F. , Druzgal Jason , Emsley Hedley C. A. , Fouche Jean-Paul , Garraux Gaëtan , Guimarães Rachel P. , Helmich Rick C. , Hu Michele , van den Heuvel Odile A. , Isaev Dmitry , Kim Ho-Bin , Klein Johannes C. , Lochner Christine , McMillan Corey T. , Melzer Tracy R. , Newman Benjamin , Parkes Laura M. , Pellicano Clelia , Piras Fabrizio , Pitcher Toni L. , Poston Kathleen L. , Rango Mario , Ribeiro Leticia F. , Rocha Cristiane S. , Rummel Christian , Santos Lucas S. R. , Schmidt Reinhold , Schwingenschuh Petra , Squarcina Letizia , Stein Dan J. , Vecchio Daniela , Vriend Chris , Wang Jiunjie , Weintraub Daniel , Wiest Roland , Yasuda Clarissa L. , Jahanshad Neda , Thompson Paul M. , van der Werf Ysbrand D. , Gutman Boris A. 
Published: November 2024

AbstractAlterations in subcortical brain regions are linked to motor and non-motor symptoms in Parkinson’s disease (PD). However, associations between clinical expression and regional morphological abnormalities of the basal ganglia, thalamus, amygdala and hippocampus are not well established. We analyzed 3D T1-weighted brain MRI and clinical data from 2525 individuals with PD and 1326 controls from 22 global sources in the ENIGMA-PD consortium. We investigated disease effects using mass univariate and multivariate models on the medial thickness of 27,120 vertices of seven bilateral subcortical structures. Shape differences were observed across all Hoehn and Yahr (HY) stages, as well as correlations with motor and cognitive symptoms. Notably, we observed incrementally thinner putamen from HY1, caudate nucleus and amygdala from HY2, hippocampus, nucleus accumbens, and thalamus from HY3, and globus pallidus from HY4–5. Subregions of the thalami were thicker in HY1 and HY2. Largely congruent patterns were associated with a longer time since diagnosis and worse motor symptoms and cognitive performance. Multivariate regression revealed patterns predictive of disease stage. These cross-sectional findings provide new insights into PD subcortical degeneration by demonstrating patterns of disease stage-specific morphology, largely consistent with ongoing degeneration.
Adipose tissue retains an epigenetic memory of obesity after weight loss
Authors: Hinte Laura C. , Castellano-Castillo Daniel , Ghosh Adhideb , Melrose Kate , Gasser Emanuel , Noé Falko , Massier Lucas , Dong Hua , Sun Wenfei , Hoffmann Anne , Wolfrum Christian , Rydén Mikael , Mejhert Niklas , Blüher Matthias , von Meyenn Ferdinand 
Published: November 2024

AbstractReducing body weight to improve metabolic health and related comorbidities is a primary goal in treating obesity1,2. However, maintaining weight loss is a considerable challenge, especially as the body seems to retain an obesogenic memory that defends against body weight changes3,4. Overcoming this barrier for long-term treatment success is difficult because the molecular mechanisms underpinning this phenomenon remain largely unknown. Here, by using single-nucleus RNA sequencing, we show that both human and mouse adipose tissues retain cellular transcriptional changes after appreciable weight loss. Furthermore, we find persistent obesity-induced alterations in the epigenome of mouse adipocytes that negatively affect their function and response to metabolic stimuli. Mice carrying this obesogenic memory show accelerated rebound weight gain, and the epigenetic memory can explain future transcriptional deregulation in adipocytes in response to further high-fat diet feeding. In summary, our findings indicate the existence of an obesogenic memory, largely on the basis of stable epigenetic changes, in mouse adipocytes and probably other cell types. These changes seem to prime cells for pathological responses in an obesogenic environment, contributing to the problematic ‘yo-yo’ effect often seen with dieting. Targeting these changes in the future could improve long-term weight management and health outcomes.
Probe set selection for targeted spatial transcriptomics
Authors: Kuemmerle Louis B. , Luecken Malte D. , Firsova Alexandra B. , Barros de Andrade e Sousa Lisa , Straßer Lena , Mekki Ilhem Isra , Campi Francesco , Heumos Lukas , Shulman Maiia , Beliaeva Valentina , Hediyeh-Zadeh Soroor , Schaar Anna C. , Mahbubani Krishnaa T. , Sountoulidis Alexandros , Balassa Tamás , Kovacs Ferenc , Horvath Peter , Piraud Marie , Ertürk Ali , Samakovlis Christos , Theis Fabian J. 
Published: November 2024

Abstract
Targeted spatial transcriptomic methods capture the topology of cell types and states in tissues at single-cell and subcellular resolution by measuring the expression of a predefined set of genes. The selection of an optimal set of probed genes is crucial for capturing the spatial signals present in a tissue. This requires selecting the most informative, yet minimal, set of genes to profile (gene set selection) for which it is possible to build probes (probe design). However, current selections often rely on marker genes, precluding them from detecting continuous spatial signals or new states. We present Spapros, an end-to-end probe set selection pipeline that optimizes both gene set specificity for cell type identification and within-cell type expression variation to resolve spatially distinct populations while considering prior knowledge as well as probe design and expression constraints. We evaluated Spapros and show that it outperforms other selection approaches in both cell type recovery and recovering expression variation beyond cell types. Furthermore, we used Spapros to design a single-cell resolution in situ hybridization on tissues (SCRINSHOT) experiment of adult lung tissue to demonstrate how probes selected with Spapros identify cell types of interest and detect spatial variation even within cell types.
Band structure database of layered intercalation compounds with various intercalant atoms and layered hosts
Authors: Kawaguchi Naoto , Shibata Kiyou , Mizoguchi Teruyasu 
Published: November 2024

AbstractHere we provide a database comprising electronic band structures of 9,004 layered intercalation compounds, where atoms are intercalated into a host layered compound with different intercalant atoms, along with 468 structures related to the layered host compounds. Additionally, we provide properties derived from the electronic states such as band gap as well as stability-related properties like formation energies. Direct comparison of the band structures before and after intercalation is generally challenging due to changes in their space group and k-path. However, in this study, we developed new k-paths consistent with the host materials, allowing for the direct comparison of band structures before and after intercalation. This enables direct and quantitative discussion of the band structure changes induced by the intercalations and provides a valuable database for intercalant-driven band engineering. Layered intercalation compounds are widely used in many fields, including superconductivity and energy applications, and understanding of electronic structures is necessary. The feature of our database holds promises for the development of layered compounds with enhanced functionalities through database utilization.
Performance of the comprehensive nutrition screening index in predicting mortality after cardiac surgery
Authors: Chung Jaeyeon , Bae Jinyoung , Park Seyong , Kim Dong Hyouk , Cho Youn Joung , Nam Karam , Jeon Yunseok , Ju Jae-Woo 
Published: November 2024

AbstractMalnutrition is a significant risk factor for postoperative outcomes in patients undergoing cardiac surgery. The Seoul National University Hospital-Nutrition Screening Index (SNUH-NSI) is an automated screening tool designed to comprehensively assess malnutrition risk. However, its predictive value in patients undergoing cardiac surgery remains unvalidated. This study included adult patients who underwent cardiac surgery at a tertiary teaching hospital between May 2008 and December 2019. Patients were classified as low-, intermediate-, or high-risk for malnutrition based on the SNUH-NSI. The association between malnutrition risk and postoperative cumulative all-cause mortality was evaluated using multivariable Cox regression analysis. The predictive ability of the SNUH-NSI was compared with conventional nutritional indices. Compared to the low-risk group, both the high-risk (adjusted hazard ratio [HR], 2.64; 95% confidence interval [CI], 2.19–3.19; P < 0.001) and intermediate-risk groups (adjusted HR, 1.54; 95% CI, 1.31–1.82; P < 0.001) demonstrated a significantly elevated risk of cumulative all-cause mortality. The multivariable model incorporating SNUH-NSI demonstrated moderate but superior predictive performance compared to that of other conventional nutritional indices. Preoperative malnutrition assessed by the SNUH-NSI was found to be a significant predictor of mortality following cardiac surgery. Implementing the SNUH-NSI for automated preoperative malnutrition screening could be an efficient and cost-effective approach.
Tumor-derived extracellular vesicles disrupt the blood–brain barrier endothelium following high-frequency irreversible electroporation
Authors: Murphy Kelsey R. , Aycock Kenneth N. , Marsh Spencer , Hay Alayna N. , Athanasiadi Ilektra , Bracha Shay , Chang Christine , Gourdie Robert , Davalos Rafael V. , Rossmeisl John H. , Dervisis Nikolaos G. 
Published: November 2024

AbstractHigh-frequency irreversible electroporation (H-FIRE), a nonthermal brain tumor ablation therapeutic, generates a central tumor ablation zone while transiently disrupting the peritumoral blood–brain barrier (BBB). We hypothesized that bystander effects of H-FIRE tumor cell ablation, mediated by small tumor-derived extracellular vesicles (sTDEV), disrupt the BBB endothelium. Monolayers of bEnd.3 cerebral endothelial cells were exposed to supernatants of H-FIRE or radiation (RT)-treated LL/2 and F98 cancer cells. Endothelial cell response was evaluated microscopically and via flow cytometry for apoptosis. sTDEV were isolated following H-FIRE and RT, characterized via nanoparticle tracking analysis (NTA) and transmission electron microscopy, and applied to a Transwell BBB endothelium model to quantify permeability changes. Supernatants of H-FIRE-treated tumor cells, but not supernatants of sham- or RT-treated cells, disrupted endothelial cell monolayer integrity while maintaining viability. sTDEV released by glioma cells treated with 3000 V/cm H-FIRE increased permeability of the BBB endothelium model compared to sTDEV released after lower H-FIRE doses and RT. NTA revealed significantly decreased sTDEV release after the 3000 V/cm H-FIRE dose. Our results demonstrate that sTDEV increase permeability of the BBB endothelium after H-FIRE ablation in vitro. sTDEV-mediated mechanisms of BBB disruption may be exploited for drug delivery to infiltrative margins following H-FIRE ablation.
Blink-induced changes in pupil dynamics are consistent and heritable
Authors: Demiral Şükrü Barış , Volkow Nora D. 
Published: November 2024

AbstractPupil size and blink rates are heritable but the extent to which they interact with one another has not been properly investigated. Though changes in pupil size due to eye blinks have been reported, they are considered a pupillary artifact. In this study we used the HCP 7T fMRI dataset with resting state eye-tracking data obtained in monozygotic and dizygotic twins to assess their heritability and their interactions. For this purpose, we characterized the pupil dilation (positive peak) and constriction (negative peak) that followed blink events, which we describe as blink-induced pupillary response (BIPR). We show that the BIPR is highly consistent with a positive dilatory peak (D-peak) around 500ms and a negative constricting peak (C-peak) around 1s. These patterns were reproducible within- and between-subjects across two time points and differed by vigilance state (vigilant versus drowsy). By comparing BIPR between monozygotic and dizygotic twins we show that BIPR have a heritable component with significant additive genetic (A) and environmental (E) factors dominating the structural equation models, particularly in the time-domain for both D- and C-peaks (a2 between 42 and 49%) and shared effects (C) as observed in the amplitude domain for the C-peak. Blink duration, pupil size and blink rate were also found to be highly heritable (a2 up to 62% for pupil size). Our study provides evidence of that shared environmental and additive genetic factors influence BIPR and indicates that BIPR should not be treated as a coincidental artefact. Instead BIPR appears to be a component of a larger oculomotor system that we label here as Oculomotor Adaptive System, that is genetically determined.
Contact toxicity of insecticides against rice weevil, Sitophilus oryzae L. and its effect on progeny production
Authors: Rajarushi C. N. , Nebapure Suresh M. , Biswas Ankur , Rajna S. , Subramanian S. 
Published: November 2024

AbstractPost-harvest losses caused by insect pests, particularly the rice weevil, Sitophilus oryzae, pose a significant challenge in food storage facilities worldwide. To combat this pest, synthetic insecticides and fumigants are widely used. However, effective contact insecticides are scarce. Hence, the present study explored the alternatives by evaluating the contact toxicity of various insecticides against S. oryzae using glass, jute, and floor tiles as surface substrates and further examining the effect on progeny production of promising candidate insecticides. Among the insecticides tested, malathion exhibited the highest toxicity on glass and jute surfaces regardless of the exposure period. On the other hand, spinetoram proved to be the most effective on tile surface with an 8 h exposure period. Among the alternate insecticides (spinosad, spinetoram, chlorfenapyr and lambda-cyhalothrin), spinetoram was most effective with LC50 values of 155.8 and 116.9 mg/m² for 4 h and 8 h exposure, respectively, on tile surface; 204.6 and 129.0 mg/m² for 4 h and 8 h exposure, respectively, on glass surface; and 271.5 and 199.5 mg/m² for 4 h and 8 h exposure, respectively, on jute surface. Relative toxicity assessments revealed spinetoram to be 2.11 and 2.51 times more effective than deltamethrin on tile surface for 4 and 8 h of exposure, respectively whereas it was 1.14 times more effective than malathion on tile surface at 8 h exposure. Principal component analysis indicated a higher demand for insecticide doses closely associated with the structural properties of surfaces, particularly evident with jute surfaces. Furthermore, the effect on adult mortality and progeny production by malathion, spinetoram, and lambda-cyhalothrin revealed malathion as the most effective insecticide followed by spinetoram. Carboxylesterase, acetylcholinesterase, and Glutathione S-transferase (GST) activities were notably higher in deltamethrin-treated insects compared to other insecticides. The studies concluded that spinetoram can be considered an alternative to conventional insecticides for the management of S. oryzae under different storage conditions.
Respiratory symptoms among e-cigarette users without an established smoking history in the VERITAS cohort
Authors: Goicoechea Jefrrey Zamora , Boughner Allison , Lee Juan José Cirion , Mahajan Aman , Yeo Kurt , Sproga Maris , Russell Christopher , Coughlan Michael , Selya Arielle , Caci Grazia , Caponnetto Pasquale , Tomaselli Venera , Polosa Riccardo 
Published: November 2024

AbstractPrior research on e-cigarettes’ health impacts is inconclusive due to confounding by previous tobacco smoking. Studies of e-cigarette use among people without an established smoking history are informative for this question. A cross-sectional survey was administered across six geopolitical world regions to adults aged 18+ without a history of established cigarette smoking or regular use of other nicotine/tobacco products. Two cohorts were defined based on e-cigarette use: “Vapers Cohort” (N = 491) who used e-cigarettes in the past 7 days and “Control Cohort” (N = 247) who never regularly used e-cigarettes. Frequency of respiratory symptoms (Respiratory Symptom Evaluation Score (RSES)) were compared between cohorts, adjusting for sociodemographics. Tobacco use history and patterns of e-cigarette use was also examined. Respiratory symptoms were rare among both the Vapers and Control Cohorts: 83.3% and 88.4%, respectively, reported “rarely” or “never” experiencing all five RSES items (p = 0.125). The Vapers (vs. Control) Cohort reported modestly more frequent respiratory symptoms (adjusted mean RSES 1.61 vs. 1.43, respectively, p < 0.001); however, this difference (0.18) did not reach the threshold of clinical relevance (0.57). The Vapers (vs. Control) Cohort more often reported former cigarette experimentation (30.8% vs. 12.1%) and former infrequent use of other nicotine/tobacco products (18.1% vs. 5.8%). The Vapers Cohort most often used disposable devices (63.7%) and multiple flavors (approximately 70–80% across primary device type). In this cohort of adults without a history of established combustible tobacco use, e-cigarette use was statistically linked to more frequent respiratory symptoms, though not in a clinically meaningful way. The cross-sectional design of this study cannot establish causality between e-cigarette use and respiratory symptoms.
Sustainable land and irrigation management to limit loss of hydropower in the Andes-Amazon headwaters
Authors: Ding Zhaowei , Angarita Hector , Albert Montesinos Cáceres Christian , Lavado-Casimiro Waldo , Goldstein Jesse A. , Batista Natasha , Wu Tong , Fisher Dave , Baudoin Farah Andrea , Zheng Hua , Schmitt Rafael J. P. 
Published: November 2024

AbstractWater plays a critical role in adapting food and energy systems to climate change in the Andes. However, robust climate solutions that work across sectors have not been explored for these working landscapes. Here we develop a framework consisting of high-fidelity catchment and hydropower models while considering climate and other uncertainties in a robust, bottom-up manner for the upper Huallaga River in Peru. We then explore adaptation strategies across sectors. Our results highlight that irrigation will be critical for maintaining food production under climate change. Yet, an unplanned expansion of irrigation could lead to a near total loss of firm hydropower downstream. Exploring 10,080 possible landuse/management adaptation pathways, we find limited opportunities for win-win solutions under climate change. In the light of such challenges, our results highlight the need for navigating structural trade-offs between upstream land and water users and downstream interests in the Andes in a strategic and equitable manner.
Novel integrated multiomics analysis reveals a key role for integrin beta-like 1 in wound scarring
Authors: Kim Sang-Eun , Noda Ryota , Liu Yu-Chen , Nakajima Yukari , Kameoka Shoichiro , Motooka Daisuke , Mizuno Seiya , Takahashi Satoru , Takaya Kento , Murase Takehiko , Ikematsu Kazuya , Tratsiakova Katsiaryna , Motoyama Takahiro , Nakashima Masahiro , Kishi Kazuo , Martin Paul , Seno Shigeto , Okuzaki Daisuke , Mori Ryoichi 
Published: November 2024

AbstractExacerbation of scarring can originate from a minority fibroblast population that has undergone inflammatory-mediated genetic changes within the wound microenvironment. The fundamental relationship between molecular and spatial organization of the repair process at the single-cell level remains unclear. We have developed a novel, high-resolution spatial multiomics method that integrates spatial transcriptomics with scRNA-Seq; we identified new characteristic features of cell–cell communication and signaling during the repair process. Data from PU.1-/- mice, which lack an inflammatory response, combined with scRNA-Seq and Visium transcriptomics, led to the identification of nine genes potentially involved in inflammation-related scarring, including integrin beta-like 1 (Itgbl1). Transgenic mouse experiments confirmed that Itgbl1-expressing fibroblasts are required for granulation tissue formation and drive fibrogenesis during skin repair. Additionally, we detected a minority population of Acta2high-expressing myofibroblasts with apparent involvement in scarring, in conjunction with Itgbl1 expression. IL1β signaling inhibited Itgbl1 expression in TGFβ1-treated primary fibroblasts from humans and mice. Our novel methodology reveal molecular mechanisms underlying fibroblast–inflammatory cell interactions that initiate wound scarring.
Salmonella cancer therapy metabolically disrupts tumours at the collateral cost of T cell immunity
Authors: Copland Alastair , Mackie Gillian M , Scarfe Lisa , Jinks Elizabeth , Lecky David A J , Gudgeon Nancy , McQuade Riahne , Ono Masahiro , Barthel Manja , Hardt Wolf-Dietrich , Ohno Hiroshi , Hoevenaar Wilma H M , Dimeloe Sarah , Bending David , Maslowski Kendle M 
Published: November 2024

AbstractBacterial cancer therapy (BCT) is a promising therapeutic for solid tumours. Salmonella enterica Typhimurium (STm) is well-studied amongst bacterial vectors due to advantages in genetic modification and metabolic adaptation. A longstanding paradox is the redundancy of T cells for treatment efficacy; instead, STm BCT depends on innate phagocytes for tumour control. Here, we used distal T cell receptor (TCR) and IFNγ reporter mice (Nr4a3-Tocky-Ifnγ-YFP) and a colorectal cancer (CRC) model to interrogate T cell activity during BCT with attenuated STm. We found that colonic tumour infiltrating lymphocytes (TILs) exhibited a variety of activation defects, including IFN-γ production decoupled from TCR signalling, decreased polyfunctionality and reduced central memory (TCM) formation. Modelling of T-cell–tumour interactions with a tumour organoid platform revealed an intact TCR signalosome, but paralysed metabolic reprogramming due to inhibition of the master metabolic controller, c-Myc. Restoration of c-Myc by deletion of the bacterial asparaginase ansB reinvigorated T cell activation, but at the cost of decreased metabolic control of the tumour by STm. This work shows for the first time that T cells are metabolically defective during BCT, but also that this same phenomenon is inexorably tied to intrinsic tumour suppression by the bacterial vector.