bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagenolysis-dependent DDR1 signalling dictates pancreatic cancer outcome
Authors: Su Hua , Yang Fei , Fu Rao , Trinh Brittney , Sun Nina , Liu Junlai , Kumar Avi , Baglieri Jacopo , Siruno Jeremy , Le Michelle , Li Yuhan , Dozier Stephen , Nair Ajay , Filliol Aveline , Sinchai Nachanok , Rosenthal Sara Brin , Santini Jennifer , Metallo Christian M. , Molina Anthony , Schwabe Robert F. , Lowy Andrew M. , Brenner David , Sun Beicheng , Karin Michael 
Published: October 2022

AbstractPancreatic ductal adenocarcinoma (PDAC) is a highly desmoplastic, aggressive cancer that frequently progresses and spreads by metastasis to the liver1. Cancer-associated fibroblasts, the extracellular matrix and type I collagen (Col I) support2,3 or restrain the progression of PDAC and may impede blood supply and nutrient availability4. The dichotomous role of the stroma in PDAC, and the mechanisms through which it influences patient survival and enables desmoplastic cancers to escape nutrient limitation, remain poorly understood. Here we show that matrix-metalloprotease-cleaved Col I (cCol I) and intact Col I (iCol I) exert opposing effects on PDAC bioenergetics, macropinocytosis, tumour growth and metastasis. Whereas cCol I activates discoidin domain receptor 1 (DDR1)–NF-κB–p62–NRF2 signalling to promote the growth of PDAC, iCol I triggers the degradation of DDR1 and restrains the growth of PDAC. Patients whose tumours are enriched for iCol I and express low levels of DDR1 and NRF2 have improved median survival compared to those whose tumours have high levels of cCol I, DDR1 and NRF2. Inhibition of the DDR1-stimulated expression of NF-κB or mitochondrial biogenesis blocks tumorigenesis in wild-type mice, but not in mice that express MMP-resistant Col I. The diverse effects of the tumour stroma on the growth and metastasis of PDAC and on the survival of patients are mediated through the Col I–DDR1–NF-κB–NRF2 mitochondrial biogenesis pathway, and targeting components of this pathway could provide therapeutic opportunities.
Inferring and perturbing cell fate regulomes in human brain organoids
Authors: Fleck Jonas Simon , Jansen Sophie Martina Johanna , Wollny Damian , Zenk Fides , Seimiya Makiko , Jain Akanksha , Okamoto Ryoko , Santel Malgorzata , He Zhisong , Camp J. Gray , Treutlein Barbara 
Published: October 2022

AbstractSelf-organizing neural organoids grown from pluripotent stem cells1–3combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. We developed Pando—a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We show that the transcription factor GLI3 is required for cortical fate establishment in humans, recapitulating previous research performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify two distinct GLI3 regulomes that are central to telencephalic fate decisions: one regulating dorsoventral patterning with HES4/5 as direct GLI3 targets, and one controlling ganglionic eminence diversification later in development. Together, we provide a framework for how human model systems and single-cell technologies can be leveraged to reconstruct human developmental biology.
Statistical inference using GLEaM model with spatial heterogeneity and correlation between regions
Authors: Tan Yixuan , Zhang Yuan , Cheng Xiuyuan , Zhou Xiao-Hua 
Published: October 2022

AbstractA better understanding of various patterns in the coronavirus disease 2019 (COVID-19) spread in different parts of the world is crucial to its prevention and control. Motivated by the previously developed Global Epidemic and Mobility (GLEaM) model, this paper proposes a new stochastic dynamic model to depict the evolution of COVID-19. The model allows spatial and temporal heterogeneity of transmission parameters and involves transportation between regions. Based on the proposed model, this paper also designs a two-step procedure for parameter inference, which utilizes the correlation between regions through a prior distribution that imposes graph Laplacian regularization on transmission parameters. Experiments on simulated data and real-world data in China and Europe indicate that the proposed model achieves higher accuracy in predicting the newly confirmed cases than baseline models.
Benthic animal-borne sensors and citizen science combine to validate ocean modelling
Authors: Lavender Edward , Aleynik Dmitry , Dodd Jane , Illian Janine , James Mark , Smout Sophie , Thorburn James 
Published: October 2022

AbstractDevelopments in animal electronic tagging and tracking have transformed the field of movement ecology, but interest is also growing in the contributions of tagged animals to oceanography. Animal-borne sensors can address data gaps, improve ocean model skill and support model validation, but previous studies in this area have focused almost exclusively on satellite-telemetered seabirds and seals. Here, for the first time, we develop the use of benthic species as animal oceanographers by combining archival (depth and temperature) data from animal-borne tags, passive acoustic telemetry and citizen-science mark-recapture records from 2016–17 for the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. By comparing temperature observations to predictions from the West Scotland Coastal Ocean Modelling System, we quantify model skill and empirically validate an independent model update. The results from bottom-temperature and temperature-depth profile validation (5,324 observations) fill a key data gap in Scotland. For predictions in 2016, we identified a consistent warm bias (mean = 0.53 °C) but a subsequent model update reduced bias by an estimated 109% and improved model skill. This study uniquely demonstrates the use of benthic animal-borne sensors and citizen-science data for ocean model validation, broadening the range of animal oceanographers in aquatic environments.
The relationship between pre-operative psoas and skeletal muscle parameters and survival following endovascular aneurysm repair: a systematic review and meta-analysis
Authors: Bradley N. A. , Roxburgh C. S. D. , McMillan D. C. , Guthrie G. J. K. 
Published: October 2022

AbstractSarcopenia is characterised by chronically reduced skeletal muscle volume and function, and is determined radiologically by psoas and skeletal muscle measurement. The present systematic review and meta-analysis aims to examine the relationship between pre-operative CT-derived psoas and skeletal muscle parameters and outcomes in patients undergoing EVAR and F/B-EVAR for aortic aneurysm. The MEDLINE database was interrogated for studies investigating the effect of pre-operative CT-diagnosed sarcopenia on outcomes following EVAR and F/B-EVAR. The systematic review was carried out in accordance with PRISMA guidelines. The primary outcome was overall mortality. RevMan 5.4.1 was used to perform meta-analysis. PROSPERO Database Registration Number: CRD42021273085. Ten relevant studies were identified, one reporting skeletal muscle parameters, and the remaining nine reporting psoas muscle parameters, which were used for meta-analysis. There were a total of 2563 patients included (2062 EVAR, 501 F/B-EVAR), with mean follow-up ranging from 25 to 101 months. 836 patients (33%) were defined as radiologically sarcopenic. In all studies, the combined HR for all-cause mortality in sarcopenic versus non-sarcopenic patients was 2.61 (1.67–4.08), p < .001. Two studies reported outcomes on patients undergoing F/B-EVAR; the combined HR for all-cause mortality in sarcopenic versus non-sarcopenic patients was 3.08 (1.66–5.71), p = .004. Radiological sarcopenia defined by psoas or skeletal muscle parameters was associated with inferior survival in patients undergoing both EVAR and F/B-EVAR. Current evidence is limited by heterogeneity in assessment of body composition and lack of a consensus definition of radiological sarcopenia.
Influence of scan direction on subfoveal choroidal vascularity index using optical coherence tomography
Authors: Kim Yung Hui , Jin Hyung Nam , Kim Hyun Jee , Lee Jong Hoon , Ji Yong-Sok 
Published: October 2022

AbstractWe investigated the influence of scan direction on subfoveal choroidal vascularity index (CVI) measurements using spectral-domain optical coherence tomography (SD-OCT) in young healthy subjects. Seventy-eight eyes of 41 healthy volunteers were included. Choroidal structures were obtained using SD-OCT with enhanced depth imaging (EDI) through radial scans at the center of the macula. The subfoveal choroidal images in the horizontal (0°), 45°, vertical (90°) and − 45° directions were recorded and CVIs were analyzed according to their respective directions using image binarization. Additionally, subfoveal choroidal thickness (SFCT), and axial eye length were measured. The SFCT and subfoveal CVI showed a negative correlation but were only significant for the 45° scan (Pearson’s r = − 0.262, P = 0.021). The axial eye length and subfoveal CVI had no significant correlation in any direction (all P > 0.05). In the Bland–Altman plot, the subfoveal CVI measurement showed high agreement among the four scan directions. When the SFCT was ≥ 300 µm, there was no difference in the measured values of the subfoveal CVI among the four scan directions; however, when the SFCT was < 300 µm, there was a significant difference in subfoveal CVI among the scan directions (one-way analysis of variance, F = 4.685, P = 0.004). In subfoveal CVI measurement, it is considered that the horizontal (0°) scan can represent the vertical (90°) or oblique (45°, − 45°) scans. However, when the SFCT is thinner, the subfoveal CVI in each direction of radial scan may vary significantly. Hence, caution is required in the interpretation.
Chimpanzees organize their social relationships like humans
Authors: Escribano Diego , Doldán-Martelli Victoria , Cronin Katherine A. , Haun Daniel B. M. , van Leeuwen Edwin J. C. , Cuesta José A. , Sánchez Angel 
Published: October 2022

AbstractHuman relationships are structured in a set of layers, ordered from higher (intimate relationships) to lower (acquaintances) emotional and cognitive intensity. This structure arises from the limits of our cognitive capacity and the different amounts of resources required by different relationships. However, it is unknown whether nonhuman primate species organize their affiliative relationships following the same pattern. We here show that the time chimpanzees devote to grooming other individuals is well described by the same model used for human relationships, supporting the existence of similar social signatures for both humans and chimpanzees. Furthermore, the relationship structure depends on group size as predicted by the model, the proportion of high-intensity connections being larger for smaller groups.
A comparative study on the analysis of hemodynamics in the athlete’s heart
Authors: Gülan Utku , Rossi Valentina A. , Gotschy Alexander , Saguner Ardan M. , Manka Robert , Brunckhorst Corinna B. , Duru Firat , Schmied Christian M. , Niederseer David 
Published: October 2022

AbstractThe pathophysiological mechanisms underlying the development of the athlete’s heart are still poorly understood. To characterize the intracavitary blood flows in the right ventricle (RV) and right-ventricular outflow tract (RVOT) in 2 healthy probands, patients with arrhythmogenic right ventricular cardiomyopathy (ARVC) and 2 endurance athletes, we performed 4D-MRI flow measurements to assess differences in kinetic energy and shear stresses. Time evolution of velocity magnitude, mean kinetic energy (MKE), turbulent kinetic energy (TKE) and viscous shear stress (VSS) were measured both along the whole RV and in the RVOT. RVOT regions had higher kinetic energy values and higher shear stresses levels compared to the global averaging over RV among all subjects. Endurance athletes had relatively lower kinetic energy and shear stresses in the RVOT regions compared to both healthy probands and ARVC patients. The athlete’s heart is characterized by lower kinetic energy and shear stresses in the RVOT, which might be explained by a higher diastolic compliance of the RV.
Identifying patients at risk of unplanned re-hospitalisation using statewide electronic health records
Authors: Brankovic Aida , Rolls David , Boyle Justin , Niven Philippa , Khanna Sankalp 
Published: October 2022

AbstractPreventing unplanned hospitalisations, including readmissions and re-presentations to the emergency department, is an important strategy for addressing the growing demand for hospital care. Significant successes have been reported from interventions put in place by hospitals to reduce their incidence. However, there is limited use of data-driven algorithms in hospital services to identify patients for enrolment into these intervention programs. Here we present the results of a study aiming to develop algorithms deployable at scale as part of a state government’s initiative to address rehospitalizations and which fills several gaps identified in the state-of-the-art literature. To the best of our knowledge, our study involves the largest-ever sample size for developing risk models. Logistic regression, random forests and gradient boosted techniques were explored as model candidates and validated retrospectively on five years of data from 27 hospitals in Queensland, Australia. The models used a range of predictor variables sourced from state-wide Emergency Department(ED), inpatient, hospital-dispensed medications and hospital-requested pathology databases. The investigation leads to several findings: (i) the advantage of looking at a longer patient data history, (ii) ED and inpatient datasets alone can provide useful information for predicting hospitalisation risk and the addition of medications and pathology test results leads to trivial performance improvements, (iii) predicting readmissions to the hospital was slightly easier than predicting re-presentations to ED after an inpatient stay, which was slightly easier again than predicting re-presentations to ED after an EDstay, (iv) a gradient boosted approach (XGBoost) was systematically the most powerful modelling approach across various tests.
Sound transmission loss of double-walled sandwich cross-ply layered magneto-electro-elastic plates under thermal environment
Authors: Refahati Nima , Jearsiripongkul Thira , Thongchom Chanachai , Saffari Peyman Roodgar , Saffari Pouyan Roodgar , Keawsawasvong Suraparb 
Published: October 2022

AbstractThis study offers a comprehensive investigation into the parameters affecting the sound transmission characteristics of a double-walled sandwich magneto-electro-elastic cross-ply layered plate resting on viscoelastic medium in thermal environment. To this end, the walls of this sandwich structure are modeled based on the assumptions of the first-order shear deformation theory. The governing equations are derived via a coupled set of equations targeting vibration and acoustic aspects of the problem after the application of Hamilton’s principle. The obtained equations are then solved by the implementation of double Fourier series and the second velocity potential, giving an accurate estimation of sound transmission loss under initial magnetic and electric potentials, variations of temperature, ply angle, acoustic cavity depth, incident angle of sound waves, and viscoelastic parameters.
Association of malnutrition with renal dysfunction and clinical outcome in patients with heart failure
Authors: Otaki Yoichiro , Watanabe Tetsu , Shimizu Mari , Tachibana Shingo , Sato Junya , Kobayashi Yuta , Saito Yuji , Aono Tomonori , Tamura Harutoshi , Kato Shigehiko , Nishiyama Satoshi , Takahashi Hiroki , Arimoto Takanori , Watanabe Masafumi 
Published: October 2022

AbstractMalnutrition, glomerular damage (GD), and renal tubular damage (RTD) are common morbidities associated with poor clinical outcomes in heart failure (HF) patients. However, the association between malnutrition and renal dysfunction and its impact on clinical outcomes in HF patients have not yet been fully elucidated. We assessed the nutritional status and renal function of 1061 consecutive HF patients. Malnutrition, GD, and RTD were defined as a controlling nutritional status (CONUT) score of ≥ 5, reduced eGFR or microalbuminuria, and levels of N-acetyl-beta-d-glucosamidase of > 14.2 U/gCr according to previous reports, respectively. Patients with RTD had a higher CONUT score and a lower prognostic nutritional index and geriatric nutritional risk index than those without. Multivariate logistic analysis demonstrated that RTD, but not GD, was significantly associated with malnutrition. There were 360 cardiac events during the median follow-up period of 688 days. Multivariate Cox proportional hazard regression analysis demonstrated that comorbid malnutrition and renal dysfunction, rather than simple malnutrition, were significantly associated with cardiac events in HF patients. We found a close relationship between malnutrition and renal dysfunction in HF patients. Comorbid malnutrition and renal dysfunction were risk factors for cardiac events in HF patients, suggesting the importance of managing and treating these.
Patient positioning during pediatric cardiothoracic computed tomography using a high-resilience pad system and pre-scan measurement of chest thickness
Authors: Higuchi Satoshi , Nishii Tatsuya , Hirota Atsushi , Harumoto Shota , Horinouchi Hiroki , Tateishi Emi , Ohta Yasutoshi , Kiso Keisuke , Kurosaki Kenichi , Fukuda Tetsuya 
Published: October 2022

AbstractPatient positioning at the isocenter of the CT gantry is important for optimizing image quality and radiation dose, but accurate positioning is challenging in pediatric patients. We evaluated whether the high-resilience pad and pre-scan measurement of chest thickness allow accurate positioning in pediatric patients with congenital heart disease. Sixty-seven patients aged 7 years or younger who underwent cardiothoracic CT were enrolled. The ideal table height, defined as the position at which the scanner’s and patient’s isocenters coincided, was determined by radiographers either manually (manual group) or based on the pad’s and chest’s thickness (calculated group). The distance between the two isocenters and image quality were evaluated. The calculated group demonstrated smaller isocenter distance and standard deviation (distance: 0.2 ± 5.8 mm vs. − 8.3 ± 11.6 mm, p < 0.01; absolute value: 4.1 [1.9–8.0] mm vs. 12.3 [5.1–16.3] mm, p < 0.01), and higher signal-to-noise ratio (SNR) and dose-normalized SNR (SNRD) in the descending aorta than the manual group (SNR: 39.8 [31.0–53.7] vs. 31.9 [28.9–36.6], p = 0.048, SNRD: 39.8 [31.0–53.7] vs. 31.9 [28.9–36.6], p = 0.04). The system allowed for more accurate positioning in pediatric cardiothoracic CT, yielding higher image quality.
Artificial neural network-based model to predict the effect of γ-aminobutyric acid on salinity and drought responsive morphological traits in pomegranate
Authors: Zarbakhsh Saeedeh , Shahsavar Ali Reza 
Published: October 2022

AbstractRecently, γ-Aminobutyric acid (GABA) has been introduced as a treatment with high physiological activity induction to enhance the ability of plants against drought and salinity stress, which led to a decline in plant growth. Since changes in morphological traits to drought and salinity stress are influenced by multiple factors, advanced computational analysis has great potential for computing nonlinear and multivariate data. In this work, the effect of four input variables including GABA concentration, pomegranate cultivars, days of treatment, and drought and salinity stress evaluated to predict and modeling of morphological traits using artificial neural network (ANN) models including multilayer perceptron (MLP) and radial basis function (RBF). Image processing technique was used to measure the LLI, LWI, and LAI parameters. Among the ANNs applied, the MLP algorithm was chosen as the best model based on the highest accuracy. Furthermore, to predict and estimate the optimal values of input variables for achieving the best morphological parameters, the MLP algorithm was linked to a non-dominated sorting genetic algorithm-II (NSGA-II). Based on the results of MLP-NSGA-II, the best values of crown diameter (18.42 cm), plant height (151.82 cm), leaf length index (5.67 cm), leaf width index (1.76 cm), and leaf area index (13.82 cm) could be achieved with applying 10.57 mM GABA on ‘Atabaki’ cultivar under control (non-stress) condition after 20.8 days. The results of modeling and optimization can be helpful to predict the morphological responses to drought and salinity conditions.
Optically driven liquid crystal droplet rotator
Authors: Saito Keita , Kimura Yasuyuki 
Published: October 2022

AbstractIn this study, the rotation of liquid crystal droplets induced by elliptically polarized laser light was investigated using optical tweezers. The rotation mechanism was analyzed based on the arrangement of liquid crystal molecules within the droplets. The change in the rotation behavior of nematic liquid crystal (NLC) droplets was evaluated by varying the droplet size. The experimental results were analyzed based on the waveplate effect and light-scattering process. The rotation behavior of cholesteric liquid crystal droplets was examined by varying the droplet size and helical pitch, which was controlled by the chiral dopant concentration. The results are discussed in terms of the selective reflection of the incident beam by the helical structure. The dependence of the rotation frequency on the ellipticity of the incident beam was also studied. The main contribution to the rotation gradually changes from light transmission to reflection with increasing chirality of the droplet. An NLC rotator system was constructed using holographic optical tweezers. Such an optically controllable rotator is a typical micro-optomechanical device. Complex flow fields, including multiple vortex and localized shear fields, were realized at the micron scale.