bluuebunny/crossref_metadata_2025_split huggingface dataset:
surviveR: a flexible shiny application for patient survival analysis
Authors: Sessler Tamas , Quinn Gerard P. , Wappett Mark , Rogan Emily , Sharkey David , Ahmaderaghi Baharak , Lawler Mark , Longley Daniel B. , McDade Simon S. 
Published: December 2023

AbstractKaplan–Meier (KM) survival analyses based on complex patient categorization due to the burgeoning volumes of genomic, molecular and phenotypic data, are an increasingly important aspect of the biomedical researcher’s toolkit. Commercial statistics and graphing packages for such analyses are functionally limited, whereas open-source tools have a high barrier-to-entry in terms of understanding of methodologies and computational expertise. We developed surviveR to address this unmet need for a survival analysis tool that can enable users with limited computational expertise to conduct routine but complex analyses. surviveR is a cloud-based Shiny application, that addresses our identified unmet need for an easy-to-use web-based tool that can plot and analyse survival based datasets. Integrated customization options allows a user with limited computational expertise to easily filter patients to enable custom cohort generation, automatically calculate log-rank test and Cox hazard ratios. Continuous datasets can be integrated, such as RNA or protein expression measurements which can be then used as categories for survival plotting. We further demonstrate the utility through exemplifying its application to a clinically relevant colorectal cancer patient dataset. surviveR is a cloud-based web application available at https://generatr.qub.ac.uk/app/surviveR, that can be used by non-experts users to perform complex custom survival analysis.
Ultrasound performance in pediatric deep soft-tissue tumor characterization
Authors: Li Cong , Chen Wenyi , Jin Ya , Xu Hong , Luo Hong 
Published: December 2023

AbstractThis study investigated the performance of ultrasonography in diagnosing deep soft-tissue tumors and tumor-like lesions in children with histological results. Demographic information and ultrasound characteristics of benign and malignant masses were statistically analyzed. Three radiologists (Radiologists 1, 2, and 3) independently reviewed the ultrasonography studies while being blinded to the medical history and other imaging findings. The 82 lesions included in the study were histopathologically classified as malignant (n = 25) or benign (n = 57). No statistically significant differences were observed between the benign and malignant subgroups regarding age (p = 0.059), sex (p = 1.0), disease course (p = 0.812), presence or absence of symptoms (p = 0.534), maximum diameter (p = 0.359), margin (p = 1.0), calcification (p = 0.057), or blood Adler type (p = 0.563). However, statistically significant differences were observed between the benign and malignant subgroups in terms of isolated or Multiple occurrences (p < 0.001), history of malignancy (p < 0.001), shape (p < 0.001), and echogenicity (p < 0.001). Parameters such as tumor shape (p = 0.042, OR = 6.222), single or multiple occurrences (p = 0.008, OR = 17.000), and history of malignancy (p = 0.038, OR = 13.962) were identified as independent predictors of benign and malignant tumors. The diagnostic sensitivities evaluated by the three radiologists were 68.0%, 72.0%, 96.0%, respectively, while the specificities were 77.2%, 82.5%, 77.2%, respectively. Ultrasound demonstrates good performance in the diagnosis of benign deep lesions such as hemangiomas/venous malformation and adipocytic tumors. Multiple irregular morphologies and a history of malignancy were identified as independent risk factors for malignant masses. The experience of radiologists in recognizing specific tumors is important. Careful attention should be paid to masses with ambiguous ultrasound features, as well as small lesions.
Longing for touch post-COVID-19: current observations and future directions
Authors: Hasenack Birgit , Meijer Larissa L. , van Harmelen Anna , Overvliet Krista E. , Keizer Anouk 
Published: December 2023

AbstractPrevious studies have reported an association between the COVID-19 pandemic, social distancing regulations and longing for touch (LFT; i.e., a discrepancy between actual touch frequency and one’s desire to be touched). However, less is known about the prevalence and severity of LFT in the general population in the absence of social distancing regulations. The aim of this study was therefore to exploratively compare data collected during and after the pandemic. Pandemic data was collected online in an international sample (n = 1982), of which a matched subsample (n = 115) was used in the reported analyses. Post-pandemic data was collected one week after social distancing regulations restrictions were lifted in the Netherlands (n = 60) and when virtually no restrictions were in place (n = 55). The severity of LFT was significantly higher during the pandemic than afterwards. Although there were no significant differences in the general prevalence of LFT, significantly more participants reported high levels of LFT (score of 75–100) during the pandemic. We cautiously conclude that, although LFT may have peaked during the pandemic, a large portion of the general population desires to experience more interpersonal touch, even in the absence of social distancing regulations.
Combination of melt-electrospun poly-ε-caprolactone scaffolds and hepatocyte-like cells from footprint-free hiPSCs to create 3D biohybrid constructs for liver tissue engineering
Authors: Weber Josefin , Linti Carsten , Lörch Christiane , Weber Marbod , Andt Madelene , Schlensak Christian , Wendel Hans Peter , Doser Michael , Avci-Adali Meltem 
Published: December 2023

AbstractThe liver is a vital organ with numerous functions, including metabolic functions, detoxification, and the synthesis of secretory proteins. The increasing prevalence of liver diseases requires the development of effective treatments, models, and regenerative approaches. The field of liver tissue engineering represents a significant advance in overcoming these challenges. In this study, 3D biohybrid constructs were created by combining hepatocyte-like cells (HLCs) derived from patient-specific footprint-free human induced pluripotent stem cells (hiPSCs) and 3D melt-electrospun poly-ε-caprolactone (PCL) scaffolds. First, a differentiation procedure was established to obtain autologous HCLs from hiPSCs reprogrammed from renal epithelial cells using self-replicating mRNA. The obtained cells expressed hepatocyte-specific markers and exhibited important hepatocyte functions, such as albumin synthesis, cytochrome P450 activity, glycogen storage, and indocyanine green metabolism. Biocompatible PCL scaffolds were fabricated by melt-electrospinning and seeded with pre-differentiated hepatoblasts, which uniformly attached to the fibers of the scaffolds and successfully matured into HLCs. The use of patient-specific, footprint-free hiPSC-derived HLCs represents a promising cell source for personalized liver regeneration strategies. In combination with biocompatible 3D scaffolds, this innovative approach has a broader range of applications spanning liver tissue engineering, drug testing and discovery, and disease modeling.
Human iPSC-derived microglia carrying the LRRK2-G2019S mutation show a Parkinson’s disease related transcriptional profile and function
Authors: Ohtonen Sohvi , Giudice Luca , Jäntti Henna , Fazaludeen Mohammad Feroze , Shakirzyanova Anastasia , Gómez-Budia Mireia , Välimäki Nelli-Noora , Niskanen Jonna , Korvenlaita Nea , Fagerlund Ilkka , Koistinaho Jari , Amiry-Moghaddam Mahmood , Savchenko Ekaterina , Roybon Laurent , Lehtonen Šárka , Korhonen Paula , Malm Tarja 
Published: December 2023

AbstractLRRK2-G2019S is one of the most common Parkinson’s disease (PD)-associated mutations and has been shown to alter microglial functionality. However, the impact of LRRK2-G2019S on transcriptional profile of human induced pluripotent stem cell-derived microglia-like cells (iMGLs) and how it corresponds to microglia in idiopathic PD brain is not known. Here we demonstrate that LRRK2-G2019S carrying iMGL recapitulate aspects of the transcriptional signature of human idiopathic PD midbrain microglia. LRRK2-G2019S induced subtle and donor-dependent alterations in iMGL mitochondrial respiration, phagocytosis and cytokine secretion. Investigation of microglial transcriptional state in the midbrains of PD patients revealed a subset of microglia with a transcriptional overlap between the in vitro PD-iMGL and human midbrain PD microglia. We conclude that LRRK2-G2019S iMGL serve as a model to study PD-related effects in human microglia.
Discrimination of finger movements by magnetomyography with optically pumped magnetometers
Authors: Greco Antonino , Baek Sangyeob , Middelmann Thomas , Mehring Carsten , Braun Christoph , Marquetand Justus , Siegel Markus 
Published: December 2023

AbstractOptically pumped magnetometers (OPM) are quantum sensors that offer new possibilities to measure biomagnetic signals. Compared to the current standard surface electromyography (EMG), in magnetomyography (MMG), OPM sensors offer the advantage of contactless measurements of muscle activity. However, little is known about the relative performance of OPM-MMG and EMG, e.g. in their ability to detect and classify finger movements. To address this in a proof-of-principle study, we recorded simultaneous OPM-MMG and EMG of finger flexor muscles for the discrimination of individual finger movements on a single human participant. Using a deep learning model for movement classification, we found that both sensor modalities were able to discriminate finger movements with above 89% accuracy. Furthermore, model predictions for the two sensor modalities showed high agreement in movement detection (85% agreement; Cohen’s kappa: 0.45). Our findings show that OPM sensors can be employed for contactless discrimination of finger movements and incentivize future applications of OPM in magnetomyography.
The role of captopril in leukotriene deficient type 1 diabetic mice
Authors: Guimarães João Pedro Tôrres , Queiroz Luiz A. D. , Menikdiwela Kalhara R. , Pereira Nayara , Ramalho Theresa , Jancar Sonia , Moustaid-Moussa Naima , Martins Joilson O. 
Published: December 2023

AbstractT1D can be associated with metabolic disorders and several impaired pathways, including insulin signaling, and development of insulin resistance through the renin-angiotensin system (RAS). The main precursor of RAS is angiotensinogen (Agt) and this system is often linked to autophagy dysregulation. Dysregulated autophagy has been described in T1D and linked to impairments in both glucose metabolism, and leukotrienes (LTs) production. Here, we have investigated the role of RAS and LTs in both muscle and liver from T1D mice, and its effects on insulin and autophagy pathways. We have chemically induced T1D in 129sve and 129sve 5LO−/− mice (lacking LTs) with streptozotocin (STZ). To further inhibit ACE activity, mice were treated with captopril (Cap). In muscle of T1D mice, treatment with Cap increased the expression of RAS (angiotensinogen and angiotensin II receptor), insulin signaling, and autophagy markers, regardless of the genotype. In the liver of T1D mice, the treatment with Cap increased the expression of RAS and insulin signaling markers, mostly when LTs were absent. 5LO−/− T1D mice showed increased insulin sensitivity, and decreased NEFA, after the Cap treatment. Cap treatment impacted both insulin signaling and autophagy pathways at the mRNA levels in muscle and liver, indicating the potential role of ACE inhibition on insulin sensitivity and autophagy in T1D.
Combined clinical and ultrasound criteria could accurately predict the Y chromosome in primary amenorrhea patient
Authors: Sumapraja Kanadi , Pangastuti Niken Pudji , Ikhsan Muhammad , Harzif Achmad Kemal , Maidarti Mila 
Published: December 2023

AbstractThis study aimed to assess the combined clinical and ultrasound criteria as a diagnostic tool for screening the Y chromosome related to primary amenorrhea. This cross-sectional study involving 59 subjects was taken from medical records at the Reproductive Immunoendocrinology Polyclinic of Cipto Mangunkusumo General Hospital, Jakarta, Indonesia. The medical records of subjects were then cross-checked with karyotyping analysis results. Sensitivity, specificity, and predictive values were analyzed to assess the criteria. Two subjects were presented with a Y chromosome, and one without a Y chromosome was misclassified into another group. After analysis, we found that combined clinical and ultrasound criteria could predict the Y chromosome related to primary amenorrhea with 95.9% accuracy, with sensitivity and specificity of 80% and 97.96%, respectively. Combined clinical and ultrasound criteria (introduced as Kanadi Sumapraja Criteria) could be used as a diagnostic tool for screening a Y chromosome related to primary amenorrhea.
On enhancing the noise-reduction performance of the acoustic lined duct utilizing the phase-modulating metasurface
Authors: Ou Yang , Zhao Yonghui 
Published: December 2023

AbstractThis work proposes a noise-reduction structure that integrates phase-modulating metasurface (PMM) with acoustic liners (ALs) to enhance the narrow band absorption performance of a duct with relatively small length-diameter ratio. The PMM manipulates the wavefront by introducing different transmission phase shifts based on an array of Helmholtz resonators, so that the spinning wave within the duct can be generated. Compared with the plane wave, the generated spinning wave has a lower group velocity, which results in a greater traveling distance over the ALs in the duct. The optimization design is performed to determine the final structural parameters of the PMM, which is based on the predictions of the amplitude and phase shift of the acoustic wave at the outlet of the PMM using the theory of passive phased array. With the manipulation of the PMM, the incident plane wave is modulated into a spinning wave, and then enters into the acoustic liner duct (ALD), whose structural parameters are optimized by maximizing the transmission loss using the mode-matching technique. Finally, the noise-reduction performance of this combined structure is evaluated by numerical simulations in the presence of grazing flow. The results demonstrate that, compared with the traditional ALD, the proposed structure exhibits a significant increase in transmission loss within the considered frequency band, especially near the peak frequency of the narrow band noise.
Spatio-temporal analysis of land use land cover change and its impact on land surface temperature of Sialkot City, Pakistan
Authors: Javaid Kainat , Ghafoor Gul Zareen , Sharif Faiza , Shahid Memuna Ghafoor , Shahzad Laila , Ghafoor Naghmana , Hayyat Muhammad Umar , Farhan Muhammad 
Published: December 2023

AbstractThe dynamic interplay between urbanization and its impacts on climate is a subject of recent concern, particularly in rapidly urbanizing cities of Pakistan. This research investigated the spatio-temporal effects of urban growth in terms of Land Use Land Cover changes on the thermal environment (Land Surface Temperature) of the Sialkot city, Pakistan using satellite data spanning four distinct time periods (1989, 2000, 2009 and 2020) and predicted changes for year 2030 by employing Cellular Automata Markov Chain Model. Satellite imagery (Landsat 5, 7 and 8) was processed, and maximum likelihood supervised classification was done to generate LULC maps for each of the aforementioned years. In addition to LULC classification, thermal bands of satellite data (for summer and winter) were processed to compute Land Surface Temperature (LST) of the city. The prediction of LULC changes and LST was done for year 2030 using Cellular Automata Markov Chain Model. The accuracy of classified and prediction maps was checked using Kappa Index. The LULC analysis revealed 4.14% increase in the built-up area and 3.43% decrease in vegetation cover of the city during 1989 to 2020. Both land covers are expected to change in the future (year 2030) by + 1.31% (built-up) and − 1.1% (vegetation). Furthermore, a declining trend in the barren land and water bodies was also observed over time. These LULC changes were found affecting the LST of study area. The transformation of vegetation cover into built-up area resulted in an increase in LST over time. A notable rise of 4.5 °C (summer) and 5.7 °C (winter) in the mean LST of Sialkot was observed during 1989 to 2020 and further increases are anticipated in year 2030. This study calls for attention of the policy makers to reduce human impact on the local climate of the city. The study will also help city developers in analyzing the urban population growth trend, finding suitable location to built new infrastructure by governmental authorities and how the rising temperature can affect energy demand and agriculture production of the city in future.
Environmental uncertainty and digital technologies corporate in shaping corporate green behavior and tax avoidance
Authors: Ao Xiang-Yuan , Ong Tze San , Aprile Roberto , Di Vaio Assunta 
Published: December 2023

AbstractThis study contributes to the field of sustainability by analyzing changes in firms following the adoption of new environmental protection laws to meet community sustainability needs. Focusing on the Chinese context, it examined the relationship between firms' environmental protection measures (i.e., corporate green behavior) and profitability (i.e., corporate tax avoidance). The moderating roles of environmental uncertainty and digital technology application in this relationship were also investigated. The findings offer insights into the complex dynamics linking firms’ environmental initiatives to their business outcomes and financial decisions within the framework of a sustainable community. Ultimately, this study highlights the importance and implications of sustainable practices for both the environment and corporate financial performance. Firms’ environmental behaviors are enablers of sustainable communities by deploying natural resources and creating a more resilient economy through active community participation in green production models.
Effect of freeze–thaw manipulation on phytostabilization of industrially contaminated soil with halloysite nanotubes
Authors: Radziemska Maja , Gusiatin Mariusz Z. , Cydzik-Kwiatkowska Agnieszka , Blazejczyk Aurelia , Majewski Grzegorz , Jaskulska Iwona , Brtnicky Martin 
Published: December 2023

AbstractThe latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing–thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing–thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT’s role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC’s negative effect on microbial diversity and increased Planctomycetia abundance.
Efficient agricultural practices in Africa reduce crop water footprint despite climate change, but rely on blue water resources
Authors: Giordano Vittorio , Tuninetti Marta , Laio Francesco 
Published: December 2023

AbstractAlarming projections of climate change, decline in crop yields, and increased food demand constitute daunting threats to African food production and sustainable water management. Here, we map this complex water-food nexus by combining gridded climate data and process-based crop modelling to quantify scenarios of crop water footprint under Representative Concentration Pathway 2.6 and Representative Concentration Pathway 6.0 for time horizons 2040, 2070 and 2100. We show that high-input agricultural management coupled with the expansion of irrigation infrastructure could generate an average reduction of water use intensity up to 64% for staple crops, but only 5% for cash crops, by 2040. Notwithstanding the positive effect of intensification, between 82 Km3 (2040) and 102 Km3 (2100) of additional blue water will be required to sustain the increased yields. Our scenarios are suited for identifying locations where crops are subject to high climate impacts and where crop production shows trade-offs between high-input management and irrigation demand.
Substantial blue carbon sequestration in the world’s largest seagrass meadow
Authors: Fu Chuancheng , Frappi Sofia , Havlik Michelle Nicole , Howe Wells , Harris S. David , Laiolo Elisa , Gallagher Austin J. , Masqué Pere , Duarte Carlos M. 
Published: December 2023

AbstractSeagrass meadows are important sinks for organic carbon and provide co-benefits. However, data on the organic carbon stock in seagrass sediments are scarce for many regions, particularly The Bahamas, which accounts for up to 40.7% of the documented global seagrass area, limiting formulation of blue carbon strategies. Here, we sampled 10 seagrass meadows across an extensive island chain in The Bahamas. We estimate that Bahamas seagrass meadows store 0.42–0.59 Pg organic carbon in the top-meter sediments with an accumulation rate of 2.1–2.9 Tg annually, representing a substantial global blue carbon hotspot. Autochthonous organic carbon in sediments decreased from ~1980 onwards, with concomitant increases in cyanobacterial and mangrove contributions, suggesting disturbance of seagrass ecosystems, likely caused by tourism and maritime traffic activities. This study provides seagrass blue carbon data from a vast, understudied region and contributes to improving climate action for The Bahamas and the Greater Caribbean region.
Language guided 3D object detection in point clouds for MEP scenes
Authors: Li Junjie , Du Shengli , Liu Jianfeng , Chen Weibiao , Tang Manfu , Zheng Lei , Wang Lianfa , Ji Chunle , Yu Xiao , Yu Wanli 
Published: December 2023

AbstractIn recent years, contrastive language‐image pre‐training (CLIP) has gained popularity for processing 2D data. However, the application of cross‐modal transferable learning to 3D data remains a relatively unexplored area. In addition, high‐quality, labelled point cloud data for Mechanical, Electrical, and Plumbing (MEP) scenarios are in short supply. To address this issue, the authors introduce a novel object detection system that employs 3D point clouds and 2D camera images, as well as text descriptions as input, using image‐text matching knowledge to guide dense detection models for 3D point clouds in MEP environments. Specifically, the authors put forth the proposition of a language‐guided point cloud modelling (PCM) module, which leverages the shared image weights inherent in the CLIP backbone. This is done with the aim of generating pertinent category information for the target, thereby augmenting the efficacy of 3D point cloud target detection. After sufficient experiments, the proposed point cloud detection system with the PCM module is proven to have a comparable performance with current state‐of‐the‐art networks. The approach has 5.64% and 2.9% improvement in KITTI and SUN‐RGBD, respectively. In addition, the same good detection results are obtained in their proposed MEP scene dataset.