bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative multi-omics analysis to gain new insights into COVID-19
Authors: Eshetie Setegn , Choi Karmel W. , Hyppönen Elina , Benyamin Beben , Lee S. Hong 
Published: November 2024

AbstractMultidimensional host and viral factors determine the clinical course of COVID-19. While the virology of the disease is well studied, investigating host-related factors, including genome, transcriptome, metabolome, and exposome, can provide valuable insights into the underlying pathophysiology. We conducted integrative omics analyses to explore their intricate interplay in COVID-19. We used data from the UK Biobank (UKB), and employed single-omics, pairwise-omics, and multi-omics models to illustrate the effects of different omics layers. The dataset included COVID-19 phenotypic data as well as genome, imputed-transcriptome, metabolome and exposome data. We examined the main, interaction effects and correlations between omics layers underlying COVID-19. Single-omics analyses showed that the transcriptome (derived from the coronary artery tissue) and exposome captured 3–4% of the variation in COVID-19 susceptibility, while the genome and metabolome contributed 2–2.5% of the phenotypic variation. In the omics-exposome model, where individual omics layers were simultaneously fitted with exposome data, the contributions of genome and metabolome were diminished and considered negligible, whereas the effects of the transcriptome showed minimal change. Through mediation analysis, the findings revealed that exposomic factors mediated about 60% of the genome and metabolome’s effects, while having a relatively minor impact on the transcriptome, mediating only 7% of its effects. In conclusion, our integrative-omics analyses shed light on the contribution of omics layers to the variance of COVID-19.
Modified neuroimmune processes and emotional behaviour in weaned and late adolescent male and female mice born via caesarean section
Authors: Di Miceli Mathieu , Rossitto Moïra , Martinat Maud , Marchaland Flore , Kharbouche Sarah , Graland Marion , Younes Farah , Séré Alexandra , Aubert Agnès , Khabbaz Lydia Rabbaa , Madore Charlotte , Delpech Jean-Christophe , Martín Rebeca , Layé Sophie 
Published: November 2024

Abstract
Elective and emergency Caesarean section (C-section) procedures are on the rise, exceeding the recommended guidelines by the World Health Organization. Higher morbidities and long-term health conditions are correlated to C-section deliveries, including neurodevelopmental disorders. During C-section delivery, newborns are not exposed to the vaginal commensal flora, which impedes the early establishment of the gut microbiota. The latter is essential for adequate neuro-immune processes to take place during infancy. In this study, we used a validated model of mice born by C-section (CSD), which mimics clinical observations of dysregulated gut microbiota. Animals were either born naturally or by CSD, before being adopted by dams who underwent delivery within the 12 preceding hours. Behavioural analyses were conducted at post-natal day (PND) 21 and 55. Our results indicate that animals born by C-section present significantly higher body weight in late (PND40-P53) but not early adolescence (PND21-P27), compared to animals born by vaginal delivery (VD). Male animals delivered by C-section presented significantly lower exploration time of the novel arm in the Y Maze test at PND55. However, at PND21, abnormal social interaction was witnessed in male and female animals born by CSD, with significantly decreased time spent interacting during the social interaction test. At both PND21 and PND55, animals from both sexes born by C-section presented significantly decreased time spent in the open arm of the Elevated Plus Maze test, compared to control animals. We then measured the expression of genes associated to neuroimmune interactions (microglia phenotype), inflammatory mediators and lipids in several brain structures of VD and CSD mice at PND21 and PND55. At weaning, animals born by CSD presented altered microglia, inflammatory and lipid metabolism signatures, with increased expression of Cd36, Csf1r and Tnfα in different brain regions of males, but not in females. At PND64, Csf1r, Tmem119 as well as C3ar1 were significantly increased in males born by C-section, but not in females. In males born by vaginal delivery, the expression of Cd36 at PND64 was correlated to anxiety at PND55, whilst a correlation between the expression of Clec7a and the number of head dippings in the elevated plus maze was also noted in males born by CSD. Altogether, our study shows altered emotional behaviour in animals delivered by CSD, which is likely explained by underlying neuro-inflammatory processes in different brain regions. Our work further supports the long-term consequences of CSD on brain health.
Screening great ape museum specimens for DNA viruses
Authors: Hämmerle Michelle , Guellil Meriam , Trgovec-Greif Lovro , Cheronet Olivia , Sawyer Susanna , Ruiz-Gartzia Irune , Lizano Esther , Rymbekova Aigerim , Gelabert Pere , Bernardi Paolo , Han Sojung , Rattei Thomas , Schuenemann Verena J. , Marques-Bonet Tomas , Guschanski Katerina , Calvignac-Spencer Sebastien , Pinhasi Ron , Kuhlwilm Martin 
Published: November 2024

AbstractNatural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.
A technical survey on practical applications and guidelines for IoT sensors in precision agriculture and viticulture
Authors: Pascoal David , Silva Nuno , Adão Telmo , Lopes Rui Diogo , Peres Emanuel , Morais Raul 
Published: November 2024

Abstract
Climate change pose significant challenges to modern agriculture management systems, threatening food production and security. Therefore, tackling its effects has never been so imperative to attain sustainable food access and nutrition worldwide. In the case of viticulture, besides jeopardizing grape production, climate change has severe impact in quality, which has becoming more challenging to manage, due to the increasingly frequent fungal contamination, with consequences for relevant quality parameters such as the aromatic profiles of grapes and wines and their phenolic compounds. This has been leading to a reconfiguration of the wine industry geostrategic landscape and economy dynamics, particularly in Southern Europe. To address these and other emerging challenges, in-field deployable proximity-based precision technologies have been enabling real-time monitoring of crops ecosystems, including climate, soil and plants, by performing relevant data gathering and storage, paving the way for advanced decision support under the Internet of Things (IoT) paradigm. This paper explores the integration of agronomic and technological knowledge, emphasizing the proper selection of IoT-capable sensors for viticulture, while considering more general ones from agriculture to fill gaps when specialized options are unavailable. Moreover, advisable practices for sensor installation are provided, according to respective types, data acquisition capabilities and applicability.
Evaluation of the advanced air mobility potential for organ transplantation in Austria and Germany
Authors: Karpstein Robin , Brolli Jakob , Stiegler Philipp , Sucher Robert , Holzapfel Florian , Biberthaler Peter 
Published: November 2024

AbstractSolid organ transplantation continues to be the only or most efficient therapeutic solution for several end-stage diseases. The success of such transplantation is largely dependent on the swift transportation of organs from donors to recipients, as Cold Ischemia Time (CIT) plays a critical role in determining the recipient’s medical outcome. This study explores the potential of Advanced Air Mobility (AAM) in the context of organ transplantation in Austria and Germany. AAM, in the healthcare sector, is associated with potential overall process time savings via air transportation, thereby reducing CIT. However, the application of AAM for organ transplantation has not yet been implemented in Europe. This study employs a Monte Carlo simulation to derive the trip length distributions for organ transplantation in Austria and Germany. By utilizing data from Eurotransplant (2018–2021) and ÖBIG (2017–2021), it was found that 48% of organ transports within Germany, and 80% of organ transports within Austria, fall within a trip length of less than 150 km. This distance is within the capabilities of today’s AAM technology. Anticipated time benefits of up to 30 min compared to ground-based transport can be expected. Furthermore, the optimization of the organ transport process, facilitated by AAM, promises greater potential for CIT reduction.
Comparative analysis of amino acid sequence level in plant GATA transcription factors
Authors: Kim Mangi 
Published: November 2024

AbstractTranscription factors (TFs) are essential regulators of gene expression, influencing numerous biological processes such as development, growth, and cellular responses in plants. Among these, GATA TFs are distinguished by their highly conserved DNA-binding domain, characterized by a class IV zinc finger motif (CX2CX18-20CX2C). This study investigates the amino acid sequence patterns of 5,335 GATA TFs across 165 plant species sourced from the PlantTFDB database (http://planttfdb.gao-lab.org/), encompassing diverse taxonomic groups. Through comparative sequence analysis, I identify conserved domains and structural features that enhance the understanding functional roles, evolutionary conservation, and lineage-specific adaptations of GATA TFs. These findings provide valuable insights into the diversification and functional specialization of GATA TFs, with implications for improving stress tolerance and adaptability in crops. This study contributes to the broader knowledge of transcriptional regulation in plant biology.
Experimental and numerical investigation of a cold-formed steel system used to restore old buildings floor
Authors: Fahmy Ahmed Shamel , Swelem Sherine Mostafa , Farrag Rowida Saad , Mobarak Wael F. M. 
Published: November 2024

AbstractThis paper presents a novel configuration of built-up cold-formed steel (CFS) flooring system in the shape of a box section. A new technique is applied to produce the components of the flooring system, which are fastened by self-drilling screws. This box section consists of a cast-in-situ concrete slab, trapezoidal steel decking, two sigma section, steel plate and stiffening equal angles. The main objectives of this system is to enable rapid construction and decrease the time, requirements, and cost. As a result, the proposed system is designed to use the decking in a longitudinal direction. Many old buildings have sturdy structures but their floors were ruined due to being fabricated from timber. This flooring system will be implemented to increase their quality of life and be reused. The loading experiments of four specimens were carried out. The failure modes of the CFS flooring system, load-deflection relation curves, longitudinal strain distribution at different heights were obtained. The experimental results show that the flooring system has high stiffness and flexural performance and can reach ultimate strength without local buckling failure. The failure occurs due to distortion at the end supports. Then, the capacity of the flooring system was calculated theoretically. Then, the practical and theoretical results were compared. The calculated results agree well with the test results. A three-dimensional finite element model is also established to investigate structural performance of the proposed system.
Seasonal hotspots of beach litter in the North-East Atlantic linked to aquaculture and river runoff
Authors: Rieger Niclas , Olmedo Estrella , Thiel Martin , Salvo Vanessa Sarah , Honorato-Zimmer Daniela , Vásquez Nelson , Turiel Antonio , Piera Jaume 
Published: November 2024

AbstractMacroplastic pollution is a pervasive global environmental challenge, adversely affecting marine ecosystems, wildlife and human health. Understanding temporal variations is crucial for identifying pollution sources and developing effective mitigation policies. However, in-situ data from beach surveys are often irregular, both spatially and temporally, and highly variable, complicating robust statistical conclusions. Here we employ a Bayesian machine learning framework to investigate seasonal variations, identify regional hotspots and elucidate their anthropogenic drivers. Using data from 3866 surveys across 168 western European beaches, we leverage a spatial log-Gaussian Cox Process to enhance statistical inference by integrating information from nearby beaches. Distinct seasonal patterns emerge, with winter and spring exhibiting the highest pollution levels, while pronounced regional differences highlight seasonal pollution hotspots in the western Iberian Peninsula, French coastline, Irish Sea and Skagerrak region. These peaks are attributed to riverine emissions and aquaculture activities, highlighting the potential impact of these sources on beach pollution. Our findings advocate for enhanced, time-specific monitoring to effectively manage litter hotspots, emphasizing the importance of aquaculture-related plastic emissions.
Biofouling changes the settling dynamics of macroplastic plates
Authors: Lofty James , Wilson Catherine , Ouro Pablo 
Published: November 2024

AbstractPlastic pollution transported in rivers remains poorly understood due to the diversity of shapes, sizes, and densities of plastics, as well as their complex interactions with biofilms. While previous studies have explored the settling velocities of plastics and their interactions with biofilms, they often overlook how biofouling alters plastic dynamics and settling behaviour. To address this, over 800 settling experiments were conducted to demonstrate that the dynamics and falling velocities of isotropic (spheres) and anisotropic (square and rectangle plates) macroplastics of different densities (1050 to 2200 kg/m3) are significantly impacted by biofouling. Three-dimensional tracking of plastic trajectories revealed that biofilm colonisation on the surface of anisotropic plastic plates triggered them to exhibit more chaotic trajectories, larger horizontal dispersion and higher oscillatory frequencies. These dynamics reduced the average vertical settling velocity of anisotropic biofouled plates by up to 12%—despite greater plastic densities and considering the multimodal distribution of a plate’s fall velocity—compared to their pristine counterparts. Results highlight the necessity of accounting for the intricate multimodal settling dynamics of plastics, including their interactions with biofilms, to provide more reliable predictions of plastic transport and fate in aquatic environments.
Achieving at-scale seascape restoration by optimising cross-habitat facilitative processes
Authors: Vozzo Maria L. , Buelow Christina A. , Sievers Michael , Adame M. Fernanda , Branson Paul , Brown Maddison , Crosswell Joseph R. , Doropoulos Christopher , Gilby Ben L. , Martinez-Baena Francisco , Reeves Simon , Rullens Vera , Steven Andy , Xiao Ziyu , Dahle Kirk , Silliman Brian , ter Hofstede Remment , van Koningsveld Mark , Saunders Megan I. 
Published: November 2024

AbstractCross-habitat facilitative processes can enhance seascape restoration outcomes but there is uncertainty around the spatial dependencies of these processes across habitats. We synthesised the influence of environmental parameters on six processes underpinning cross-habitat facilitation and identified the linear distances over which they operate between habitats. All six process types occur at distances commonly used in seascape restoration demonstrating how harnessing facilitation can scale-up restoration to meet national and international goals.
TBN-promoted regioselective C–C bond cleavage: a new strategy for the synthesis of unsymmetrically substituted N-aryl oxalamides
Authors: Liu Guiqin , Zhang Zheyan , Wang Huifeng , Chen Ruiling , Tian Haiying , Chen Xiuling 
Published: November 2024

The intermolecular regioselective C–C and C–O bond cleavage and amination was accomplished by CuCl2-TBN system under mild reaction conditions for the synthesis of unsymmetrically substituted N-aryl oxalamides.
Reducing overfitting in vehicle recognition by decorrelated sparse representation regularisation
Authors: Wei Wanyu , Fu Xinsha , Ma Siqi , Zhu Yaqiao , Lu Ning 
Published: November 2024

AbstractMost state‐of‐the‐art vehicle recognition methods benefit from the excellent feature extraction capabilities of convolutional neural networks (CNNs), which allow the models to perform well on the intra‐dataset. However, they often show poor generalisation when facing cross‐datasets due to the overfitting problem. For this issue, numerous studies have shown that models do not generalise well in new scenarios due to the high correlation between the representations in CNNs. Furthermore, over‐parameterised CNNs have a large number of redundant representations. Therefore, we propose a novel Decorrelated Sparse Representation (DSR) regularisation. (1) It tries to minimise the correlation between feature maps to obtain decorrelated representations. (2) It forces the convolution kernels to extract meaningful features by allowing the sparse kernels to have additional optimisation. The DSR regularisation encourages diverse representations to reduce overfitting. Meanwhile, DSR can be applied to a wide range of vehicle recognition methods based on CNNs, and it does not require additional computation in the testing phase. In the experiments, DSR performs better than the original model on the intra‐dataset and cross‐dataset. Through ablation analysis, we find that DSR can drive the model to focus on the essential differences among all kinds of vehicles.
280–300 GHz SiGe‐InP hybrid‐integrated transmitter with 21.9 dBm EIRP and 10 Gbps data rate
Authors: Lu Haiyan , Chen Jixin , Yan Pinpin , Tang Si‐Yuan , Zheng Yu , Zheng Sidou , Cheng Wei , Sun Yan , Zhou Peigen , Chang Long , Cai Longzhu , Jiang Zhi Hao , Tao Hongqi , Chen Tangsheng , Hong Wei 
Published: November 2024

AbstractIn this paper, a 280–300 GHz hybrid‐integrated transmitter is proposed. The advantages of the SiGe and InP chips are fully made use by integrating these two chips. For low cost and high integration, the local oscillator chain and mixer are based on chips in SiGe technology, and the 300‐GHz power amplifier and on‐chip antenna are realised in InP technology for high output power and small die size. The low‐cost bonding wires are introduced for the interconnection between these two chips, and the lens are attached above the on‐chip antenna for further EIRP enhancement. Finally, the proposed transmitter is fabricated and measured, which shows comparable performances with 21.9 dBm EIRP (equivalent isotropic radiated power) and 10 Gbps data rate.
Effect of phase centre variation on tropospheric delay in PPP‐AR with low‐cost global navigation satellite systems receiver and antenna
Authors: Wu Jizhong , Wang Xiaoying , Ma Hongyang 
Published: November 2024

AbstractAs low‐cost global navigation satellite systems receiver and antenna become increasingly prevalent for water vapour monitoring, precise millimetre‐level characterisation of instrument biases is crucial for maintaining measurement accuracy and reliability. This study examines the impact of phase centre variation (PCV) corrections on zenith wet delay (ZWD) accuracy in precise point positioning (PPP) solutions using low‐cost systems. The results show that PCV corrections significantly improve ZWD estimation, reducing bias and RMS by 66% and 31% in ambiguity float PPP, and by 71% and 38% in ambiguity fixed PPP. In addition, integer ambiguity resolution offers no significant improvement in ZWD accuracy without PCV correction. When PCV corrections and ambiguity fixing are applied, low‐cost receivers demonstrate ZWD estimates comparable to those of high‐precision geodetic receivers, with a deviation of 0.2 mm and an RMS of 2 mm. However, variations in signal tracking and multipath suppression can still influence ambiguity fixing rates, resulting in slightly lower performance for low‐cost receivers compared to their high‐precision counterparts. The study concludes that deploying low‐cost receivers with calibrated antennas offers a cost‐effective approach to increasing the spatial resolution of atmospheric water vapour measurements, thereby enhancing weather monitoring and early warning systems, particularly for localised extreme weather events.
Antibiotikaanwendung 2012/13 bis 2021/22 in deutschen Akutkrankenhäusern
Authors: Kern Winfried V. , Steib-Bauert Michaela , Fellhauer Matthias , Baumann Jürgen , Först Gesche , Kramme Evelyn , Dörje Frank , de With Katja 
Published: November 2024

ZusammenfassungEine wichtige Voraussetzung für die Sicherung einer rationalen Antibiotika-Verordnung ist die Verfügbarkeit und Prüfung von Verbrauchsdaten. Wir haben erstmals vor 10 Jahren solche Daten für Akutkrankenhäuser in Deutschland vorgestellt und möchten die Entwicklungen seither beschreiben.Die jährlichen Antibiotika-Verordnungsmengen aus Akutkrankenhäusern wurden für den Zeitraum 2012/13 bis 2021/22 analysiert, dargestellt als Tagesdosen pro 100 Pflegetage, wobei die Tagesdosis-Definition speziell für den Krankenhausbereich adaptiert wurde („recommended daily dose“, RDD). Zusätzlich wurde eine Hochrechnung auf die Gesamtbevölkerung unter Verwendung der seitens der WHO definierten Tagesdosen („defined daily doses“, DDD) vorgenommen.Die Antibiotika-Verbrauchsdichte in deutschen Akutkrankenhäusern ist im betrachteten 10-Jahres-Zeitraum nicht angestiegen. Sie betrug im Median im Jahre 2012/13 insgesamt 41,9 RDD/100 Pflegetage (n=169, Interquartilbereich 35–48 RDD/100) im Vergleich zu 42,1 RDD/100 im Jahre 2021/22 (n=329, Interquartilbereich 35–48 RDD/100). Auf die Bevölkerung bezogen lag der Verbrauch 2021/22 bei 1,85 DDD pro 1000 Bewohner und Tag. Die Verbrauchsdichte war in Universitätskliniken (54,0 RDD/100) signifikant höher als in den nicht universitären Krankenhäusern unterschiedlicher Größe, deren Verbrauchswerte sich nur wenig unterschieden (Mediane 39,8–44,0 RDD/100). Penicilline wurden zunehmend häufiger (Anstieg des Anteils an allen Wirkstoffen +63%), Fluorchinolone (– 54%) und Cephalosporine der ersten und zweiten Generation (– 41%) seltener eingesetzt. Auf Intensivstationen war die Verordnungsdichte rund doppelt so hoch wie auf den Normalstationen. Hohe Verordnungsdichten wurden
auch in universitären hämatologisch-onkologischen Abteilungen (Median 96,8 RDD/100) und in Fachabteilungen für Urologie (Mediane 65,1–70,5 RDD/100) und HNO-Heilkunde (Mediane 49,1–60,9 RDD/100) beobachtet.Bei gleichbleibender Antibiotika-Verordnungsdichte im Krankenhaus insgesamt gab es Verschiebungen im Spektrum der Wirkstoffgruppen, mit einer zunehmenden Bevorzugung von Penicillin-Derivaten. Auf die Bevölkerung hochgerechnet lag der Verbrauch leicht oberhalb des europäischen Durchschnitts.