bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sinus, middle-ear and mastoid radiological findings of severe acute respiratory syndrome coronavirus-2
Authors: Watts E , Balai E , Kwatra D , Banerjee S , Hoskison E 
Published: October 2022

AbstractObjectiveTo assess the incidence of radiological inflammation within the paranasal sinuses, middle ear and mastoid in patients with confirmed severe acute respiratory syndrome coronavirus-2.MethodsA retrospective cohort study was conducted to examine consecutive adults (aged over 18 years) with coronavirus disease 2019 (confirmed on polymerase chain reaction within 7 days of imaging) who underwent computed tomography of the head between 1 March 2020 and 24 June 2020. Lund–Mackay and mastoid and middle-ear opacification scores were used to categorise the extent of sinus and mastoid opacification on axial and coronal computed tomography images.ResultsOf 147 patients originally identified, only 83 met the inclusion criteria. Sinus opacification was present in 51.8 per cent of patients (n = 43), and middle-ear or mastoid opacification was observed in 24.1 per cent (n = 20). There was no statistically significant difference in sinus or middle-ear and mastoid opacification between patients after stratification based on 30-day all-cause mortality.ConclusionRadiological computed tomography findings suggest mild mucosal disease within the sinuses, middle ear and mastoid. There was no statistical correlation between such opacification and 30-day mortality.
An Application of a Runtime Epistemic Probabilistic Event Calculus to Decision-making in e-Health Systems
Authors: D’ASARO FABIO AURELIO , RAGGIOLI LUCA , MALEK SALIM , GRAZIOSO MARCO , ROSSI SILVIA 
Published: October 2022

AbstractWe present and discuss a runtime architecture that integrates sensorial data and classifiers with a logic-based decision-making system in the context of an e-Health system for the rehabilitation of children with neuromotor disorders. In this application, children perform a rehabilitation task in the form of games. The main aim of the system is to derive a set of parameters the child’s current level of cognitive and behavioral performance (e.g., engagement, attention, task accuracy) from the available sensors and classifiers (e.g., eye trackers, motion sensors, emotion recognition techniques) and take decisions accordingly. These decisions are typically aimed at improving the child’s performance by triggering appropriate re-engagement stimuli when their attention is low, by changing the game or making it more difficult when the child is losing interest in the task as it is too easy. Alongside state-of-the-art techniques for emotion recognition and head pose estimation, we use a runtime variant of a probabilistic and epistemic logic programming dialect of the Event Calculus, known as the Epistemic Probabilistic Event Calculus. In particular, the probabilistic component of this symbolic framework allows for a natural interface with the machine learning techniques. We overview the architecture and its components, and show some of its characteristics through a discussion of a running example and experiments.
The Key Factors Controlling the Seasonality of Planetary Climate
Authors: Guendelman Ilai , Kaspi Yohai 
Published: October 2022

AbstractSeveral different factors influence the seasonal cycle of a planet. This study uses a general circulation model and an energy balance model (EBM) to assess the parameters that govern the seasonal cycle. We define two metrics to describe the seasonal cycle, ϕs, the latitudinal shift of the maximum temperature, and ΔT, the maximum seasonal temperature variation amplitude. We show that alongside the expected dependence on the obliquity and orbital period, where seasonality generally strengthens with an increase in these parameters, the seasonality depends in a nontrivial way on the rotation rate. While the seasonal amplitude decreases as the rotation rate slows down, the latitudinal shift, ϕs, shifts poleward. A similar result occurs in a diffusive EBM with increasing diffusivity. These results suggest that the influence of the rotation rate on the seasonal cycle stems from the effect of the rotation rate on the atmospheric heat transport.
Tunable High‐Resolution Synthetic Aperture Radar Imaging
Authors: Kim Arnold D. , Tsogka Chrysoula 
Published: October 2022

AbstractWe have recently introduced a modification of the multiple signal classification method for synthetic aperture radar. This method incorporates a user‐defined parameter, ϵ, that allows for tunable quantitative high‐resolution imaging. However, this method requires relatively large single‐to‐noise ratios (SNR) to work effectively. Here, we first identify the fundamental mechanism in that method that produces high‐resolution images. Then we introduce a modification to Kirchhoff Migration (KM) that uses the same mechanism to produce tunable, high‐resolution images. This modified KM method can be applied to low SNR measurements. We show simulation results that demonstrate the features of this method.
Light People: Professor Martin Booth spoke about adaptive optics and its applications
Authors: Cui Jiahe , He Chao , Chang Wei 
Published: October 2022

EditorialAdaptive optics (AO), a technique originally introduced by astronomers to correct for optical distortions when looking at distant stars, now benefits the entire optics and photonics society. Prof. Martin Booth, who leads his research lab at the University of Oxford where he started his career, was one of the first people to take advantage of AO for microscopy. Since then, he has been continuously promoting the wide application of AO in all aspects of biological research and material science. As one of the few people who has witnessed the growth of AO in various communities, Prof. Martin Booth talks about their major differences, as well as their current challenges and future development. He discusses how AO can benefit emerging areas and the key challenges that may be faced. Prof. Martin Booth has also been making continuous efforts in removing the barriers of AO so that it can be promoted towards the wider community. Finally, he shares his experience from actively taking up different roles in education and in various societies and provides valuable advice to all early career researchers on the wisdom of being successful in their future careers. It is an honour for us to invite Prof. Martin Booth on this issue, and to learn from his inspirations, enthusiasm, and dedication.
Validation of a multi-frequency bioelectrical impedance analysis device for the assessment of body composition in older adults with type 2 diabetes
Authors: Buch Assaf , Ben-Yehuda Arie , Rouach Vanessa , Maier Andrea B. , Greenman Yona , Izkhakov Elena , Stern Naftali , Eldor Roy 
Published: October 2022

Abstract
Background
Aging and type 2 diabetes (T2DM) are associated with an increased risk of sarcopenia. Diagnosis of sarcopenia is commonly done using dual-energy X-ray absorptiometry (DXA) in specialized settings. Another available method for assessing body composition is direct segmental multi-frequency bioelectrical impedance analysis (DSMF-BIA). Here, we examine the accuracy of a DSMF-BIA (InBody-770) for assessing body composition in older adults with T2DM when compared to DXA.

Methods
Eighty-four obese/overweight older adults (49 women, 71 ± 5 years) with T2DM who were recruited for the CEV-65 study and had both DSMF-BIA and DXA assessments at baseline were included. The analysis included Bland–Altman plots and intra class correlation coefficients. Sub-analyses were performed according to gender and following 10 weeks of interventions (diet, circuit training, and Empagliflozin).

Results
The leg lean mass results according to DSMF-BIA and DXA were 14.76 ± 3.62 kg and 15.19 ± 3.52 kg, respectively, with no difference between devices according to Bland–Altman analyses (p = 0.353). Assessment of appendicular skeletal mass index did not differ between DSMF-BIA and DXA (7.43 vs. 7.47 kg/m2; p = 0.84; ICC = 0.965, p < 0.0001; mean difference −0.068, p = 0.595). Gender and treatment interventions did not modify the accuracy of the DSMF-BIA when compared to DXA.

Conclusions
In older adults with T2DM the degree of agreement between DSMF-BIA and DXA, was high, supporting the use of DSMF-BIA to measure muscle mass.
Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
Authors: Herbst Sophie A. , Vesterlund Mattias , Helmboldt Alexander J. , Jafari Rozbeh , Siavelis Ioannis , Stahl Matthias , Schitter Eva C. , Liebers Nora , Brinkmann Berit J. , Czernilofsky Felix , Roider Tobias , Bruch Peter-Martin , Iskar Murat , Kittai Adam , Huang Ying , Lu Junyan , Richter Sarah , Mermelekas Georgios , Umer Husen Muhammad , Knoll Mareike , Kolb Carolin , Lenze Angela , Cao Xiaofang , Österholm Cecilia , Wahnschaffe Linus , Herling Carmen , Scheinost Sebastian , Ganzinger Matthias , Mansouri Larry , Kriegsmann Katharina , Kriegsmann Mark , Anders Simon , Zapatka Marc , Del Poeta Giovanni , Zucchetto Antonella , Bomben Riccardo , Gattei Valter , Dreger Peter , Woyach Jennifer , Herling Marco , Müller-Tidow Carsten , Rosenquist Richard , Stilgenbauer Stephan , Zenz Thorsten , Huber Wolfgang , Tausch Eugen , Lehtiö Janne , Dietrich Sascha 
Published: October 2022

AbstractCancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.
Rapid antibiotic susceptibility testing and species identification for mixed samples
Authors: Kandavalli Vinodh , Karempudi Praneeth , Larsson Jimmy , Elf Johan 
Published: October 2022

AbstractAntimicrobial resistance is an increasing problem on a global scale. Rapid antibiotic susceptibility testing (AST) is urgently needed in the clinic to enable personalized prescriptions in high-resistance environments and to limit the use of broad-spectrum drugs. Current rapid phenotypic AST methods do not include species identification (ID), leaving time-consuming plating or culturing as the only available option when ID is needed to make the sensitivity call. Here we describe a method to perform phenotypic AST at the single-cell level in a microfluidic chip that allows subsequent genotyping by in situ FISH. By stratifying the phenotypic AST response on the species of individual cells, it is possible to determine the susceptibility profile for each species in a mixed sample in 2 h. In this proof-of-principle study, we demonstrate the operation with four antibiotics and mixed samples with combinations of seven species.
Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3
Authors: Georges Romain O. , Sepulveda Hugo , Angel J. Carlos , Johnson Eric , Palomino Susan , Nowak Roberta B. , Desai Arshad , López-Moyado Isaac F. , Rao Anjana 
Published: October 2022

AbstractTET (Ten-Eleven Translocation) dioxygenases effect DNA demethylation through successive oxidation of the methyl group of 5-methylcytosine (5mC) in DNA. In humans and in mouse models, TET loss-of-function has been linked to DNA damage, genome instability and oncogenesis. Here we show that acute deletion of all three Tet genes, after brief exposure of triple-floxed, Cre-ERT2-expressing mouse embryonic stem cells (mESC) to 4-hydroxytamoxifen, results in chromosome mis-segregation and aneuploidy; moreover, embryos lacking all three TET proteins showed striking variation in blastomere numbers and nuclear morphology at the 8-cell stage. Transcriptional profiling revealed that mRNA encoding a KH-domain protein, Khdc3 (Filia), was downregulated in triple TET-deficient mESC, concomitantly with increased methylation of CpG dinucleotides in the vicinity of the Khdc3 gene. Restoring KHDC3 levels in triple Tet-deficient mESC prevented aneuploidy. Thus, TET proteins regulate Khdc3 gene expression, and TET deficiency results in mitotic infidelity and genome instability in mESC at least partly through decreased expression of KHDC3.
Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts
Authors: Jensen Emil D. , Deichmann Marcus , Ma Xin , Vilandt Rikke U. , Schiesaro Giovanni , Rojek Marie B. , Lengger Bettina , Eliasson Line , Vento Justin M. , Durmusoglu Deniz , Hovmand Sandie P. , Al’Abri Ibrahim , Zhang Jie , Crook Nathan , Jensen Michael K. 
Published: October 2022

AbstractG protein-coupled receptors (GPCRs) enable cells to sense environmental cues and are indispensable for coordinating vital processes including quorum sensing, proliferation, and sexual reproduction. GPCRs comprise the largest class of cell surface receptors in eukaryotes, and for more than three decades the pheromone-induced mating pathway in baker’s yeast Saccharomyces cerevisiae has served as a model for studying heterologous GPCRs (hGPCRs). Here we report transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast and use a model-guided approach to correlate gene expression to morphological changes. From this we demonstrate mating between haploid cells armed with hGPCRs and endogenous biosynthesis of their cognate ligands. Furthermore, we devise a ligand-free screening strategy for hGPCR compatibility with the yeast mating pathway and enable hGPCR-signaling in the probiotic yeast Saccharomyces boulardii. Combined, our findings enable new means to study mating, hGPCR-signaling, and cell-cell communication in a model eukaryote and yeast probiotics.
Slow light in a 2D semiconductor plasmonic structure
Authors: Klein Matthew , Binder Rolf , Koehler Michael R. , Mandrus David G. , Taniguchi Takashi , Watanabe Kenji , Schaibley John R. 
Published: October 2022

AbstractSpectrally narrow optical resonances can be used to generate slow light, i.e., a large reduction in the group velocity. In a previous work, we developed hybrid 2D semiconductor plasmonic structures, which consist of propagating optical frequency surface-plasmon polaritons interacting with excitons in a semiconductor monolayer. Here, we use coupled exciton-surface plasmon polaritons (E-SPPs) in monolayer WSe2 to demonstrate slow light with a 1300 fold decrease of the SPP group velocity. Specifically, we use a high resolution two-color laser technique where the nonlinear E-SPP response gives rise to ultra-narrow coherent population oscillation (CPO) resonances, resulting in a group velocity on order of 105 m/s. Our work paves the way toward on-chip actively switched delay lines and optical buffers that utilize 2D semiconductors as active elements.
Promiscuity of response regulators for thioredoxin steers bacterial virulence
Authors: Kim Ju-Sim , Born Alexandra , Till James Karl A. , Liu Lin , Kant Sashi , Henen Morkos A. , Vögeli Beat , Vázquez-Torres Andrés 
Published: October 2022

AbstractThe exquisite specificity between a sensor kinase and its cognate response regulator ensures faithful partner selectivity within two-component pairs concurrently firing in a single bacterium, minimizing crosstalk with other members of this conserved family of paralogous proteins. We show that conserved hydrophobic and charged residues on the surface of thioredoxin serve as a docking station for structurally diverse response regulators. Using the OmpR protein, we identify residues in the flexible linker and the C-terminal β-hairpin that enable associations of this archetypical response regulator with thioredoxin, but are dispensable for interactions of this transcription factor to its cognate sensor kinase EnvZ, DNA or RNA polymerase. Here we show that the promiscuous interactions of response regulators with thioredoxin foster the flow of information through otherwise highly dedicated two-component signaling systems, thereby enabling both the transcription of Salmonella pathogenicity island-2 genes as well as growth of this intracellular bacterium in macrophages and mice.
Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium
Authors: Kumar Sandeep , Altermann Eric , Leahy Sinead C. , Jauregui Ruy , Jonker Arjan , Henderson Gemma , Kittelmann Sandra , Attwood Graeme T. , Kamke Janine , Waters Sinéad M. , Patchett Mark L. , Janssen Peter H. 
Published: October 2022

AbstractQuinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH4) relative to their feed intake, but whether Quinella contributes to low CH4 emissions is not known. Here, we concentrate Quinella cells from sheep rumen contents, extract and sequence DNA, and reconstruct Quinella genomes that are >90% complete with as little as 0.20% contamination. Bioinformatic analyses of the encoded proteins indicate that lactate and propionate formation are major fermentation pathways. The presence of a gene encoding a potential uptake hydrogenase suggests that Quinella might be able to use free hydrogen (H2). None of the inferred metabolic pathways is predicted to produce H2, a major precursor of CH4, which is consistent with the lower CH4 emissions from those sheep with high abundances of this bacterium.
Epidemic spreading under mutually independent intra- and inter-host pathogen evolution
Authors: Zhang Xiyun , Ruan Zhongyuan , Zheng Muhua , Zhou Jie , Boccaletti Stefano , Barzel Baruch 
Published: October 2022

AbstractThe dynamics of epidemic spreading is often reduced to the single control parameter R0 (reproduction-rate), whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, R0 may change over time, potentially leading to a mutation-driven spread, in which an initially sub-pandemic pathogen undergoes a breakthrough mutation. To predict the boundaries of this pandemic phase, we introduce here a modeling framework to couple the inter-host network spreading patterns with the intra-host evolutionary dynamics. We find that even in the extreme case when these two process are driven by mutually independent selection forces, mutations can still fundamentally alter the pandemic phase-diagram. The pandemic transitions, we show, are now shaped, not just by R0, but also by the balance between the epidemic and the evolutionary timescales. If mutations are too slow, the pathogen prevalence decays prior to the appearance of a critical mutation. On the other hand, if mutations are too rapid, the pathogen evolution becomes volatile and, once again, it fails to spread. Between these two extremes, however, we identify a broad range of conditions in which an initially sub-pandemic pathogen can breakthrough to gain widespread prevalence.
Combining mass spectrometry and machine learning to discover bioactive peptides
Authors: Madsen Christian T. , Refsgaard Jan C. , Teufel Felix G. , Kjærulff Sonny K. , Wang Zhe , Meng Guangjun , Jessen Carsten , Heljo Petteri , Jiang Qunfeng , Zhao Xin , Wu Bo , Zhou Xueping , Tang Yang , Jeppesen Jacob F. , Kelstrup Christian D. , Buckley Stephen T. , Tullin Søren , Nygaard-Jensen Jan , Chen Xiaoli , Zhang Fang , Olsen Jesper V. , Han Dan , Grønborg Mads , de Lichtenberg Ulrik 
Published: October 2022

AbstractPeptides play important roles in regulating biological processes and form the basis of a multiplicity of therapeutic drugs. To date, only about 300 peptides in human have confirmed bioactivity, although tens of thousands have been reported in the literature. The majority of these are inactive degradation products of endogenous proteins and peptides, presenting a needle-in-a-haystack problem of identifying the most promising candidate peptides from large-scale peptidomics experiments to test for bioactivity. To address this challenge, we conducted a comprehensive analysis of the mammalian peptidome across seven tissues in four different mouse strains and used the data to train a machine learning model that predicts hundreds of peptide candidates based on patterns in the mass spectrometry data. We provide in silico validation examples and experimental confirmation of bioactivity for two peptides, demonstrating the utility of this resource for discovering lead peptides for further characterization and therapeutic development.
Climate-mediated shifts in temperature fluctuations promote extinction risk
Authors: Duffy Kate , Gouhier Tarik C. , Ganguly Auroop R. 
Published: October 2022

AbstractClimate-mediated changes in thermal stress can destabilize animal populations and promote extinction risk. However, risk assessments often focus on changes in mean temperatures and thus ignore the role of temporal variability or structure. Using Earth System Model projections, we show that significant regional differences in the statistical distribution of temperature will emerge over time and give rise to shifts in the mean, variability and persistence of thermal stress. Integrating these trends into mathematical models that simulate the dynamical and cumulative effects of thermal stress on the performance of 38 globally distributed ectotherm species revealed complex regional changes in population stability over the twenty-first century, with temperate species facing higher risk. Yet despite their idiosyncratic effects on stability, projected temperatures universally increased extinction risk. Overall, these results show that the effects of climate change may be more extensive than previously predicted on the basis of the statistical relationship between biological performance and average temperature.