bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Droplet Size Distributions During the Transition of an Ultraclean Stratocumulus Cloud System to Open Cell Structure: An LES Investigation Using Lagrangian Microphysics
Authors: Chandrakar Kamal Kant , Morrison Hugh , Witte Mikael 
Published: September 2022

AbstractA state‐of‐the‐art Lagrangian microphysics scheme is used in a large‐eddy simulation to investigate the stratocumulus transition from closed to open cell structure. Processes controlling precipitation development, which is a key to the transition, are analyzed by leveraging unique benefits of Lagrangian microphysics, particularly the ability to track computational drops in the flow. Sufficient time is needed for coalescence growth of cloud drops to drizzle within the updraft‐downdraft cycle of large eddies. This favors broad drop size distributions (DSDs) and drizzle growth in downdrafts, where drops are typically much older than in updrafts. During the closed cell stage, mean cloud drop radius is too small, and the DSDs are too narrow, so that the timescale for coalescence is much longer than the large eddy turnover time and drizzle growth is limited. The closed‐to‐open cell transition occurs when these timescales become comparable and the precipitation flux increases sharply.
Metabolic flux between organs measured by arteriovenous metabolite gradients
Authors: Bae Hosung , Lam Katie , Jang Cholsoon 
Published: September 2022

AbstractMammalian organs convert dietary nutrients into circulating metabolites and share them to maintain whole-body metabolic homeostasis. While the concentrations of circulating metabolites have been frequently measured in a variety of pathophysiological conditions, the exchange flux of circulating metabolites between organs is not easily measurable due to technical difficulties. Isotope tracing is useful for measuring such fluxes for a metabolite of interest, but the shuffling of isotopic atoms between metabolites requires mathematical modeling. Arteriovenous metabolite gradient measurements can complement isotope tracing to infer organ-specific net fluxes of many metabolites simultaneously. Here, we review the historical development of arteriovenous measurements and discuss their advantages and limitations with key example studies that have revealed metabolite exchange flux between organs in diverse pathophysiological contexts.
Broadband 1-GHz mid-infrared frequency comb
Authors: Hoghooghi Nazanin , Xing Sida , Chang Peter , Lesko Daniel , Lind Alexander , Rieker Greg , Diddams Scott 
Published: September 2022

AbstractMid-infrared (MIR) spectrometers are invaluable tools for molecular fingerprinting and hyper-spectral imaging. Among the available spectroscopic approaches, GHz MIR dual-comb absorption spectrometers have the potential to simultaneously combine the high-speed, high spectral resolution, and broad optical bandwidth needed to accurately study complex, transient events in chemistry, combustion, and microscopy. However, such a spectrometer has not yet been demonstrated due to the lack of GHz MIR frequency combs with broad and full spectral coverage. Here, we introduce the first broadband MIR frequency comb laser platform at 1 GHz repetition rate that achieves spectral coverage from 3 to 13 µm. This frequency comb is based on a commercially available 1.56 µm mode-locked laser, robust all-fiber Er amplifiers and intra-pulse difference frequency generation (IP-DFG) of few-cycle pulses in χ(2) nonlinear crystals. When used in a dual comb spectroscopy (DCS) configuration, this source will simultaneously enable measurements with μs time resolution, 1 GHz (0.03 cm−1) spectral point spacing and a full bandwidth of >5 THz (>166 cm−1) anywhere within the MIR atmospheric windows. This represents a unique spectroscopic resource for characterizing fast and non-repetitive events that are currently inaccessible with other sources.
Photo-induced macro/mesoscopic scale ion displacement in mixed-halide perovskites: ring structures and ionic plasma oscillations
Authors: Sun Xiaoxiao , Zhang Yong , Ge Weikun 
Published: September 2022

AbstractContrary to the common belief that the light-induced halide ion segregation in a mixed halide alloy occurs within the illuminated area, we find that the Br ions released by light are expelled from the illuminated area, which generates a macro/mesoscopic size anion ring surrounding the illuminated area, exhibiting a photoluminescence ring. This intriguing phenomenon can be explained as resulting from two counter-balancing effects: the outward diffusion of the light-induced free Br ions and the Coulombic force between the anion deficit and surplus region. Right after removing the illumination, the macro/mesoscopic scale ion displacement results in a built-in voltage of about 0.4 V between the ring and the center. Then, the displaced anions return to the illuminated area, and the restoring force leads to a damped ultra-low-frequency oscillatory ion motion, with a period of about 20–30 h and lasting over 100 h. This finding may be the first observation of an ionic plasma oscillation in solids. Our understanding and controlling the “ion segregation” demonstrate that it is possible to turn this commonly viewed “adverse phenomenon” into novel electronic applications, such as ionic patterning, self-destructive memory, and energy storage.
Galectin-3 critically mediates the hepatoprotection conferred by M2-like macrophages in ACLF by inhibiting pyroptosis but not necroptosis signalling
Authors: Bai Li , Lu Wang , Tang Shan , Tang Huixin , Xu Manman , Liang Chen , Zheng Sujun , Liu Shuang , Kong Ming , Duan Zhongping , Chen Yu 
Published: September 2022

AbstractWe previously documented that M2-like macrophages exert a hepatoprotective effect in acute-on-chronic liver failure (ACLF) by inhibiting necroptosis signalling. Nevertheless, the molecular mechanism behind this hepatoprotection still needs to be further dissected. Galectin-3 (GAL3) has been reported to be critically involved in the pathogenesis of multiple liver diseases, whereas the potential role of GAL3 in ACLF remains to be explored. Herein, we hypothesised that GAL3 plays a pivotal role in the hepatoprotection conferred by M2-like macrophages in ACLF by inhibiting necroptosis. To test this hypothesis, we first assessed the expression of GAL3 in control and fibrotic mice with or without acute insult. Second, loss- and gain-of-function experiments of GAL3 were performed. Third, the correlation between GAL3 and M2-like macrophage activation was analysed, and the potential role of GAL3 in M2-like macrophage-conferred hepatoprotection was confirmed. Finally, the molecular mechanism underlying GAL3-mediated hepatoprotection was dissected. GAL3 was found to be obviously upregulated in fibrotic mice with or without acute insult but not in acutely injured mice. Depletion of GAL3 aggravated hepatic damage in fibrotic mice upon insult. Conversely, adoptive transfer of GAL3 provided normal mice enhanced resistance against acute insult. The expression of GAL3 is closely correlated with M2-like macrophage activation. Through adoptive transfer and depletion experiments, M2-like macrophages were verified to act as a major source of GAL3. Importantly, GAL3 was confirmed to hold a pivotal place in the hepatoprotection conferred by M2-like macrophages through loss- and gain-of-function experiments. Unexpectedly, the depletion and adoptive transfer of GAL3 resulted in significant differences in the expression levels of pyroptosis but not necroptosis signalling molecules. Taken together, GAL3 plays a pivotal role in the hepatoprotection conferred by M2-like macrophages in ACLF by inhibiting pyroptosis but not necroptosis signalling. Our findings provide novel insights into the pathogenesis and therapy of ACLF.
Circ-TRIO promotes TNBC progression by regulating the miR-432-5p/CCDC58 axis
Authors: Wang Zekun , Li Yaming , Yang Jingwen , Liang Yiran , Wang Xiaolong , Zhang Ning , Kong Xiaoli , Chen Bing , Wang Lijuan , Zhao Wenjing , Yang Qifeng 
Published: September 2022

AbstractNumerous studies have shown that circRNAs are aberrantly expressed in various cancers and play a significant role in tumor progression. However, the molecular mechanisms of circRNAs in triple-negative breast cancer (TNBC) remain ambiguous. By intersecting throughput data and qRT-PCR results from tissues and cell lines, circ-TRIO was identified as a potential oncogenic regulator of TNBC. Moreover, circ-TRIO expression was detected in TNBC tissues and was correlated with the recurrence and prognosis of TNBC patients. The circular characteristics of circ-TRIO were verified by RNase R and CHX assays. Functionally, the knockdown of circ-TRIO inhibited the proliferation, migration and invasion of TNBC cells, while the overexpression of circ-TRIO resulted in the opposite impacts. Mechanistically, a dual luciferase reporter assay and RNA immunoprecipitation were performed and indicated that circ-TRIO could combine with miR-432-5p to regulate the expression of coiled-coil domain containing 58 (CCDC58). In summary, our study illustrates that circ-TRIO plays an important role in the progression of TNBC by regulating the miR-432-5p/CCDC58 axis, which could broaden our insight into the underlying mechanisms and provide a novel prognostic marker of TNBC in the clinic.
Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle
Authors: Keller Philipp , Reiter Michael A. , Kiefer Patrick , Gassler Thomas , Hemmerle Lucas , Christen Philipp , Noor Elad , Vorholt Julia A. 
Published: September 2022

AbstractMethanol is a liquid with high energy storage capacity that holds promise as an alternative substrate to replace sugars in the biotechnology industry. It can be produced from CO2 or methane and its use does not compete with food and animal feed production. However, there are currently only limited biotechnological options for the valorization of methanol, which hinders its widespread adoption. Here, we report the conversion of the industrial platform organism Escherichia coli into a synthetic methylotroph that assimilates methanol via the energy efficient ribulose monophosphate cycle. Methylotrophy is achieved after evolution of a methanol-dependent E. coli strain over 250 generations in continuous chemostat culture. We demonstrate growth on methanol and biomass formation exclusively from the one-carbon source by 13C isotopic tracer analysis. In line with computational modeling, the methylotrophic E. coli strain optimizes methanol oxidation by upregulation of an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway and downregulating tricarboxylic acid cycle enzymes. En route towards sustainable bioproduction processes, our work lays the foundation for the efficient utilization of methanol as the dominant carbon and energy resource.
Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3
Authors: Peters Christine E. , Schulze-Gahmen Ursula , Eckhardt Manon , Jang Gwendolyn M. , Xu Jiewei , Pulido Ernst H. , Bardine Conner , Craik Charles S. , Ott Melanie , Gozani Or , Verba Kliment A. , Hüttenhain Ruth , Carette Jan E. , Krogan Nevan J. 
Published: September 2022

AbstractEnteroviruses cause a number of medically relevant and widespread human diseases with no approved antiviral therapies currently available. Host-directed therapies present an enticing option for this diverse genus of viruses. We have previously identified the actin histidine methyltransferase SETD3 as a critical host factor physically interacting with the viral protease 2A. Here, we report the 3.5 Å cryo-EM structure of SETD3 interacting with coxsackievirus B3 2A at two distinct interfaces, including the substrate-binding surface within the SET domain. Structure-function analysis revealed that mutations of key residues in the SET domain resulted in severely reduced binding to 2A and complete protection from enteroviral infection. Our findings provide insight into the molecular basis of the SETD3-2A interaction and a framework for the rational design of host-directed therapeutics against enteroviruses.
Impact of basic network motifs on the collective response to perturbations
Authors: Bao Xiaoge , Hu Qitong , Ji Peng , Lin Wei , Kurths Jürgen , Nagler Jan 
Published: September 2022

AbstractMany collective phenomena such as epidemic spreading and cascading failures in socioeconomic systems on networks are caused by perturbations of the dynamics. How perturbations propagate through networks, impact and disrupt their functions may depend on the network, the type and location of the perturbation as well as the spreading dynamics. Previous work has analyzed the retardation effects of the nodes along the propagation paths, suggesting a few transient propagation "scaling” regimes as a function of the nodes’ degree, but regardless of motifs such as triangles. Yet, empirical networks consist of motifs enabling the proper functioning of the system. Here, we show that basic motifs along the propagation path jointly determine the previously proposed scaling regimes of distance-limited propagation and degree-limited propagation, or even cease their existence. Our results suggest a radical departure from these scaling regimes and provide a deeper understanding of the interplay of self-dynamics, interaction dynamics, and topological properties.
Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome
Authors: Guillén-García Alejandra , Gibson Savannah E. R. , Jordan Caleb J. C. , Ramaswamy Venkata K. , Linthwaite Victoria L. , Bromley Elizabeth H. C. , Brown Adrian P. , Hodgson David R. W. , Blower Tim R. , Verlet Jan R. R. , Degiacomi Matteo T. , Pålsson Lars-Olof , Cann Martin J. 
Published: September 2022

AbstractLight harvesting is fundamental for production of ATP and reducing equivalents for CO2 fixation during photosynthesis. However, electronic energy transfer (EET) through a photosystem can harm the photosynthetic apparatus when not balanced with CO2. Here, we show that CO2 binding to the light-harvesting complex modulates EET in photosynthetic cyanobacteria. More specifically, CO2 binding to the allophycocyanin alpha subunit of the light-harvesting complex regulates EET and its fluorescence quantum yield in the cyanobacterium Synechocystis sp. PCC 6803. CO2 binding decreases the inter-chromophore distance in the allophycocyanin trimer. The result is enhanced EET in vitro and in live cells. Our work identifies a direct target for CO2 in the cyanobacterial light-harvesting apparatus and provides insights into photosynthesis regulation.
QED radiative corrections for accelerator neutrinos
Authors: Tomalak Oleksandr , Chen Qing , Hill Richard J. , McFarland Kevin S. 
Published: September 2022

AbstractNeutrino oscillation experiments at accelerator energies aim to establish charge-parity violation in the neutrino sector by measuring the energy-dependent rate ofνeappearance andνμdisappearance in aνμbeam. These experiments can precisely measureνμcross sections at near detectors, butνecross sections are poorly constrained and require theoretical inputs. In particular, quantum electrodynamics radiative corrections are different for electrons and muons. These corrections are proportional to the small quantum electrodynamics couplingα ≈ 1/137; however, the large separation of scales between the neutrino energy and the proton mass (~GeV), and the electron mass and soft-photon detection thresholds (~MeV) introduces large logarithms in the perturbative expansion. The resulting flavor differences exceed the percent-level experimental precision and depend on nonperturbative hadronic structure. We establish a factorization theorem for exclusive charged-current (anti)neutrino scattering cross sections representing them as a product of two factors. The first factor is flavor universal; it depends on hadronic and nuclear structure and can be constrained by high-statisticsνμdata. The second factor is non-universal and contains logarithmic enhancements, but can be calculated exactly in perturbation theory. For charged-current elastic scattering, we demonstrate the cancellation of uncertainties in the predicted ratio ofνeandνμcross sections. We point out the potential impact of non-collinear energetic photons and the distortion of the visible lepton spectra, and provide precise predictions for inclusive observables.
PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications
Authors: Korlepara Divya B. , Vasavi C. S. , Jeurkar Shruti , Pal Pradeep Kumar , Roy Subhajit , Mehta Sarvesh , Sharma Shubham , Kumar Vishal , Muvva Charuvaka , Sridharan Bhuvanesh , Garg Akshit , Modee Rohit , Bhati Agastya P. , Nayar Divya , Priyakumar U. Deva 
Published: September 2022

AbstractComputational methods and recently modern machine learning methods have played a key role in structure-based drug design. Though several benchmarking datasets are available for machine learning applications in virtual screening, accurate prediction of binding affinity for a protein-ligand complex remains a major challenge. New datasets that allow for the development of models for predicting binding affinities better than the state-of-the-art scoring functions are important. For the first time, we have developed a dataset, PLAS-5k comprised of 5000 protein-ligand complexes chosen from PDB database. The dataset consists of binding affinities along with energy components like electrostatic, van der Waals, polar and non-polar solvation energy calculated from molecular dynamics simulations using MMPBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. The calculated binding affinities outperformed docking scores and showed a good correlation with the available experimental values. The availability of energy components may enable optimization of desired components during machine learning-based drug design. Further, OnionNet model has been retrained on PLAS-5k dataset and is provided as a baseline for the prediction of binding affinities.
Low-cost yield-driven design of antenna structures using response-variability essential directions and parameter space reduction
Authors: Pietrenko-Dabrowska Anna , Koziel Slawomir , Golunski Lukasz 
Published: September 2022

AbstractQuantifying the effects of fabrication tolerances and uncertainties of other types is fundamental to improve antenna design immunity to limited accuracy of manufacturing procedures and technological spread of material parameters. This is of paramount importance especially for antenna design in the industrial context. Degradation of electrical and field properties due to geometry parameter deviations often manifests itself as, e.g., center frequency shifts or compromised impedance matching. Improving antenna performance at the presence of uncertainties is typically realized through maximization of the fabrication yield. This is normally carried out at the accuracy level of full-wave electromagnetic (EM) analysis, which incurs considerable computational expenses. The involvement of surrogate modeling techniques is the most common approach to alleviating these difficulties, yet conventional modeling methods suffer to a great extent form the curse of dimensionality. This work proposes a technique for low-cost yield optimization of antenna structures. It capitalizes on meticulous definition of the domain of the metamodel constructed for statistical analysis purposes. The domain is spanned by a limited number of essential directions being the most influential in terms of affecting antenna responses in the frequency bands of interest. These directions are determined through an automated decision-making process based on the assessment of the circuit response variability. Our approach permits maintaining small domain volume, which translates into low cost of surrogate model setup, while providing sufficient room for yield improvement. The presented method is validated using three antenna structures and favorably compared to several surrogate-assisted benchmark methods. EM-driven Monte Carlo simulation is also conducted to verify reliability of the yield optimization process.
Predicting Grade group 2 or higher cancer at prostate biopsy by 4Kscore in blood and uCaP microRNA model in urine
Authors: Fredsøe Jacob , Rasmussen Martin , Tin Amy L. , Vickers Andrew J. , Borre Michael , Sørensen Karina D. , Lilja Hans 
Published: September 2022

AbstractElevated prostate-specific antigen (PSA) levels often lead to unnecessary and possibly harmful transrectal ultrasound guided biopsy, e.g. when the biopsy is negative or contains only low-grade insignificant cancer, unlikely to become symptomatic in the man’s normal lifespan. A model based on four-kallikrein markers in blood (commercialized as 4Kscore) predicts risk of Grade group 2 or higher prostate cancer at biopsy, reducing unnecessary biopsies. We assessed whether these results extend to a single institution prostate biopsy cohort of Danish men and are enhanced by three microRNAs from urine (referred to as uCaP). The 4Kscore measured in cryopreserved blood from 234 men referred for 10+ core biopsy to Aarhus University Hospital, 29 with PSA > 25 ng/ml. We explored uCaP in urine from 157 of these men. Combined with age and DRE findings, both 4Kscore and uCaP could accurately predict Grade group 2 or higher prostate cancer (all patients: AUC = 0.802 and 0.797; PSA ≤ 25: AUC = 0.763 and 0.759). There was no additive effect when combining the 4Kscore and uCaP. Limitations include a study cohort with higher risk than commonly reported for biopsy cohorts. Our findings further support the clinical use of the 4Kscore to predict Grade group 2 or higher cancers in men being considered for biopsy.
People with chronic low back pain display spatial alterations in high-density surface EMG-torque oscillations
Authors: Arvanitidis Michail , Jiménez-Grande David , Haouidji-Javaux Nadège , Falla Deborah , Martinez-Valdes Eduardo 
Published: September 2022

AbstractWe quantified the relationship between spatial oscillations in surface electromyographic (sEMG) activity and trunk-extension torque in individuals with and without chronic low back pain (CLBP), during two submaximal isometric lumbar extension tasks at 20% and 50% of their maximal voluntary torque. High-density sEMG (HDsEMG) signals were recorded from the lumbar erector spinae (ES) with a 64-electrode grid, and torque signals were recorded with an isokinetic dynamometer. Coherence and cross-correlation analyses were applied between the filtered interference HDsEMG and torque signals for each submaximal contraction. Principal component analysis was used to reduce dimensionality of HDsEMG data and improve the HDsEMG-based torque estimation. sEMG-torque coherence was quantified in the δ(0–5 Hz) frequency bandwidth. Regional differences in sEMG-torque coherence were also evaluated by creating topographical coherence maps. sEMG-torque coherence in the δ band and sEMG-torque cross-correlation increased with the increase in torque in the controls but not in the CLBP group (p = 0.018, p = 0.030 respectively). As torque increased, the CLBP group increased sEMG-torque coherence in more cranial ES regions, while the opposite was observed for the controls (p = 0.043). Individuals with CLBP show reductions in sEMG-torque relationships possibly due to the use of compensatory strategies and regional adjustments of ES-sEMG oscillatory activity.