bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of interparticle cohesion on rebounding slow impacts on rubble pile asteroids
Authors: Joeris Kolja , Schönau Laurent , Keulen Matthias , Born Philip , Kollmer Jonathan E. 
Published: August 2022

AbstractThe ballistic sorting effect has been proposed to be a driver behind the observed size sorting on the rubble pile asteroid Itokawa. This effect depends on the inelasticity of slow collisions with granular materials. The inelasticity of a collision with a granular material, in turn, depends on grain size. Here we argue that determining the inelasticity of such collisions in an asteroid-like environment is a nontrivial task. We show non-monotonic dependency of the coefficient of restitution (COR) on target particle size using experiments in microgravity. Employing numerical simulations, we explain these results with the growing influence of adhesion for smaller-sized particles. We conclude that there exists an optimum impactor to target particle size ratio for ballistic sorting.
Combined functional and structural imaging of brain white matter reveals stage-dependent impairment in multiple system atrophy of cerebellar type
Authors: Lin Hua , Lin Li , Xu Lyuan , Li Siran , Song Penghui , Li Muwei 
Published: August 2022

AbstractAdvances in fMRI of brain white matter (WM) have established the feasibility of understanding how functional signals of WM evolve with brain diseases. By combining functional signals with structural features of WM, the current study characterizes functional and structural impairments of WM in cerebelar type multiple system atrophy, with the goal to derive new mechanistic insights into the pathological progression of this disease. Our analysis of 30 well-diagnosed patients revealed pronounced decreases in functional connectivity in WM bundles of the cerebellum and brainstem, and concomitant local structural alterations that depended on the disease stage. The novel findings implicate a critical time point in the pathological evolution of the disease, which could guide optimal therapeutic interventions. Furthermore, fMRI signals of impaired WM bundles exhibited superior sensitivity in differentiating initial disease development, which demonstrates great potential of using these signals to inform disease management.
Observation of Rabi dynamics with a short-wavelength free-electron laser
Authors: Nandi Saikat , Olofsson Edvin , Bertolino Mattias , Carlström Stefanos , Zapata Felipe , Busto David , Callegari Carlo , Di Fraia Michele , Eng-Johnsson Per , Feifel Raimund , Gallician Guillaume , Gisselbrecht Mathieu , Maclot Sylvain , Neoričić Lana , Peschel Jasper , Plekan Oksana , Prince Kevin C. , Squibb Richard J. , Zhong Shiyang , Demekhin Philipp V. , Meyer Michael , Miron Catalin , Badano Laura , Danailov Miltcho B. , Giannessi Luca , Manfredda Michele , Sottocorona Filippo , Zangrando Marco , Dahlström Jan Marcus 
Published: August 2022

AbstractRabi oscillations are periodic modulations of populations in two-level systems interacting with a time-varying field1. They are ubiquitous in physics with applications in different areas such as photonics2, nano-electronics3, electron microscopy4 and quantum information5. While the theory developed by Rabi was intended for fermions in gyrating magnetic fields, Autler and Townes realized that it could also be used to describe coherent light–matter interactions within the rotating-wave approximation6. Although intense nanometre-wavelength light sources have been available for more than a decade7–9, Rabi dynamics at such short wavelengths has not been directly observed. Here we show that femtosecond extreme-ultraviolet pulses from a seeded free-electron laser10 can drive Rabi dynamics between the ground state and an excited state in helium atoms. The measured photoelectron signal reveals an Autler–Townes doublet and an avoided crossing, phenomena that are both fundamental to coherent atom–field interactions11. Using an analytical model derived from perturbation theory on top of the Rabi model, we find that the ultrafast build-up of the doublet structure carries the signature of a quantum interference effect between resonant and non-resonant photoionization pathways. Given the recent availability of intense attosecond12 and few-femtosecond13 extreme-ultraviolet pulses, our results unfold opportunities to carry out ultrafast manipulation of coherent processes at short wavelengths using free-electron lasers.
A compute-in-memory chip based on resistive random-access memory
Authors: Wan Weier , Kubendran Rajkumar , Schaefer Clemens , Eryilmaz Sukru Burc , Zhang Wenqiang , Wu Dabin , Deiss Stephen , Raina Priyanka , Qian He , Gao Bin , Joshi Siddharth , Wu Huaqiang , Wong H.-S. Philip , Cauwenberghs Gert 
Published: August 2022

AbstractRealizing increasingly complex artificial intelligence (AI) functionalities directly on edge devices calls for unprecedented energy efficiency of edge hardware. Compute-in-memory (CIM) based on resistive random-access memory (RRAM)1promises to meet such demand by storing AI model weights in dense, analogue and non-volatile RRAM devices, and by performing AI computation directly within RRAM, thus eliminating power-hungry data movement between separate compute and memory2–5. Although recent studies have demonstrated in-memory matrix-vector multiplication on fully integrated RRAM-CIM hardware6–17, it remains a goal for a RRAM-CIM chip to simultaneously deliver high energy efficiency, versatility to support diverse models and software-comparable accuracy. Although efficiency, versatility and accuracy are all indispensable for broad adoption of the technology, the inter-related trade-offs among them cannot be addressed by isolated improvements on any single abstraction level of the design. Here, by co-optimizing across all hierarchies of the design from algorithms and architecture to circuits and devices, we present NeuRRAM—a RRAM-based CIM chip that simultaneously delivers versatility in reconfiguring CIM cores for diverse model architectures, energy efficiency that is two-times better than previous state-of-the-art RRAM-CIM chips across various computational bit-precisions, and inference accuracy comparable to software models quantized to four-bit weights across various AI tasks, including accuracy of 99.0 percent on MNIST18and 85.7 percent on CIFAR-1019image classification, 84.7-percent accuracy on Google speech command recognition20, and a 70-percent reduction in image-reconstruction error on a Bayesian image-recovery task.
Evidence for intrinsic charm quarks in the proton
Authors:   The NNPDF Collaboration, Ball Richard D. , Candido Alessandro , Cruz-Martinez Juan , Forte Stefano , Giani Tommaso , Hekhorn Felix , Kudashkin Kirill , Magni Giacomo , Rojo Juan 
Published: August 2022

AbstractThe theory of the strong force, quantum chromodynamics, describes the proton in terms of quarks and gluons. The proton is a state of two up quarks and one down quark bound by gluons, but quantum theory predicts that in addition there is an infinite number of quark–antiquark pairs. Both light and heavy quarks, whose mass is respectively smaller or bigger than the mass of the proton, are revealed inside the proton in high-energy collisions. However, it is unclear whether heavy quarks also exist as a part of the proton wavefunction, which is determined by non-perturbative dynamics and accordingly unknown: so-called intrinsic heavy quarks1. It has been argued for a long time that the proton could have a sizable intrinsic component of the lightest heavy quark, the charm quark. Innumerable efforts to establish intrinsic charm in the proton2 have remained inconclusive. Here we provide evidence for intrinsic charm by exploiting a high-precision determination of the quark–gluon content of the nucleon3 based on machine learning and a large experimental dataset. We disentangle the intrinsic charm component from charm–anticharm pairs arising from high-energy radiation4. We establish the existence of intrinsic charm at the 3-standard-deviation level, with a momentum distribution in remarkable agreement with model predictions1,5.We confirm these findings by comparing them to very recent data on Z-boson production with charm jets from the Large Hadron Collider beauty (LHCb) experiment6.
Ordered and deterministic cancer genome evolution after p53 loss
Authors: Baslan Timour , Morris John P. , Zhao Zhen , Reyes Jose , Ho Yu-Jui , Tsanov Kaloyan M. , Bermeo Jonathan , Tian Sha , Zhang Sean , Askan Gokce , Yavas Aslihan , Lecomte Nicolas , Erakky Amanda , Varghese Anna M. , Zhang Amy , Kendall Jude , Ghiban Elena , Chorbadjiev Lubomir , Wu Jie , Dimitrova Nevenka , Chadalavada Kalyani , Nanjangud Gouri J. , Bandlamudi Chaitanya , Gong Yixiao , Donoghue Mark T. A. , Socci Nicholas D. , Krasnitz Alex , Notta Faiyaz , Leach Steve D. , Iacobuzio-Donahue Christine A. , Lowe Scott W. 
Published: August 2022

AbstractAlthough p53 inactivation promotes genomic instability1 and presents a route to malignancy for more than half of all human cancers2,3, the patterns through which heterogenous TP53 (encoding human p53) mutant genomes emerge and influence tumorigenesis remain poorly understood. Here, in a mouse model of pancreatic ductal adenocarcinoma that reports sporadic p53 loss of heterozygosity before cancer onset, we find that malignant properties enabled by p53 inactivation are acquired through a predictable pattern of genome evolution. Single-cell sequencing and in situ genotyping of cells from the point of p53 inactivation through progression to frank cancer reveal that this deterministic behaviour involves four sequential phases—Trp53 (encoding mouse p53) loss of heterozygosity, accumulation of deletions, genome doubling, and the emergence of gains and amplifications—each associated with specific histological stages across the premalignant and malignant spectrum. Despite rampant heterogeneity, the deletion events that follow p53 inactivation target functionally relevant pathways that can shape genomic evolution and remain fixed as homogenous events in diverse malignant populations. Thus, loss of p53—the ‘guardian of the genome’—is not merely a gateway to genetic chaos but, rather, can enable deterministic patterns of genome evolution that may point to new strategies for the treatment of TP53-mutant tumours.
A condensate dynamic instability orchestrates actomyosin cortex activation
Authors: Yan Victoria Tianjing , Narayanan Arjun , Wiegand Tina , Jülicher Frank , Grill Stephan W. 
Published: August 2022

AbstractA key event at the onset of development is the activation of a contractile actomyosin cortex during the oocyte-to-embryo transition1–3. Here we report on the discovery that, in Caenorhabditis elegans oocytes, actomyosin cortex activation is supported by the emergence of thousands of short-lived protein condensates rich in F-actin, N-WASP and the ARP2/3 complex4–8 that form an active micro-emulsion. A phase portrait analysis of the dynamics of individual cortical condensates reveals that condensates initially grow and then transition to disassembly before dissolving completely. We find that, in contrast to condensate growth through diffusion9, the growth dynamics of cortical condensates are chemically driven. Notably, the associated chemical reactions obey mass action kinetics that govern both composition and size. We suggest that the resultant condensate dynamic instability10 suppresses coarsening of the active micro-emulsion11, ensures reaction kinetics that are independent of condensate size and prevents runaway F-actin nucleation during the formation of the first cortical actin meshwork.
In vivo single-molecule analysis reveals COOLAIR RNA structural diversity
Authors: Yang Minglei , Zhu Pan , Cheema Jitender , Bloomer Rebecca , Mikulski Pawel , Liu Qi , Zhang Yueying , Dean Caroline , Ding Yiliang 
Published: August 2022

AbstractCellular RNAs are heterogeneous with respect to their alternative processing and secondary structures, but the functional importance of this complexity is still poorly understood. A set of alternatively processed antisense non-coding transcripts, which are collectively called COOLAIR, are generated at the Arabidopsis floral-repressor locus FLOWERING LOCUS C (FLC)1. Different isoforms of COOLAIR influence FLC transcriptional output in warm and cold conditions2–7. Here, to further investigate the function of COOLAIR, we developed an RNA structure-profiling method to determine the in vivo structure of single RNA molecules rather than the RNA population average. This revealed that individual isoforms of the COOLAIR transcript adopt multiple structures with different conformational dynamics. The major distally polyadenylated COOLAIR isoform in warm conditions adopts three predominant structural conformations, the proportions and conformations of which change after cold exposure. An alternatively spliced, strongly cold-upregulated distal COOLAIR isoform6 shows high structural diversity, in contrast to proximally polyadenylated COOLAIR. A hyper-variable COOLAIR structural element was identified that was complementary to the FLC transcription start site. Mutations altering the structure of this region changed FLC expression and flowering time, consistent with an important regulatory role of the COOLAIR structure in FLC transcription. Our work demonstrates that isoforms of non-coding RNA transcripts adopt multiple distinct and functionally relevant structural conformations, which change in abundance and shape in response to external conditions.
Differential gene expression in iPSC-derived human intestinal epithelial cell layers following exposure to two concentrations of butyrate, propionate and acetate
Authors: Grouls Menno , Janssen Aafke W. F. , Duivenvoorde Loes P. M. , Hooiveld Guido J. E. J. , Bouwmeester Hans , van der Zande Meike 
Published: August 2022

AbstractIntestinal epithelial cells and the intestinal microbiota are in a mutualistic relationship that is dependent on communication. This communication is multifaceted, but one aspect is communication through compounds produced by the microbiota such as the short-chain fatty acids (SCFAs) butyrate, propionate and acetate. Studying the effects of SCFAs and especially butyrate in intestinal epithelial cell lines like Caco-2 cells has been proven problematic. In contrast to the in vivo intestinal epithelium, Caco-2 cells do not use butyrate as an energy source, leading to a build-up of butyrate. Therefore, we used human induced pluripotent stem cell derived intestinal epithelial cells, grown as a cell layer, to study the effects of butyrate, propionate and acetate on whole genome gene expression in the cells. For this, cells were exposed to concentrations of 1 and 10 mM of the individual short-chain fatty acids for 24 h. Unique gene expression profiles were observed for each of the SCFAs in a concentration-dependent manner. Evaluation on both an individual gene level and pathway level showed that butyrate induced the biggest effects followed by propionate and then acetate. Several known effects of SCFAs on intestinal cells were confirmed, such as effects on metabolism and immune responses. The changes in metabolic pathways in the intestinal epithelial cell layers in this study demonstrate that there is a switch in energy homeostasis, this is likely associated with the use of SCFAs as an energy source by the induced pluripotent stem cell derived intestinal epithelial cells similar to in vivo intestinal tissues where butyrate is an important energy source.
Ultrasound-guided femoral approach for coronary angiography and interventions in the porcine model
Authors: Tsigkas Grigorios , Vasilagkos Georgios , Tousis Alexandros , Theofanis Michail , Apostolos Anastasios , Spyridonidis Ioannis , Goudas Leonidas , Karpetas Georgios , Moulias Athanasios , Katsouras Christos S. , Kitrou Panagiotis , Mplani Virginia , Moulas Anargyros N. , Karnabatidis Dimitrios , Davlouros Periklis 
Published: August 2022

AbstractCoronary angiography and percutaneous coronary intervention (PCI) procedural details in swine are similar to those performed to humans, since their heart and coronary anatomy closely resembles. However, only a few detailed descriptions of the procedure are available, containing notable differences. We present a feasible and reproducible protocol for percutaneous coronary interventions in porcine experimental models, utilizing ultrasound-guided femoral approach. Nine female pigs were studied to explore the feasibility of superficial femoral arterial (SFA) access for coronary angiography and provisional PCI, as well as the most suitable guiding coronary catheters and angiographic projections for the above interventions. Experiments were performed under general anesthesia, using ultrasound-guided puncture of the SFA to gain arterial access. The Amplatzer AR1® catheter, and the Right Coronary Bypass® catheter were used for the selective engagement of the right and the left coronary artery, respectively. Successful arterial access and subsequent cardiac catheterization were performed in all pigs. Only one animal required a second puncture for femoral artery access. None of the 9 animals presented any significant tachycardia or hypotensive episode. One animal developed an access site-related complication following the first catheterization procedure. During follow-up, 100% success of SFA catheterization was achieved using the same ultrasound-guided technique. The ultrasound-guided superficial femoral artery access for coronary angiography and provisional interventions in porcine models is a quick and safe alternative to the carotid artery approach. The RCB and AR1 catheters may be the best choice for the quick and easy selective coronary engagement of the right and left ostia, respectively.
Use of InSAR data for measuring land subsidence induced by groundwater withdrawal and climate change in Ardabil Plain, Iran
Authors: Ghorbani Zahra , Khosravi Ali , Maghsoudi Yasser , Mojtahedi Farid Fazel , Javadnia Eslam , Nazari Ali 
Published: August 2022

AbstractThe Ardabil plain, with an approximate area of 1097.2 km2in northwestern Iran, has experienced land subsidence due to intensive groundwater withdrawal and long seasons of drought in recent years. Different techniques have been used to investigate and evaluate subsidence in this region including: Global Positioning Systems (GPS), Levelling, and Geotechnical methods. These methods are typically expensive, time-consuming, and identify only a small fraction of the areas prone to subsidence. This study employs an Interferometric Synthetic Aperture Radar (InSAR) technique to measure the long-term subsidence of the plain. An open-source SAR interferometry time series analysis package, LiCSBAS, that integrates with the automated Sentinel-1 InSAR processor (COMET-LiCSAR) is used to analyze Sentinel-1 satellite images from October 2014 to January 2021. Processing of Sentinel-1 images shows that the Ardabil plain has been facing rapid subsidence due to groundwater pumping and reduced rainfall, especially between May 2018 to January 2019. The maximum subsidence rate was 45 mm/yr, measured at the southeastern part of the plain. While providing significant advantages (less processing time and disk space) over other InSAR processing packages, implementation of the LiCSBAS processing package and its accuracy for land subsidence measurements at different scales needs further evaluation. This study provides a procedure for evaluating its efficiency and accuracy for land subsidence measurements by comparing its measurements with the results of the GMTSAR and geotechnical numerical modeling. The results of geotechnical numerical modeling showed land subsidence with an average annual rate of 38 mm between 2006 and 2020, which was close to measurements using the InSAR technique. Comparison of the subsidence measurements of the Ardabil plain using the LiCSBAS package with results obtained from other techniques shows that LiCSBAS is able to accurately detect land deformation at large scales (~ km). However, they may not be optimized for more local deformations such as infrastructure monitoring.
Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system
Authors: Spangler J. R. , Leski T. A. , Schultzhaus Z. , Wang Z. , Stenger D. A. 
Published: August 2022

AbstractAll CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestislcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.
Wearable adjunct ozone and antibiotic therapy system for treatment of Gram-negative dermal bacterial infection
Authors: Roth Alexander , Maruthamuthu Murali Kannan , Nejati Sina , Krishnakumar Akshay , Selvamani Vidhya , Sedaghat Sotoudeh , Nguyen Juliane , Seleem Mohamed N. , Rahimi Rahim 
Published: August 2022

AbstractThe problematic combination of a rising prevalence of skin and soft tissue infections and the growing rate of life-threatening antibiotic resistant infections presents an urgent, unmet need for the healthcare industry. These evolutionary resistances originate from mutations in the bacterial cell walls which prevent effective diffusion of antibiotics. Gram-negative bacteria are of special consideration due to the natural resistance to many common antibiotics due to the unique bilayer structure of the cell wall. The system developed here provides one solution to this problem through a wearable therapy that delivers and utilizes gaseous ozone as an adjunct therapy with topical antibiotics through a novel dressing with drug-eluting nanofibers (NFs). This technology drastically increases the sensitivity of Gram-negative bacteria to common antibiotics by using oxidative ozone to bypass resistances created by the bacterial cell wall. To enable simple and effective application of adjunct therapy, ozone delivery and topical antibiotics have been integrated into a single application patch. The drug delivery NFs are generated via electrospinning in a fast-dissolve PVA mat without inducing decreasing gas permeability of the dressing. A systematic study found ozone generation at 4 mg/h provided optimal ozone levels for high antimicrobial performance with minimal cytotoxicity. This ozone treatment was used with adjunct therapy delivered by the system in vitro. Results showed complete eradication of Gram-negative bacteria with ozone and antibiotics typically used only for Gram-positive bacteria, which showed the strength of ozone as an enabling adjunct treatment option to sensitize bacteria strains to otherwise ineffective antibiotics. Furthermore, the treatment is shown through biocompatibility testing to exhibit no cytotoxic effect on human fibroblast cells.