bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverse centrifugal effect induced by collective motion of vortices in rotating thermal convection
Authors: Ding Shan-Shan , Chong Kai Leong , Shi Jun-Qiang , Ding Guang-Yu , Lu Hao-Yuan , Xia Ke-Qing , Zhong Jin-Qiang 
Published: September 2021

AbstractWhen a fluid system is subject to strong rotation, centrifugal fluid motion is expected, i.e., denser (lighter) fluid moves outward (inward) from (toward) the axis of rotation. Here we demonstrate, both experimentally and numerically, the existence of an unexpected outward motion of warm and lighter vortices in rotating thermal convection. This anomalous vortex motion occurs under rapid rotations when the centrifugal buoyancy is sufficiently strong to induce a symmetry-breaking in the vorticity field, i.e., the vorticity of the cold anticyclones overrides that of the warm cyclones. We show that through hydrodynamic interactions the densely distributed vortices can self-aggregate into coherent clusters and exhibit collective motion in this flow regime. Interestingly, the correlation of the vortex velocity fluctuations within a cluster is scale-free, with the correlation length being proportional ( ≈ 30%) to the cluster length. Such long-range correlation leads to the counterintuitive collective outward motion of warm vortices. Our study brings insights into the vortex dynamics that are widely present in nature.
Targeting the actin nucleation promoting factor WASp provides a therapeutic approach for hematopoietic malignancies
Authors: Biber Guy , Ben-Shmuel Aviad , Noy Elad , Joseph Noah , Puthenveetil Abhishek , Reiss Neria , Levy Omer , Lazar Itay , Feiglin Ariel , Ofran Yanay , Kedmi Meirav , Avigdor Abraham , Fried Sophia , Barda-Saad Mira 
Published: September 2021

AbstractCancer cells depend on actin cytoskeleton rearrangement to carry out hallmark malignant functions including activation, proliferation, migration and invasiveness. Wiskott–Aldrich Syndrome protein (WASp) is an actin nucleation-promoting factor and is a key regulator of actin polymerization in hematopoietic cells. The involvement of WASp in malignancies is incompletely understood. Since WASp is exclusively expressed in hematopoietic cells, we performedin silicoscreening to identify small molecule compounds (SMCs) that bind WASp and promote its degradation. We describe here one such identified molecule; this WASp-targeting SMC inhibits key WASp-dependent actin processes in several types of hematopoietic malignancies in vitro and in vivo without affecting naïve healthy cells. This small molecule demonstrates limited toxicity and immunogenic effects, and thus, might serve as an effective strategy to treat specific hematopoietic malignancies in a safe and precisely targeted manner.
Coevolutionary methods enable robust design of modular repressors by reestablishing intra-protein interactions
Authors: Jiang Xian-Li , Dimas Rey P. , Chan Clement T. Y. , Morcos Faruck 
Published: September 2021

AbstractGenetic sensors with unique combinations of DNA recognition and allosteric response can be created by hybridizing DNA-binding modules (DBMs) and ligand-binding modules (LBMs) from distinct transcriptional repressors. This module swapping approach is limited by incompatibility between DBMs and LBMs from different proteins, due to the loss of critical module-module interactions after hybridization. We determine a design strategy for restoring key interactions between DBMs and LBMs by using a computational model informed by coevolutionary traits in the LacI family. This model predicts the influence of proposed mutations on protein structure and function, quantifying the feasibility of each mutation for rescuing hybrid repressors. We accurately predict which hybrid repressors can be rescued by mutating residues to reinstall relevant module-module interactions. Experimental results confirm that dynamic ranges of gene expression induction were improved significantly in these mutants. This approach enhances the molecular and mechanistic understanding of LacI family proteins, and advances the ability to design modular genetic parts.
Intracavity incoherent supercontinuum dynamics and rogue waves in a broadband dissipative soliton laser
Authors: Meng Fanchao , Lapre Coraline , Billet Cyril , Sylvestre Thibaut , Merolla Jean-Marc , Finot Christophe , Turitsyn Sergei K. , Genty Goëry , Dudley John M. 
Published: September 2021

AbstractUnderstanding dynamical complexity is one of the most important challenges in science. Significant progress has recently been made in optics through the study of dissipative soliton laser systems, where dynamics are governed by a complex balance between nonlinearity, dispersion, and energy exchange. A particularly complex regime of such systems is associated with noise-like pulse multiscale instabilities, where sub-picosecond pulses with random characteristics evolve chaotically underneath a much longer envelope. However, although observed for decades in experiments, the physics of this regime remains poorly understood, especially for highly-nonlinear cavities generating broadband spectra. Here, we address this question directly with a combined numerical and experimental study that reveals the physical origin of instability as nonlinear soliton dynamics and supercontinuum turbulence. Real-time characterisation reveals intracavity extreme events satisfying statistical rogue wave criteria, and both real-time and time-averaged measurements are in quantitative agreement with modelling.
Identification of lead vacancy defects in lead halide perovskites
Authors: Keeble David J. , Wiktor Julia , Pathak Sandeep K. , Phillips Laurie J. , Dickmann Marcel , Durose Ken , Snaith Henry J. , Egger Werner 
Published: September 2021

AbstractPerovskite photovoltaics advance rapidly, but questions remain regarding point defects: while experiments have detected the presence of electrically active defects no experimentally confirmed microscopic identifications have been reported. Here we identify lead monovacancy (VPb) defects in MAPbI3 (MA = CH3NH3+) using positron annihilation lifetime spectroscopy with the aid of density functional theory. Experiments on thin film and single crystal samples all exhibited dominant positron trapping to lead vacancy defects, and a minimum defect density of ~3 × 1015 cm−3 was determined. There was also evidence of trapping at the vacancy complex $$({{{{{\rm{V}}}}}}_{{{{{\rm{Pb}}}}}}{{{{{\rm{V}}}}}}_{{{{{\rm{I}}}}}})^{-}$$

(

V

Pb

V

I

)

−

in a minority of samples, but no trapping to MA-ion vacancies was observed. Our experimental results support the predictions of other first-principles studies that deep level, hole trapping, $${{{{{{\rm{V}}}}}}}_{{{{{{\rm{Pb}}}}}}}^{2-}$$

V

Pb

2
−

, point defects are one of the most stable defects in MAPbI3. This direct detection and identification of a deep level native defect in a halide perovskite, at technologically relevant concentrations, will enable further investigation of defect driven mechanisms.
Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
Authors: Peters Kristian , Herman Stephanie , Khoonsari Payam Emami , Burman Joachim , Neumann Steffen , Kultima Kim 
Published: September 2021

AbstractChronic diseases affecting the central nervous system (CNS) like Alzheimer’s or Parkinson’s disease typically develop with advanced chronological age. Yet, aging at the metabolic level has been explored only sporadically in humans using biofluids in close proximity to the CNS such as the cerebrospinal fluid (CSF). We have used an untargeted liquid chromatography high-resolution mass spectrometry (LC-HRMS) based metabolomics approach to measure the levels of metabolites in the CSF of non-neurological control subjects in the age of 20 up to 74. Using a random forest-based feature selection strategy, we extracted 69 features that were strongly related to age (page < 0.001, rage = 0.762, R2Boruta age = 0.764). Combining an in-house library of known substances with in silico chemical classification and functional semantic annotation we successfully assigned putative annotations to 59 out of the 69 CSF metabolites. We found alterations in metabolites related to the Cytochrome P450 system, perturbations in the tryptophan and kynurenine pathways, metabolites associated with cellular energy (NAD+, ADP), mitochondrial and ribosomal metabolisms, neurological dysfunction, and an increase of adverse microbial metabolites. Taken together our results point at a key role for metabolites found in CSF related to the Cytochrome P450 system as most often associated with metabolic aging.
Robust neuronal differentiation of human iPSC-derived neural progenitor cells cultured on densely-spaced spiky silicon nanowire arrays
Authors: Harberts Jann , Siegmund Malte , Schnelle Matteo , Zhang Ting , Lei Yakui , Yu Linwei , Zierold Robert , Blick Robert H. 
Published: September 2021

AbstractNanostructured cell culture substrates featuring nanowire (NW) arrays have been applied to a variety of basic cell lines and rodent neurons to investigate cellular behavior or to stimulate cell responses. However, patient-derived human neurons—a prerequisite for studying e.g. neurodegenerative diseases efficiently—are rarely employed due to sensitive cell culture protocols and usually long culturing periods. Here, we present human patient induced pluripotent stem cell-derived neurons cultured on densely-spaced spiky silicon NW arrays (600 NWs/ 100 µm$$^2$$

2

with NW lengths of 1 µm) which show mature electrophysiological characteristics after only 20 days of culturing. Exemplary neuronal growth and network formation on the NW arrays are demonstrated using scanning electron microscopy and immunofluorescence microscopy. The cells and neurites rest in a fakir-like settling state on the NWs only in contact with the very NW tips shown by cross-sectional imaging of the cell/NW interface using focused ion beam milling and confocal laser scanning microscopy. Furthermore, the NW arrays promote the cell culture by slightly increasing the share of differentiated neurons determined by the quantification of immunofluorescence microscopy images. The electrophysiological functionality of the neurons is confirmed with patch-clamp recordings showing the excellent capability to fire action potentials. We believe that the short culturing time to obtain functional human neurons generated from patient-derived neural progenitor cells and the robustness of this differentiation protocol to produce these neurons on densely-spaced spiky nanowire arrays open up new pathways for stem cell characterization and neurodegenerative disease studies.
Deep mutational scanning of the plasminogen activator inhibitor-1 functional landscape
Authors: Huttinger Zachary M. , Haynes Laura M. , Yee Andrew , Kretz Colin A. , Holding Matthew L. , Siemieniak David R. , Lawrence Daniel A. , Ginsburg David 
Published: September 2021

AbstractThe serine protease inhibitor (SERPIN) plasminogen activator inhibitor-1 (PAI-1) is a key regulator of the fibrinolytic system, inhibiting the serine proteases tissue- and urokinase-type plasminogen activator (tPA and uPA, respectively). Missense variants render PAI-1 non-functional through misfolding, leading to its turnover as a protease substrate, or to a more rapid transition to the latent/inactive state. Deep mutational scanning was performed to evaluate the impact of amino acid sequence variation on PAI-1 inhibition of uPA using an M13 filamentous phage display system. Error prone PCR was used to construct a mutagenized PAI-1 library encompassing ~ 70% of potential single amino acid substitutions. The relative effects of 27% of all possible missense variants on PAI-1 inhibition of uPA were determined using high-throughput DNA sequencing. 826 missense variants demonstrated conserved inhibitory activity while 1137 resulted in loss of PAI-1 inhibitory function. The least evolutionarily conserved regions of PAI-1 were also identified as being the most tolerant of missense mutations. The results of this screen confirm previous low-throughput mutational studies, including those of the reactive center loop. These data provide a powerful resource for explaining structure–function relationships for PAI-1 and for the interpretation of human genomic sequence variants.
Temporal lobe activation during episodic memory encoding following traumatic brain injury
Authors: Taing Abbie S. , Mundy Matthew E. , Ponsford Jennie L. , Spitz Gershon 
Published: September 2021

AbstractThe temporal lobes are critical for encoding and retrieving episodic memories. The temporal lobes are preferentially disrupted following a traumatic brain injury (TBI), likely contributing to the difficulties observed in episodic memory. However, the underlying neural changes that precipitate or maintain these difficulties in individuals with TBI remains poorly understood. Here, we use functional magnetic resonance imaging (fMRI) to interrogate the relationship between temporal lobe activation and encoding of episodic stimuli. Participants encoded face, scene, and animal stimuli during an fMRI run. In an out-of-scanner task, participants were required to correctly identify previously displayed stimuli over two presentation runs (each in-scanner stimuli presented twice). Forty-three patients with moderate-severe TBI were recruited and compared with 38 demographically similar healthy controls. The pattern of behavioural performance between groups depended on the stimuli presentation run. The TBI group demonstrated poorer episodic memory for faces and scenes during the first presentation, but not the second presentation. When episodic memory was analysed across all presentation runs, behavioural deficits were only apparent for faces. Interestingly, processing of faces emerged as the only between group-difference on fMRI, whereby TBI participants had an increased signal in the middle temporal gyrus extending to the superior temporal sulcus. These findings provide evidence to suggest that following TBI: (a) episodic memory is preferentially impaired for complex stimuli such as faces, and (b) robust behavioural inefficiencies are reflected in increased activation in specific temporal lobe structures during encoding.
A comparative biomechanical study of the Distal Tibia Nail against compression plating for the osteosynthesis of supramalleolar corrective osteotomies
Authors: Greenfield Julia , Appelmann Philipp , Lafon Yoann , Bruyère-Garnier Karine , Rommens Pol Maria , Kuhn Sebastian 
Published: September 2021

AbstractThe Distal Tibia Nail (DTN; Mizuho, Japan) has demonstrated higher biomechanical stiffness to locking plates in previous research for A3 distal tibia fractures. It is here investigated as a fixation option for supramalleolar corrective osteotomies (SMOT). Sixteen Sawbones tibiae were implanted with either a DTN (n = 8) or Medial Distal Tibia Plate (MDTP; n = 8) and a SMOT simulated. Two surgical outcome scenarios were envisaged: “best-case” representing an intact lateral cortex, and “worst-case” representing a fractured lateral cortex. All samples were subjected to compressive (350 N, 700 N) and torsional (± 4 Nm, ± 8 Nm) testing. Samples were evaluated using calculated construct stiffness from force–displacement data, interfragmentary movement and Von Mises’ strain distribution. The DTN demonstrated a greater compressive stiffness for the best-case surgical scenario, whereas the MDTP showed higher stiffness (p < 0.05) for the worst-case surgical scenario. In torsional testing, the DTN proved more resistant to torsion in the worst-case surgical setup (p < 0.05) for both ± 4 Nm and ± 8 Nm. The equivalent stiffness of the DTN against the MDTP supports the use of this implant for SMOT fixation and should be considered as a treatment option particularly in patients presenting vascularisation problems where the MDTP is an inappropriate choice.
Application of water based drilling clay-nanoparticles in heat transfer of fractional Maxwell fluid over an infinite flat surface
Authors: Asjad Muhammad Imran , Ali Rizwan , Iqbal Azhar , Muhammad Taseer , Chu Yu-Ming 
Published: September 2021

AbstractIn the present paper, unsteady free convection flow of Maxwell fluid containing clay-nanoparticles is investigated. These particles are hanging in water, engine oil and kerosene. The values for nanofluids based on the Maxwell-Garnett and Brinkman models for effective thermal conductivity and viscosity are calculated numerically. The integer order governing equations are being extended to the novel non-integer order fractional derivative. Analytical solutions of temperature and velocity for Maxwell fluid are build using Laplace transform technique and expressed in such a way that they clearly satisfied the boundary conditions. To see the impact of different flow parameters on the velocity, we have drawn some graphs. As a result, we have seen that the fractional model is superior in narrate the decay property of field variables. Some limiting solutions are obtained and compared with the latest existing literature. Moreover, significant results can be observed for clay nanoparticles with different base fluids.
Combined agonists act synergistically to increase mucociliary clearance in a cystic fibrosis airway model
Authors: Joo Nam Soo , Cho Hyung-Ju , Shinbashi Meagan , Choi Jae Young , Milla Carlos E. , Engelhardt John F. , Wine Jeffrey J. 
Published: September 2021

AbstractMucus clearance, a primary innate defense mechanism of airways, is defective in patients with cystic fibrosis (CF) and CF animals. In previous work, the combination of a low dose of the cholinergic agonist, carbachol with forskolin or a β adrenergic agonist, isoproterenol synergistically increased mucociliary clearance velocity (MCCV) in ferret tracheas. Importantly, the present study shows that synergistic MCCV can also be produced in CF ferrets, with increases ~ 55% of WT. Synergistic MCCV was also produced in pigs. The combined agonists increased MCCV by increasing surface fluid via multiple mechanisms: increased fluid secretion from submucosal glands, increased anion secretion across surface epithelia and decreased Na+absorption. To avoid bronchoconstriction, the cAMP agonist was applied 30 min before carbachol. This approach to increasing mucus clearance warrants testing for safety and efficacy in humans as a potential therapeutic for muco-obstructive diseases.
Sustainable intensification of maize and wheat cropping system through pulse intercropping
Authors: Tripathi S. C. , Venkatesh Karnam , Meena Raj Pal , Chander Subhash , Singh G. P. 
Published: September 2021

AbstractThe intercropping of legumes with cereals help to achieve sustainable intensification by their mutual complementarity at efficiently using radiation, nutrients, etc. Several studies indicated such beneficial effects on the other component crop however, little research has been conducted to quantify their effects on the subsequent crop in a cropping system. In this study, the effect of the legume intercropping on the entire cropping system, particularly the maize + legume-wheat system was studied. Four legumes intercropped to maize followed by wheat crop were studied for intensification measures such as wheat equivalent yield (WEY), land equivalent ratio (LER), sustainable value index (SVI), and economic returns. N saving effect of legumes on the subsequent wheat crop was quantified with two N levels. Maize + cowpea-wheat combination was the most productive and economic intercrop combination (LER = 1.71, SVI = 0.96) with an increase in net economic return (43.63%) with a B:C ratio of 1.94. An additional 25% N (37.5 kg ha−1) was saved in the wheat crop when the legume intercropping was undertaken with maize. The results suggest that intercropping is the key to diversification and reduces the risk of crop failures by enhancing land-use efficiency, soil fertility, and economic returns under weather vagaries. This will be beneficial to small and marginal farmers of many countries.
Relative density of United States forests has shifted to higher levels over last two decades with important implications for future dynamics
Authors: Woodall C. W. , Weiskittel A. R. 
Published: September 2021

AbstractTree size-density dynamics can inform key trends in forest productivity along with opportunities to increase ecosystem resiliency. Here, we employ a novel approach to estimate the relative density (RD, range 0–1) of any given forest based on its current size-density relationship compared to a hypothetical maximum using the coterminous US national forest inventory between 1999 and 2020. The analysis suggests a static forest land area in the US with less tree abundance but greatly increased timber volume and tree biomass. Coupled with these resource trends, an increase in RD was identified with 90% of US forest land now reaching a biologically-relevant threshold of canopy closure and/or self-thinning induced mortality (RD > 0.3), particularly in areas prone to future drought conditions (e.g., West Coast). Notably, the area of high RD stands (RD > 0.6) has quintupled over the past 20 years while the least stocked stands (RD < 0.3) have decreased 3%. The evidence from the coterminous US forest RD distribution suggest opportunities to increase live tree stocking in understocked stands, while using density management to address tree mortality and resilience to disturbances in increasingly dense forests.
Computing molecular excited states on a D-Wave quantum annealer
Authors: Teplukhin Alexander , Kendrick Brian K. , Mniszewski Susan M. , Zhang Yu , Kumar Ashutosh , Negre Christian F. A. , Anisimov Petr M. , Tretiak Sergei , Dub Pavel A. 
Published: September 2021

AbstractThe possibility of using quantum computers for electronic structure calculations has opened up a promising avenue for computational chemistry. Towards this direction, numerous algorithmic advances have been made in the last five years. The potential of quantum annealers, which are the prototypes of adiabatic quantum computers, is yet to be fully explored. In this work, we demonstrate the use of a D-Wave quantum annealer for the calculation of excited electronic states of molecular systems. These simulations play an important role in a number of areas, such as photovoltaics, semiconductor technology and nanoscience. The excited states are treated using two methods, time-dependent Hartree–Fock (TDHF) and time-dependent density-functional theory (TDDFT), both within a commonly used Tamm–Dancoff approximation (TDA). The resulting TDA eigenvalue equations are solved on a D-Wave quantum annealer using the Quantum Annealer Eigensolver (QAE), developed previously. The method is shown to reproduce a typical basis set convergence on the example $$\hbox {H}_2$$

H
2

molecule and is also applied to several other molecular species. Characteristic properties such as transition dipole moments and oscillator strengths are computed as well. Three potential energy profiles for excited states are computed for $$\hbox {NH}_3$$

NH
3

as a function of the molecular geometry. Similar to previous studies, the accuracy of the method is dependent on the accuracy of the intermediate meta-heuristic software called qbsolv.