bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward more accurate surface properties of ceria using many-body perturbation theory
Authors: Wei Ziyang , Yan George , Sautet Philippe
Published: August 2023

Despite the wide applications, the ab initio modeling of the ceria based catalyst is challenging. The partial occupation in the 4f orbitals creates a fundamental challenge for commonly used density functional theory (DFT) methods, including semilocal functionals with Hubbard U correction to force localization and hybrid functionals. In this work, we benchmark the random phase approximation (RPA) for ceria surface properties, including surface energy and hydrogenation energy, compared to the results utilizing the DFT + U approach or hybrid functionals. We show that, for the latter approaches, different surface properties require opposite directions of parameter tuning. This forms a dilemma for the parameter based DFT methods, as the improvement of a certain property by tuning parameters will inevitably lead to the worsening of other properties. Our results suggest that the parameter-free many-body perturbation theory methods exemplified by RPA are a promising strategy to escape the dilemma and provide highly accurate descriptions, which will allow us to better understand the catalytic reactions in ceria related systems.
Gradient-descent-like scheme for the Allen–Cahn equation
Authors: Lee Dongsun
Published: August 2023

The phase-field equations have many attractive characteristics. First, phase separation can be induced by the phase-field equations. It transforms from a single homogeneous mixture to two distinct phases in a nascent state. Second, the solution of the phase-field equations is bounded by a finite value. It is beneficial to ensure numerical stability. Third, the motion of the interface can be described by geometric features. It is helpful for expressing natural phenomena in mathematical terms. Fourth, the phase-field equations possess the energy dissipation law. This law is about degeneration and decay. It tells us in thermodynamics that all occurrences are irreversible processes. In this paper, we would like to investigate the numerical implementation of the Allen–Cahn (AC) equation, which is the classical one of the phase-field equations. In phase field modeling, the binary phase system is described using a continuous variable called the order parameter. The order parameter can be categorized into two forms: conserved, which represents the physical property such as concentration or mass, and non-conserved, which does not have the conserved physical property. We consider both the non-conservative and conservative AC equations. Our interest is more precisely to scrutinize the utilization of the discrete Laplacian operator in the AC equation by considering the conservative and non-conservative order parameter ϕ. Constructing linearly implicit methods for solving the AC equation, we formulate a gradient-descent-like scheme. Therefore, reinterpreting the implicit scheme for the AC equation, we propose a novel numerical scheme in which solutions are bounded by 1 for all t > 0. Together with the conservative Allen–Cahn equation, our proposed scheme is consistent when mass is conserved as well. From a numerical point of view, a linear, unconditionally energy stable splitting scheme is transformed into a gradient-descent-like scheme. Various numerical simulations are illustrated to demonstrate the validity of the proposed scheme. We also make distinctions between the proposed one and existing numerical schemes.
Mechanisms of the imbibition behavior in shales: A critical review
Authors: Wang Mingcan , Shen Weijun , Ma Tianran , Zeng Zhi , Yang Fengchang
Published: August 2023

Despite the success of hydraulic fracturing in yielding large production increases from shale gas reservoirs, uncertainties associated with basic transport processes require understanding in order to improve the efficiency and minimize environmental impacts. The hydraulic fracturing process brings in large volumes of water into shale reservoir formations, most of which remains unrecoverable and interferes with shale gas production. The imbibition behavior in shales is commonly observed during the hydraulic fracturing process, and the mechanism greatly influences the hydrocarbon recovery in shale gas reservoirs. In this review, the imbibition models in shales are briefly summarized using the Lucas–Washburn model, piston repulsion model, capillary bundle model, and scalar model. Then the experimental study and numerical simulation of shale imbibition are discussed. Moreover, the influencing factors of the imbibition behavior in shales are analyzed, such as shale and fluid properties. Finally, the main conclusions and the future research direction prospects of the imbibition behavior in shale gas reservoirs are summarized. An accurate description of the imbibition behavior in shale is crucial for optimizing the hydraulic fracturing design and enhancing shale gas production in the development of shale gas reservoirs. It is proposed that the research on the individual influencing factors of shale percolation and the geological mechanism under coupling should be strengthened and that the research on the experimental aspects of shale powder percolation should be emphasized.
Iron dissolution and speciation from combustion particles under environmentally relevant conditions
Authors: Szady Cecily , Picarillo Grace , Davis Emily J. , Drapanauskaite Donata , Buneviciene Kristina , Baltrusaitis Jonas , Navea Juan G.
Published: August 2023

Environmental context Iron-containing combustion particles are likely to contribute to environmental iron deposition, while atmospheric acidic processing of such particles can promote their dissolution. Here we report the surface-mediated dissolution of iron from ashes generated by biomass burning power plants and kilns. Examination of the dissolution process at several environmentally relevant pHs, suggests that pH has little impact on the fraction of bioavailable Fe(II) that dissolves into the aqueous phase, although Fe(III) is heavily pH dependent. Rationale Anthropogenic combustion particles, such as ash produced in power plants or kilns, are byproducts with limited use that accumulate in large deposits and become materials of environmental concern. While stored, these particles can be carried by winds into the atmosphere or into soil or near water bodies. Recent studies suggest that a fraction of metals present in the environment come from combustion particles. Methodology In this study, we carry out a comparative study of iron dissolution and speciation from two different combustion particles: bottom ash from a biomass-fired power plant (BA) and lime kiln dust (LKD). Samples were fully characterised and their iron leaching was investigated in aqueous suspensions under environmentally relevant acidic conditions. Iron analysis and speciation was carried out calorimetrically. Results For the combustion particles examined, the fraction of bioavailable Fe2+ is lower than Fe3+. The solubility of Fe3+ is highly dependent on pH, dropping significantly at pHs higher than 3. On the other hand, the solubility of Fe2+ from both BA and LKD was found to be relatively constant over the range of pH investigated. Discussion Iron availability from combustion particles with similar mineralogy is driven by the particle’s surface properties. While iron from LKD dissolves faster than that from BA, the initial rate of dissolution of iron remains statistically constant at pHs relevant for the atmospheric aerosol deliquescent layer, decreasing at pHs above 3. This work provides insight into the ability of combustion particles to provide iron micronutrients under different environmentally relevant acidic conditions.
sccomp: Robust differential composition and variability analysis for single-cell data
Authors: Mangiola Stefano , Roth-Schulze Alexandra J. , Trussart Marie , Zozaya-Valdés Enrique , Ma Mengyao , Gao Zijie , Rubin Alan F. , Speed Terence P. , Shim Heejung , Papenfuss Anthony T.
Published: August 2023

Cellular omics such as single-cell genomics, proteomics, and microbiomics allow the characterization of tissue and microbial community composition, which can be compared between conditions to identify biological drivers. This strategy has been critical to revealing markers of disease progression, such as cancer and pathogen infection. A dedicated statistical method for differential variability analysis is lacking for cellular omics data, and existing methods for differential composition analysis do not model some compositional data properties, suggesting there is room to improve model performance. Here, we introduce sccomp, a method for differential composition and variability analyses that jointly models data count distribution, compositionality, group-specific variability, and proportion mean–variability association, being aware of outliers. sccomp provides a comprehensive analysis framework that offers realistic data simulation and cross-study knowledge transfer. Here, we demonstrate that mean–variability association is ubiquitous across technologies, highlighting the inadequacy of the very popular Dirichlet-multinomial distribution. We show that sccomp accurately fits experimental data, significantly improving performance over state-of-the-art algorithms. Using sccomp, we identified differential constraints and composition in the microenvironment of primary breast cancer.
Near-term tropical cyclone risk and coupled Earth system model biases
Authors: Sobel Adam H. , Lee Chia-Ying , Bowen Steven G. , Camargo Suzana J. , Cane Mark A. , Clement Amy , Fosu Boniface , Hart Megan , Reed Kevin A. , Seager Richard , Tippett Michael K.
Published: August 2023

Most current climate models predict that the equatorial Pacific will evolve under greenhouse gas–induced warming to a more El Niño-like state over the next several decades, with a reduced zonal sea surface temperature gradient and weakened atmospheric Walker circulation. Yet, observations over the last 50 y show the opposite trend, toward a more La Niña-like state. Recent research provides evidence that the discrepancy cannot be dismissed as due to internal variability but rather that the models are incorrectly simulating the equatorial Pacific response to greenhouse gas warming. This implies that projections of regional tropical cyclone activity may be incorrect as well, perhaps even in the direction of change, in ways that can be understood by analogy to historical El Niño and La Niña events: North Pacific tropical cyclone projections will be too active, North Atlantic ones not active enough, for example. Other perils, including severe convective storms and droughts, will also be projected erroneously. While it can be argued that these errors are transient, such that the models’ responses to greenhouse gases may be correct in equilibrium, the transient response is relevant for climate adaptation in the next several decades. Given the urgency of understanding regional patterns of climate risk in the near term, it would be desirable to develop projections that represent a broader range of possible future tropical Pacific warming scenarios—including some in which recent historical trends continue—even if such projections cannot currently be produced using existing coupled earth system models.
Sterically driven current reversal in a molecular motor model
Authors: Albaugh Alex , Gu Geyao , Gingrich Todd R.
Published: August 2023

Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor’s structure can cause the motor’s typical dynamical behavior to reverse directions. Inspired by autonomous synthetic catenane motors, we study the molecular dynamics of a minimal motor model, consisting of a shuttling ring that moves along a track containing interspersed binding sites and catalytic sites. The binding sites attract the shuttling ring while the catalytic sites speed up a reaction between molecular species, which can be thought of as fuel and waste. When that fuel and waste are held in nonequilibrium steady-state concentrations, the free energy from the reaction drives directed motion of the shuttling ring along the track. Using this model and nonequilibrium molecular dynamics, we show that the shuttling ring’s direction can be reversed by simply adjusting the spacing between binding and catalytic sites on the track. We present a steric mechanism behind the current reversal, supported by kinetic measurements from the simulations. These results demonstrate how molecular simulation can guide future development of artificial molecular motors.
SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1
Authors: Wang Zifeng , Petricca Jessica , Liu Mingyu , Zhang Songqi , Chen Sujun , Li Muqing , Besschetnova Anna , Patalano Susan , Venkataramani Kavita , Siegfried Kellee R. , Macoska Jill A. , Han Dong , Gao Shuai , Vedadi Masoud , Arrowsmith Cheryl H. , He Housheng Hansen , Cai Changmeng
Published: August 2023

Dysregulation of histone lysine methyltransferases and demethylases is one of the major mechanisms driving the epigenetic reprogramming of transcriptional networks in castration-resistant prostate cancer (CRPC). In addition to their canonical histone targets, some of these factors can modify critical transcription factors, further impacting oncogenic transcription programs. Our recent report demonstrated that LSD1 can demethylate the lysine 270 of FOXA1 in prostate cancer (PCa) cells, leading to the stabilization of FOXA1 chromatin binding. This process enhances the activities of the androgen receptor and other transcription factors that rely on FOXA1 as a pioneer factor. However, the identity of the methyltransferase responsible for FOXA1 methylation and negative regulation of the FOXA1-LSD1 oncogenic axis remains unknown. SETD7 was initially identified as a transcriptional activator through its methylation of histone 3 lysine 4, but its function as a methyltransferase on nonhistone substrates remains poorly understood, particularly in the context of PCa progression. In this study, we reveal that SETD7 primarily acts as a transcriptional repressor in CRPC cells by functioning as the major methyltransferase targeting FOXA1-K270. This methylation disrupts FOXA1-mediated transcription. Consistent with its molecular function, we found that SETD7 confers tumor suppressor activity in PCa cells. Moreover, loss of SETD7 expression is significantly associated with PCa progression and tumor aggressiveness. Overall, our study provides mechanistic insights into the tumor-suppressive and transcriptional repression activities of SETD7 in mediating PCa progression and therapy resistance.
Warming may offset impact of precipitation changes on riverine nitrogen loading
Authors: Zhao Gang , Merder Julian , Ballard Tristan C. , Michalak Anna M.
Published: August 2023

Climate change, especially in the form of precipitation and temperature changes, can alter the transformation and delivery of nitrogen on the land surface and to aquatic systems, impacting the trophic states of downstream water bodies. While the expected impacts of changes in precipitation have been explored, a quantitative understanding of the impact of temperature on nitrogen loading is lacking at landscape scales. Here, using several decades of nitrogen loading observations, we quantify how individual and combined future changes in precipitation and temperature will affect riverine nitrogen loading. We find that, contrary to recent decades, rising temperatures are likely to offset or even reverse previously reported impacts of future increases in total and extreme precipitation on nitrogen runoff across the majority of the contiguous United States. These findings highlight the multifaceted impacts of climate change on the global nitrogen cycle.
DNA methylation in the mouse cochlea promotes maturation of supporting cells and contributes to the failure of hair cell regeneration
Authors: Nguyen John D. , Llamas Juan , Shi Tuo , Crump J. Gage , Groves Andrew K. , Segil Neil
Published: August 2023

Mammalian hair cells do not functionally regenerate in adulthood but can regenerate at embryonic and neonatal stages in mice by direct transdifferentiation of neighboring supporting cells into new hair cells. Previous work showed loss of transdifferentiation potential of supporting cells is in part due to H3K4me1 enhancer decommissioning of the hair cell gene regulatory network during the first postnatal week. However, inhibiting this decommissioning only partially preserves transdifferentiation potential. Therefore, we explored other repressive epigenetic modifications that may be responsible for this loss of plasticity. We find supporting cells progressively accumulate DNA methylation at promoters of developmentally regulated hair cell genes. Specifically, DNA methylation overlaps with binding sites of Atoh1, a key transcription factor for hair cell fate. We further show that DNA hypermethylation replaces H3K27me3-mediated repression of hair cell genes in mature supporting cells, and is accompanied by progressive loss of chromatin accessibility, suggestive of facultative heterochromatin formation. Another subset of hair cell loci is hypermethylated in supporting cells, but not in hair cells. Ten-eleven translocation (TET) enzyme-mediated demethylation of these hypermethylated sites is necessary for neonatal supporting cells to transdifferentiate into hair cells. We also observe changes in chromatin accessibility of supporting cell subtypes at the single-cell level with increasing age: Gene programs promoting sensory epithelium development loses chromatin accessibility, in favor of gene programs that promote physiological maturation and function of the cochlea. We also find chromatin accessibility is partially recovered in a chronically deafened mouse model, which holds promise for future translational efforts in hearing restoration.
Plasticity of thalamocortical axons is regulated by serotonin levels modulated by preterm birth
Authors: Sinclair-Wilson Alexander , Lawrence Akindé , Ferezou Isabelle , Cartonnet Hugues , Mailhes Caroline , Garel Sonia , Lokmane Ludmilla
Published: August 2023

Sensory inputs are conveyed to distinct primary areas of the neocortex through specific thalamocortical axons (TCA). While TCA have the ability to reorient postnatally to rescue embryonic mistargeting and target proper modality-specific areas, how this remarkable adaptive process is regulated remains largely unknown. Here, using a mutant mouse model with a shifted TCA trajectory during embryogenesis, we demonstrated that TCA rewiring occurs during a short postnatal time window, preceded by a prenatal apoptosis of thalamic neurons—two processes that together lead to the formation of properly innervated albeit reduced primary sensory areas. We furthermore showed that preterm birth, through serotonin modulation, impairs early postnatal TCA plasticity, as well as the subsequent delineation of cortical area boundary. Our study defines a birth and serotonin-sensitive period that enables concerted adaptations of TCA to primary cortical areas with major implications for our understanding of brain wiring in physiological and preterm conditions.
Signatures of a magnetic superstructure phase induced by ultrahigh magnetic fields in a breathing pyrochlore antiferromagnet
Authors: Gen Masaki , Ikeda Akihiko , Aoyama Kazushi , Jeschke Harald O. , Ishii Yuto , Ishikawa Hajime , Yajima Takeshi , Okamoto Yoshihiko , Zhou Xuguang , Nakamura Daisuke , Takeyama Shojiro , Kindo Koichi , Matsuda Yasuhiro H. , Kohama Yoshimitsu
Published: August 2023

The mutual coupling of spin and lattice degrees of freedom is ubiquitous in magnetic materials and potentially creates exotic magnetic states in response to the external magnetic field. Particularly, geometrically frustrated magnets serve as a fertile playground for realizing magnetic superstructure phases. Here, we observe an unconventional two-step magnetostructural transition prior to a half-magnetization plateau in a breathing pyrochlore chromium spinel by means of state-of-the-art magnetization and magnetostriction measurements in ultrahigh magnetic fields available up to 600 T. Considering a microscopic magnetoelastic theory, the intermediate-field phase can be assigned to a magnetic superstructure with a three-dimensional periodic array of 3-up-1-down and canted 2-up-2-down spin molecules. We attribute the emergence of the magnetic superstructure to a unique combination of the strong spin–lattice coupling and large breathing anisotropy.
Ezh2 promotes mammary tumor initiation through epigenetic regulation of the Wnt and mTORC1 signaling pathways
Authors: Liu Linshan , Xiao Bin , Hirukawa Alison , Smith Harvey W. , Zuo Dongmei , Sanguin-Gendreau Virginie , McCaffrey Luke , Nam Alice Jisoo , Muller William J.
Published: August 2023

The regulation of gene expression through histone posttranslational modifications plays a crucial role in breast cancer progression. However, the molecular mechanisms underlying the contribution of histone modification to tumor initiation remain unclear. To gain a deeper understanding of the role of the histone modifier Enhancer of Zeste homology 2 (Ezh2) in the early stages of mammary tumor progression, we employed an inducible mammary organoid system bearing conditional
Ezh2
alleles that faithfully recapitulates key events of luminal B breast cancer initiation. We showed that the loss of Ezh2 severely impairs oncogene-induced organoid growth, with Ezh2-deficient organoids maintaining a polarized epithelial phenotype. Transcriptomic profiling showed that Ezh2-deficient mammary epithelial cells up-regulated the expression of negative regulators of Wnt signaling and down-regulated genes involved in mTORC1 (mechanistic target of rapamycin complex 1) signaling. We identified
Sfrp1
, a Wnt signaling suppressor, as an Ezh2 target gene that is derepressed and expressed in Ezh2-deficient epithelium. Furthermore, an analysis of breast cancer data revealed that
Sfrp1
expression was associated with favorable clinical outcomes in luminal B breast cancer patients. Finally, we confirmed that targeting Ezh2 impairs mTORC1 activity through an indirect mechanism that up-regulates the expression of the tumor suppressor Pten. These findings indicate that Ezh2 integrates the mTORC1 and Wnt signaling pathways during early mammary tumor progression, arguing that inhibiting Ezh2 or therapeutically targeting Ezh2-dependent programs could be beneficial for the treatment of early-stage luminal B breast cancer.
Human white matter myelinates faster in utero than ex utero
Authors: Grotheer Mareike , Bloom David , Kruper John , Richie-Halford Adam , Zika Stephanie , Aguilera González Vicente A. , Yeatman Jason D. , Grill-Spector Kalanit , Rokem Ariel
Published: August 2023

The formation of myelin, the fatty sheath that insulates nerve fibers, is critical for healthy brain function. A fundamental open question is what impact being born has on myelin growth. To address this, we evaluated a large (
n
= 300) cross-sectional sample of newborns from the Developing Human Connectome Project (dHCP). First, we developed software for the automated identification of 20 white matter bundles in individual newborns that is well suited for large samples. Next, we fit linear models that quantify how T1w/T2w (a myelin-sensitive imaging contrast) changes over time at each point along the bundles. We found faster growth of T1w/T2w along the lengths of all bundles before birth than right after birth. Further, in a separate longitudinal sample of preterm infants (
N
= 34), we found lower T1w/T2w than in full-term peers measured at the same age. By applying the linear models fit on the cross-section sample to the longitudinal sample of preterm infants, we find that their delay in T1w/T2w growth is well explained by the amount of time they spent developing in utero and ex utero. These results suggest that white matter myelinates faster in utero than ex utero. The reduced rate of myelin growth after birth, in turn, explains lower myelin content in individuals born preterm and could account for long-term cognitive, neurological, and developmental consequences of preterm birth. We hypothesize that closely matching the environment of infants born preterm to what they would have experienced in the womb may reduce delays in myelin growth and hence improve developmental outcomes.
Astrocyte-targeting therapy rescues cognitive impairment caused by neuroinflammation via the Nrf2 pathway
Authors: Nakano-Kobayashi Akiko , Canela Andres , Yoshihara Toru , Hagiwara Masatoshi
Published: August 2023

Neuroinflammation is a common feature of neurodegenerative disorders such as Alzheimer’s disease (AD). Neuroinflammation is induced by dysregulated glial activation, and astrocytes, the most abundant glial cells, become reactive upon neuroinflammatory cytokines released from microglia and actively contribute to neuronal loss. Therefore, blocking reactive astrocyte functions is a viable strategy to manage neurodegenerative disorders. However, factors or therapeutics directly regulating astrocyte subtypes remain unexplored. Here, we identified transcription factor NF-E2-related factor 2 (Nrf2) as a therapeutic target in neurotoxic reactive astrocytes upon neuroinflammation. We found that the absence of Nrf2 promoted the activation of reactive astrocytes in the brain tissue samples obtained from AD model 5xFAD mice, whereas enhanced Nrf2 expression blocked the induction of reactive astrocyte gene expression by counteracting NF-κB subunit p65 recruitment. Neuroinflammatory astrocytes robustly up-regulated genes associated with type I interferon and the antigen-presenting pathway, which were suppressed by Nrf2 pathway activation. Moreover, impaired cognitive behaviors observed in AD mice were rescued upon ALGERNON2 treatment, which potentiated the Nrf2 pathway and reduced the induction of neurotoxic reactive astrocytes. Thus, we highlight the potential of astrocyte-targeting therapy by promoting the Nrf2 pathway signaling for neuroinflammation-triggered neurodegeneration.
Collaborative privacy-preserving analysis of oncological data using multiparty homomorphic encryption
Authors: Geva Ravit , Gusev Alexander , Polyakov Yuriy , Liram Lior , Rosolio Oded , Alexandru Andreea , Genise Nicholas , Blatt Marcelo , Duchin Zohar , Waissengrin Barliz , Mirelman Dan , Bukstein Felix , Blumenthal Deborah T. , Wolf Ido , Pelles-Avraham Sharon , Schaffer Tali , Lavi Lee A. , Micciancio Daniele , Vaikuntanathan Vinod , Badawi Ahmad Al , Goldwasser Shafi
Published: August 2023

Real-world healthcare data sharing is instrumental in constructing broader-based and larger clinical datasets that may improve clinical decision-making research and outcomes. Stakeholders are frequently reluctant to share their data without guaranteed patient privacy, proper protection of their datasets, and control over the usage of their data. Fully homomorphic encryption (FHE) is a cryptographic capability that can address these issues by enabling computation on encrypted data without intermediate decryptions, so the analytics results are obtained without revealing the raw data. This work presents a toolset for collaborative privacy-preserving analysis of oncological data using multiparty FHE. Our toolset supports survival analysis, logistic regression training, and several common descriptive statistics. We demonstrate using oncological datasets that the toolset achieves high accuracy and practical performance, which scales well to larger datasets. As part of this work, we propose a cryptographic protocol for interactive bootstrapping in multiparty FHE, which is of independent interest. The toolset we develop is general-purpose and can be applied to other collaborative medical and healthcare application domains.
Reconstructing household transmission dynamics to estimate the infectiousness of asymptomatic influenza virus infections
Authors: Tsang Tim K. , Wang Can , Fang Vicky J. , Perera Ranawaka A. P. M. , So Hau Chi , Ip Dennis K. M. , Leung Gabriel M. , Peiris J. S. Malik , Cauchemez Simon , Cowling Benjamin J.
Published: August 2023

There has long been controversy over the potential for asymptomatic cases of the influenza virus to have the capacity for onward transmission, but recognition of asymptomatic transmission of COVID-19 stimulates further research into this topic. Here, we develop a Bayesian methodology to analyze detailed data from a large cohort of 727 households and 2515 individuals in the 2009 pandemic influenza A(H1N1) outbreak in Hong Kong to characterize household transmission dynamics and to estimate the relative infectiousness of asymptomatic versus symptomatic influenza cases. The posterior probability that asymptomatic cases [36% of cases; 95% credible interval (CrI): 32%, 40%] are less infectious than symptomatic cases is 0.82, with estimated relative infectiousness 0.57 (95% CrI: 0.11, 1.54). More data are required to strengthen our understanding of the contribution of asymptomatic cases to the spread of influenza.
Partial cytological diploidization of neoautotetraploid meiosis by induced cross-over rate reduction
Authors: Gonzalo Adrián , Parra-Nunez Pablo , Bachmann Andreas L. , Sanchez-Moran Eugenio , Bomblies Kirsten
Published: August 2023

Polyploids, which arise from whole-genome duplication events, have contributed to genome evolution throughout eukaryotes. Among plants, novel features of neopolyploids include traits that can be evolutionarily or agriculturally beneficial, such as increased abiotic stress tolerance. Thus, in addition to being interesting from an evolutionary perspective, genome duplication is also increasingly recognized as a promising crop improvement tool. However, newly formed (neo)polyploids commonly suffer from fertility problems, which have been attributed to abnormal associations among the multiple homologous chromosome copies during meiosis (multivalents). Here, we test the long-standing hypothesis that reducing meiotic cross-over number may be sufficient to limit multivalent formation, favoring diploid-like bivalent associations (cytological diploidization). To do so, we developed
Arabidopsis thaliana
lines with low cross-over rates by combining mutations for
HEI10
and
TAF4b
. Double mutants showed a reduction of ~33% in cross-over numbers in diploids without compromising meiotic stability. Neopolyploids derived from the double mutant show a cross-over rate reduction of about 40% relative to wild-type neotetraploids, and groups of four homologs indeed formed fewer multivalents and more bivalents. However, we also show that the reduction in multivalents comes with the cost of a slightly increased frequency of univalents and that it does not rescue neopolyploid fertility. Thus, while our results do show that reducing cross-over rates can reduce multivalent frequency in neopolyploids, they also emphasize that there are additional factors affecting both meiotic stability and neopolyploid fertility that will need to be considered in solving the neopolyploid fertility challenge.
Nanomechanoelectrical approach to highly sensitive and specific label-free DNA detection
Authors: Zhang Xiaoyu , Fan Xiao , Bao Huilu , Ping Jinglei
Published: August 2023

Electronic detection of DNA oligomers offers the promise of rapid, miniaturized DNA analysis across various biotechnological applications. However, known all-electrical methods, which solely rely on measuring electrical signals in transducers during probe–target DNA hybridization, are prone to nonspecific electrostatic and electrochemical interactions, subsequently limiting their specificity and detection limit. Here, we demonstrate a nanomechanoelectrical approach that delivers ultra-robust specificity and a 100-fold improvement in detection limit. We drive nanostructural DNA strands tethered to a graphene transistor to oscillate in an alternating electric field and show that the transistor-current spectra are characteristic and indicative of DNA hybridization. We find that the inherent difference in pliability between unpaired and paired DNA strands leads to the spectral characteristics with minimal influence from nonspecific electrostatic and electrochemical interactions, resulting in high selectivity and sensitivity. Our results highlight the potential of high-performance DNA analysis based on miniaturized all-electronic settings.
Patients resist, doctors manage
Authors: Mao Yansheng , Wei Shuang , Wang Xiaojiang
Published: August 2023

Although there are abundant studies on the management of patient resistance in traditional face-to-face clinical settings, scant attention has been paid to that in the online context. This study thus delves into the types of patient resistance and the strategies Chinese doctors employ to manage such resistance in Online Medical Consultation (OMC). A dataset of 148 online doctor-patient conversations was collected from Chunyu Doctor. Three types of patient resistance – expertise-oriented, experience-oriented, and emotion-oriented – are identified and analyzed in Chinese OMC. Accordingly, Chinese doctors generally adopt linguistic strategies such as interpretives to justify decisions, supportives to facilitate relational work, and imperatives in the event of persistent resistance. Furthermore, the management of patient resistance is discussed as a joint goal-centered activity in Chinese OMC, aiming to contribute to a comprehensive understanding of the shared decision-making process in Chinese health communication.
Endocytic myosin-1 is a force-insensitive, power-generating motor
Authors: Pedersen Ross T.A. , Snoberger Aaron , Pyrpassopoulos Serapion , Safer Daniel , Drubin David G. , Ostap E. Michael
Published: August 2023

Myosins are required for clathrin-mediated endocytosis, but their precise molecular roles in this process are not known. This is, in part, because the biophysical properties of the relevant motors have not been investigated. Myosins have diverse mechanochemical activities, ranging from powerful contractility against mechanical loads to force-sensitive anchoring. To better understand the essential molecular contribution of myosin to endocytosis, we studied the in vitro force-dependent kinetics of the Saccharomyces cerevisiae endocytic type I myosin called Myo5, a motor whose role in clathrin-mediated endocytosis has been meticulously studied in vivo. We report that Myo5 is a low-duty-ratio motor that is activated ∼10-fold by phosphorylation and that its working stroke and actin-detachment kinetics are relatively force-insensitive. Strikingly, the in vitro mechanochemistry of Myo5 is more like that of cardiac myosin than that of slow anchoring myosin-1s found on endosomal membranes. We, therefore, propose that Myo5 generates power to augment actin assembly-based forces during endocytosis in cells.
Role of site–site interaction on the phase equilibria of multiple-site associating fluids in a functionalized slit pore
Authors: Mandal Sashanka Sekhar , Singh Sudhir Kumar , Khan Sandip
Published: August 2023

Vapor–liquid phase equilibria for multiple sites associating fluids with different associating strengths are investigated in a slit pore using grand-canonical transition matrix Monte Carlo method. The increase of critical temperature from two-site to four-site associating fluids at constant site strength is quite significant as compared to that of the one-site to two-site associating fluids, which is more pronounced at higher associating strength (ϵ* = 6). Monomer fraction and cluster size distribution are used to investigate the association of fluid particles in coexistence phases. The monomer fraction for both phases decreases with increased associating sites on the fluid particles due to more site–site interaction with neighboring fluid particles and forming a larger cluster. Therefore, the number of associating sites and their distribution play a vital role in the association of fluid particles. Moreover, the saturation chemical potential changes with the arrangement of the sites. For two-site associating fluids, we observe early vapor–liquid transition when the sites are oppositely placed, and when the sites are placed at 90°, the vapor–liquid transition is observed at the higher chemical potential. Moreover, four-site associating fluids with a square arrangement show early vapor–liquid phase transition, mainly because these arrangements of sites effectively interact with surface sites and the molecules in the next layer.
Roadmap on electronic structure codes in the exascale era
Authors: Gavini Vikram , Baroni Stefano , Blum Volker , Bowler David R , Buccheri Alexander , Chelikowsky James R , Das Sambit , Dawson William , Delugas Pietro , Dogan Mehmet , Draxl Claudia , Galli Giulia , Genovese Luigi , Giannozzi Paolo , Giantomassi Matteo , Gonze Xavier , Govoni Marco , Gygi François , Gulans Andris , Herbert John M , Kokott Sebastian , Kühne Thomas D , Liou Kai-Hsin , Miyazaki Tsuyoshi , Motamarri Phani , Nakata Ayako , Pask John E , Plessl Christian , Ratcliff Laura E , Richard Ryan M , Rossi Mariana , Schade Robert , Scheffler Matthias , Schütt Ole , Suryanarayana Phanish , Torrent Marc , Truflandier Lionel , Windus Theresa L , Xu Qimen , Yu Victor W-Z , Perez D
Published: August 2023

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry, and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.
CT2X-IRA: CT to x-ray image registration agent using domain-cross multi-scale-stride deep reinforcement learning
Authors: Geng Haixiao , Xiao Deqiang , Yang Shuo , Fan Jingfan , Fu Tianyu , Lin Yucong , Bai Yanhua , Ai Danni , Song Hong , Wang Yongtian , Duan Feng , Yang Jian
Published: August 2023

Objective. In computer-assisted minimally invasive surgery, the intraoperative x-ray image is enhanced by overlapping it with a preoperative CT volume to improve visualization of vital anatomical structures. Therefore, accurate and robust 3D/2D registration of CT volume and x-ray image is highly desired in clinical practices. However, previous registration methods were prone to initial misalignments and struggled with local minima, leading to issues of low accuracy and vulnerability. Approach. To improve registration performance, we propose a novel CT/x-ray image registration agent (CT2X-IRA) within a task-driven deep reinforcement learning framework, which contains three key strategies: (1) a multi-scale-stride learning mechanism provides multi-scale feature representation and flexible action step size, establishing fast and globally optimal convergence of the registration task. (2) A domain adaptation module reduces the domain gap between the x-ray image and digitally reconstructed radiograph projected from the CT volume, decreasing the sensitivity and uncertainty of the similarity measurement. (3) A weighted reward function facilitates CT2X-IRA in searching for the optimal transformation parameters, improving the estimation accuracy of out-of-plane transformation parameters under large initial misalignments. Main results. We evaluate the proposed CT2X-IRA on both the public and private clinical datasets, achieving target registration errors of 2.13 mm and 2.33 mm with the computation time of 1.5 s and 1.1 s, respectively, showing an accurate and fast workflow for CT/x-ray image rigid registration. Significance. The proposed CT2X-IRA obtains the accurate and robust 3D/2D registration of CT and x-ray images, suggesting its potential significance in clinical applications.
A capacitive method and experiment for measurement of sedimentation of magnetorheological fluid
Authors: Xie Lei , Li Pei , Yang Xunyong , Yin Jianfei , Lu Chuan , Shao Xiangyang , Zhang Xiang , Wang Pengsai , Liao Changrong
Published: August 2023

Sedimentation is one of the key issues in the practical engineering applications of magnetorheological fluids (MRFs). Testing and evaluation of the suspension stability of MRFs should be a prerequisite procedure before their applications. There are a few reported methods of measurement of sedimentation of MRFs. The opaque zone below the mudline, especially the sediment zone at the bottom in the MRF column, is the true key factor that affects the applications of MRF due to the possible irreversibility caused by the caking of the sediment zone. This study proposes a novel capacitive method on the basis of the change in dielectric constant resulting from the change in concentration of the magnetic metal particles of MRF upon sedimentation. First, an analytic model was established to present a positive correlation between the dielectric constant and volume fraction of particles throughout the entire MRF column and the theoretical expression of the dielectric constant of MRF in a test tube was obtained. Second, a capacitive sensor and the relevant experimental set-up were designed and fabricated. Especially, the effect of eccentricity error of the capacitor sensor structure on the measurement was analyzed. Then, a sedimentation experiment for prepared MRF samples was carried out, and the testing results were discussed and verified by a visual mudline observation of the supernatant zone, indicating the feasibility of testing and evaluating the suspension stability of MRF by the capacitive method.
Initial-condition effects on ReLU-type hyper-jerk system and its application in image encryption
Authors: Zhang Yunzhen , Peng Daao , Chen Chengjie , Zhao Guangzhe , Zhang Xiangqun
Published: August 2023

The memristive hyper-jerk system described in this study has a non-smooth Rectified Linear Unit (ReLU) memductance function. A non-smooth memductance function of this kind might cause the system to have three line equilibria within it, bring about the arrival of extreme multistability with infinitely many coexisting attractors. Analyzing the three line equilibria’s stabilities and researching the intricate dynamical effects triggered by memristor and non-memristor initial conditions are related topic. Phase portraits, bifurcation diagrams, Lyapunov exponent spectra, and the basins of attraction all show the dynamical tendencies. According to the results, the novel system’s dynamical behaviors depend on both the memristor initial condition and the non-memristor initial conditions. Moreover, PSIM circuit simulations and MCU-based hardware measurements are run to confirm the coexisting infinitely many attractors. The ReLU-type hyper-jerk system is then utilized to encrypt images. Experimental findings support its exceptional robustness against a range of potential attacks.
Predicting temperature field in keyhole-mode selective laser melting with combined heat sources: a rapid model
Authors: Li Bing , Li Changyou , Chunlei Hua
Published: August 2023

Predicting the temperature field during selective laser melting (SLM) is crucial for improving the performance of printed parts. However, there is still a lack of an efficient and accurate model for predicting the temperature field of keyhole-mode melting in SLM. Based on the physical phenomena of keyhole-mode melting observed in experiments and simulations, this study proposes an analytical model for rapidly predicting the temperature distribution during SLM keyhole-mode melting. The model considers vapor depression in the molten pool and the interaction between the laser and molten pool during keyhole-mode melting. The model was validated using numerical simulations and experimental data. The variation trend of the laser energy distribution and molten pool size with respect to the laser energy density was revealed. As the laser energy density increased, the depth of the molten pool and the vapor depression increased linearly, and the molten pool width increased to a peak and then remained constant. The process parameter window to avoid a lack-of-fusion was also investigated. With a computation time of 15 s and a prediction error of less than 10%, this model is an effective way to simulate SLM processes and guide the optimization of process parameters.
Determination of the angular momentum of the Kerr black hole from equatorial geodesic motion
Authors: Villegas Laura O. , Ramírez-Codiz Eduardo , Jaramillo Víctor , Degollado Juan Carlos , Moreno Claudia , Núñez Darío , Romero-Cruz Fernando J.
Published: August 2023

We present a method to determine the angular momentum of a black hole based on observations of the trajectories of the bodies in the Kerr spacetime. We use the Hamilton equations to describe the dynamics of a particle and present results for equatorial trajectories, obtaining an algebraic equation for the magnitude of the black hole's angular momentum with coefficients given by observable quantities. We tailor a numerical code to solve the dynamical equations and use it to generate synthetic data. We apply the method in some representative examples, obtaining the parameters of the trajectories as well as the black hole's angular momentum in good agreement with the input data.
General black-hole metric mimicking Schwarzschild spacetime
Authors: Konoplya R.A. , Zhidenko A.
Published: August 2023

Using the general parametrization of spherically symmetric and asymptotically flat black holes in arbitrary metric theories of gravity and implying that: a) the post-Newtonian constraints are taken into account and b) basic astrophysically relevant characteristics (such as, dominant quasinormal modes, frequency at the innermost stable circular orbit, binding energy, radius of the shadow etc.) are indistinguishable from their Schwarzschild values, we propose a simple metric which depends on three independent parameters (coefficients of the parametrization). Variation of these three parameters can, nevertheless, lead to the two distinctive features. The first is the black-hole temperature, and consequently the Hawking radiation, which can differ a lot from its Schwarzschild limit. The second is the outburst of overtones which become extremely sensitive to small changes of the parameters.
Investigation on the scaling of magneto-Rayleigh–Taylor instability to the current rise time of Z-pinch plasmas
Authors: Xiaoguang Wang , Xiaodong Ren , Shijian Meng , Chongyang Mao , Delong Xiao , Qiang Yi , Shaotong Zhou , Xianbin Huang , Xiuwen Zhou , Wenqian Weng , Zhanchang Huang , Chuang Xue , Guanqiong Wang , Shunkai Sun , Xiaojian Shu
Published: August 2023

Understanding how the magneto-Rayleigh–Taylor instability (MRTI) scales to the current rise time is vital for Z-pinch dynamic hohlraum driven inertial confinement fusion. Wang et al discovered in prior theoretical work that the perturbation amplitude of MRTI before stagnation increases linearly with the current rise time when the implosion velocity of Z-pinch plasma is held constant. In the present work, three types of wire-array experiments with similar implosion dynamics and constant implosion velocity are performed on an 8 MA pulse power generator to investigate the scaling of MRTI to the rise time. It is successfully accomplished for the first time to obtain the similar wire-array Z-pinch implosions in which the current rise time is scaled up to three times on the generator by controlling the trigger time of its 24 modules. Both the experimental results, which include x-ray radiation pulses and x-ray images of imploding plasmas, and the related numerical analysis have shown that the MRTI before stagnation grows linearly with the rise time, as predicted by the theoretical model.