bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Polar Mesocyclone and Associated Environmental Characteristics During the Heavy Snowfall Event in Sapporo, Japan, in Early February 2022
Authors: Honda T. 
Published: June 2023

AbstractIn early February 2022, the Sapporo region, north Japan, experienced record‐breaking snowfall. During this period, a mesoscale cyclonic rotation corresponding to a polar mesocyclone (PMC) was observed over the Sea of Japan by a geostationary satellite. This study investigates important processes involved in this heavy snowfall event with attention to the role of the PMC using a 100‐member regional ensemble forecast. The initial conditions for the ensemble forecast are obtained by a regional‐scale ensemble data assimilation system that assimilates conventional observations only. Several ensemble members successfully predict heavy snowfall in the Sapporo region with an 18 hr lead time. Composite analyses reveal that these better ensemble members predict that a southward‐moving PMC with a precipitation system develops from small vortices over the ocean and approaches to the Sapporo region, whereas worse members instead predict precipitation systems shifted to the north of the Sapporo region. Further composite analyses demonstrate that the better ensemble members have environmental characteristics such as a deeper and colder upper‐level trough and large low‐level baroclinicity, which are favorable for the development of PMCs. In particular, the latter is associated with reverse shear in which PMCs tend to move southward. Therefore, these environmental factors are key to predicting the heavy snowfall event in Sapporo associated with the PMC.
Effects of Unsaturated Flow on Salt Distributions in Tidally Influenced Coastal Unconfined Aquifers
Authors: Luo Zhaoyang , Kong Jun , Yu Xiayang , Lu Chunhui , Werner Adrian D. , Barry David A. 
Published: June 2023

AbstractUnsaturated flow influences both the seawater extent under steady‐state conditions and the propagation of tides in coastal aquifers. However, its effects on salt distributions in tidally influenced coastal aquifers are little investigated. The present study used numerical simulations and data from laboratory experiments to analyze the effects of unsaturated flow on density‐dependent solute transport in coastal unconfined aquifers. The effects of the inland boundary condition (i.e., constant‐head or constant‐flux) were tested. Compared to a stable sea level, the results show that unsaturated flow has a more pronounced influence on salt distributions in coastal unconfined aquifers when tides are considered, regardless of the type of inland boundary condition. Neglect of unsaturated flow effects leads to expansion of the upper saline plume (USP), shrinkage of the saltwater wedge (seaward movement of saltwater wedge), and overestimation of water and salt exchange across the aquifer‐ocean interface. This is caused by a lower head in the nearshore area during high‐tide periods with the unsaturated zone effects removed. Thus, without the unsaturated zone, stronger head gradients within the nearshore aquifer occur at high tide, leading to stronger tidally driven seawater infiltration and hence a larger USP. Counterintuitively, ignoring unsaturated flow effects leads to greater average inland head over a tidal period, which shifts the saltwater wedge seaward. It is concluded that unsaturated zone effects should not be neglected for modeling tide‐affected seawater intrusion, especially if quantification of near‐shore conditions is important.
Understanding the Food‐Energy‐Water Nexus in Mixed Irrigation Regimes Using a Regional Hydroeconomic Optimization Modeling Framework
Authors: Kumar Hemant , Zhu Tingju , Sankarasubramanian A. 
Published: June 2023

AbstractUnderstanding the nexus between food, energy, and water systems (FEW) is critical for basins with intensive agricultural water use as they face significant challenges under changing climate and regional development. We investigate the food, energy, and water nexus through a regional hydroeconomic optimization (RHEO) modeling framework. The crop production in RHEO is estimated through a hierarchical regression model developed using a biophysical model, AquaCropOS, forced with daily climatic inputs. Incorporating the hierarchical model within the RHEO also reduces the computation time by enabling parallel programming within the AquaCropOS and facilitates mixed irrigation—rainfed, fully irrigated and deficit irrigation—strategies. To demonstrate the RHEO framework, we considered a groundwater‐dominated basin, South Flint River Basin, Georgia, for developing mixed irrigation strategies over 31 years. Our analyses show that optimal deficit irrigation is economically better than full irrigation, which increases the groundwater pumping cost. Thus, considering deficit irrigation in a groundwater‐dominated basin reduces the water, carbon, and energy footprints, thereby reducing FEW vulnerability. The RHEO also could be employed for analyzing FEW nexus under potential climate change and future regional development scenarios.
Rapid Fault Healing After Seismic Slip
Authors: Bedford John D. , Hirose Takehiro , Hamada Yohei 
Published: June 2023

AbstractFault strength recovery (healing) following an earthquake is a key process in controlling the recurrence of future events; however, the rates and mechanisms of fault healing are poorly constrained. Here, by performing high‐velocity friction experiments at seismic slip rates (0.57 m/s), we show that granite and gabbro fault gouges recover their strength rapidly after experiencing dynamic weakening. The healing rates are one to two orders of magnitude faster than those observed in typical frictional healing experiments performed at slow slip velocities (micrometers to millimeters per second). Analysis of the sheared gouges using Raman spectroscopy suggests that enhanced healing after seismic slip is associated with thermally activated chemical bonding at frictional contacts in the gouge. Our results indicate that seismogenic faults can potentially regain their strength early during interseismic periods, which would imply that healing may not be the dominant control on earthquake recurrence, with other processes, such as far‐field tectonic loading or frictional stability transitions, possibly dictating the occurrence of future events.
Modeling Crustal Structure in the Permian Basin by Waveform‐Matching P Receiver Functions and Autocorrelograms With Particle Swarm Optimization
Authors: Sadler B. , Pulliam J. 
Published: June 2023

AbstractWe model basin and Moho structure in the Permian Basin region of west Texas and southeastern New Mexico using a method for waveform matching via global optimization of P‐to‐S receiver functions, vertical autocorrelograms, and horizontal autocorrelograms. The algorithm is driven by Particle Swarm Optimization, whose search history can be used to assess the strength of data constraints on model parameters. A common drawback in receiver function modeling is the need to assume a value for Vp before Vs and layer thickness can be estimated. But constraints on Vp can be provided by vertical autocorrelograms of teleseismic arrivals, which detect reverberating P waves, because the phase delay times depend only on Vp and interface depth. P‐to‐S receiver functions and vertical and radial autocorrelograms are computed for M > 5.5 events at 30°–100° epicentral distance, then edited and binned by ray parameter. Synthetic seismograms are computed for layered models using a 1D reflectivity method. The free parameters in the algorithm include basin depth, basin Vp, basin Vp/Vs, and thickness and Vp/Vs of the crystalline crust. Where vertical autocorrelograms prove insufficient for determining basin Vp, Vp is assumed from nearby stations that were modeled successfully. We find an average basin Vp of 4.57 km/s and basin depths to ∼8 km. Moho depths are generally 40–48 km. A basin depth of at least 3.5 km is typically needed to produce sufficient phase separation to allow an average Vp to be determined with confidence. Modeling autocorrelograms jointly with receiver functions therefore improves constraints on deep basin structure.
Electrically-pumped compact topological bulk lasers driven by band-inverted bound states in the continuum
Authors: Han Song , Cui Jieyuan , Chua Yunda , Zeng Yongquan , Hu Liangxing , Dai Mingjin , Wang Fakun , Sun Fangyuan , Zhu Song , Li Lianhe , Davies Alexander Giles , Linfield Edmund Harold , Tan Chuan Seng , Kivshar Yuri , Wang Qi Jie 
Published: June 2023

AbstractOne of the most exciting breakthroughs in physics is the concept of topology that was recently introduced to photonics, achieving robust functionalities, as manifested in the recently demonstrated topological lasers. However, so far almost all attention was focused on lasing from topological edge states. Bulk bands that reflect the topological bulk-edge correspondence have been largely missed. Here, we demonstrate an electrically pumped topological bulk quantum cascade laser (QCL) operating in the terahertz (THz) frequency range. In addition to the band-inversion induced in-plane reflection due to topological nontrivial cavity surrounded by a trivial domain, we further illustrate the band edges of such topological bulk lasers are recognized as the bound states in the continuum (BICs) due to their nonradiative characteristics and robust topological polarization charges in the momentum space. Therefore, the lasing modes show both in-plane and out-of-plane tight confinements in a compact laser cavity (lateral size ~3λlaser). Experimentally, we realize a miniaturized THz QCL that shows single-mode lasing with a side-mode suppression ratio (SMSR) around 20 dB. We also observe a cylindrical vector beam for the far-field emission, which is evidence for topological bulk BIC lasers. Our demonstration on miniaturization of single-mode beam-engineered THz lasers is promising for many applications including imaging, sensing, and communications.
The human genome harbours widespread exclusive yin yang haplotypes
Authors: Curtis David , Amos William 
Published: June 2023

AbstractThere have been reports of examples of exclusive yin yang haplotypes, differing at every locus, but there has been no systematic search for them. Unphased whole genome sequence data for 2504 unrelated 1000 Genomes subjects was searched for chains of SNPs having global minor allele frequency (MAF) > =0.1 made up of at least 20 SNPs in complete linkage disequilibrium with each other and with no pair being separated by more than 9 other SNPs. The global distribution of these haplotypes was investigated, along with their ancestral origins and associations with genes and phenotypes. A number of previously unrecognised repeats were noted, flagged by all or most subjects being called as heterozygotes, and these were discarded. There were 5114 exclusive yin yang haplotypes each consisting of on average 34.8 SNPs, each spanning on average 15.7 kb and cumulatively covering 80 Mb. Although for some haplotypes the MAF varied markedly between populations the average global fixation index was similar to that for SNPs elsewhere in the genome and there was no evidence of enrichment for genes or gene ontologies. For all but 92 haplotypes there were partial forms present in the chimpanzee and/or Neanderthal genome, indicating that they had been formed in a gradual process but that intermediate haplotypes were now absent from modern humans. Exclusive yin yang haplotypes cover over 2% of the human genome. The mechanisms accounting for their formation and preservation are unclear. They may serve as useful markers of the dispersal of chromosomal regions through human history.
Modelling genetic stability in engineered cell populations
Authors: Ingram Duncan , Stan Guy-Bart 
Published: June 2023

AbstractPredicting the evolution of engineered cell populations is a highly sought-after goal in biotechnology. While models of evolutionary dynamics are far from new, their application to synthetic systems is scarce where the vast combination of genetic parts and regulatory elements creates a unique challenge. To address this gap, we here-in present a framework that allows one to connect the DNA design of varied genetic devices with mutation spread in a growing cell population. Users can specify the functional parts of their system and the degree of mutation heterogeneity to explore, after which our model generates host-aware transition dynamics between different mutation phenotypes over time. We show how our framework can be used to generate insightful hypotheses across broad applications, from how a device’s components can be tweaked to optimise long-term protein yield and genetic shelf life, to generating new design paradigms for gene regulatory networks that improve their functionality.
Mechanism of small molecule inhibition of Plasmodium falciparum myosin A informs antimalarial drug design
Authors: Moussaoui Dihia , Robblee James P. , Robert-Paganin Julien , Auguin Daniel , Fisher Fabio , Fagnant Patricia M. , Macfarlane Jill E. , Schaletzky Julia , Wehri Eddie , Mueller-Dieckmann Christoph , Baum Jake , Trybus Kathleen M. , Houdusse Anne 
Published: June 2023

AbstractMalaria results in more than 500,000 deaths per year and the causative Plasmodium parasites continue to develop resistance to all known agents, including different antimalarial combinations. The class XIV myosin motor PfMyoA is part of a core macromolecular complex called the glideosome, essential for Plasmodium parasite mobility and therefore an attractive drug target. Here, we characterize the interaction of a small molecule (KNX-002) with PfMyoA. KNX-002 inhibits PfMyoA ATPase activity in vitro and blocks asexual blood stage growth of merozoites, one of three motile Plasmodium life-cycle stages. Combining biochemical assays and X-ray crystallography, we demonstrate that KNX-002 inhibits PfMyoA using a previously undescribed binding mode, sequestering it in a post-rigor state detached from actin. KNX-002 binding prevents efficient ATP hydrolysis and priming of the lever arm, thus inhibiting motor activity. This small-molecule inhibitor of PfMyoA paves the way for the development of alternative antimalarial treatments.
Chemoselectivity change in catalytic hydrogenolysis enabling urea-reduction to formamide/amine over more reactive carbonyl compounds
Authors: Iwasaki Takanori , Tsuge Kazuki , Naito Naoki , Nozaki Kyoko 
Published: June 2023

AbstractThe selective transformation of a less reactive carbonyl moiety in the presence of more reactive ones can realize straightforward and environmentally benign chemical processes. However, such a transformation is highly challenging because the reactivity of carbonyl compounds, one of the most important functionalities in organic chemistry, depends on the substituents on the carbon atom. Herein, we report an Ir catalyst for the selective hydrogenolysis of urea derivatives, which are the least reactive carbonyl compounds, affording formamides and amines. Although formamide, as well as ester, amide, and carbamate substituents, are considered to be more reactive than urea, the proposed Ir catalyst tolerated these carbonyl groups and reacted with urea in a highly chemoselective manner. The proposed chemo- and regioselective hydrogenolysis allows the development of a strategy for the chemical recycling of polyurea resins.
Machine learning optimization of candidate antibody yields highly diverse sub-nanomolar affinity antibody libraries
Authors: Li Lin , Gupta Esther , Spaeth John , Shing Leslie , Jaimes Rafael , Engelhart Emily , Lopez Randolph , Caceres Rajmonda S. , Bepler Tristan , Walsh Matthew E. 
Published: June 2023

AbstractTherapeutic antibodies are an important and rapidly growing drug modality. However, the design and discovery of early-stage antibody therapeutics remain a time and cost-intensive endeavor. Here we present an end-to-end Bayesian, language model-based method for designing large and diverse libraries of high-affinity single-chain variable fragments (scFvs) that are then empirically measured. In a head-to-head comparison with a directed evolution approach, we show that the best scFv generated from our method represents a 28.7-fold improvement in binding over the best scFv from the directed evolution. Additionally, 99% of designed scFvs in our most successful library are improvements over the initial candidate scFv. By comparing a library’s predicted success to actual measurements, we demonstrate our method’s ability to explore tradeoffs between library success and diversity. Results of our work highlight the significant impact machine learning models can have on scFv development. We expect our method to be broadly applicable and provide value to other protein engineering tasks.
Non-volatile electrically programmable integrated photonics with a 5-bit operation
Authors: Chen Rui , Fang Zhuoran , Perez Christopher , Miller Forrest , Kumari Khushboo , Saxena Abhi , Zheng Jiajiu , Geiger Sarah J. , Goodson Kenneth E. , Majumdar Arka 
Published: June 2023

AbstractScalable programmable photonic integrated circuits (PICs) can potentially transform the current state of classical and quantum optical information processing. However, traditional means of programming, including thermo-optic, free carrier dispersion, and Pockels effect result in either large device footprints or high static energy consumptions, significantly limiting their scalability. While chalcogenide-based non-volatile phase-change materials (PCMs) could mitigate these problems thanks to their strong index modulation and zero static power consumption, they often suffer from large absorptive loss, low cyclability, and lack of multilevel operation. Here, we report a wide-bandgap PCM antimony sulfide (Sb2S3)-clad silicon photonic platform simultaneously achieving low loss (<1.0 dB), high extinction ratio (>10 dB), high cyclability (>1600 switching events), and 5-bit operation. These Sb2S3-based devices are programmed via on-chip silicon PIN diode heaters within sub-ms timescale, with a programming energy density of $$\sim 10\,{fJ}/n{m}^{3}$$
~
10

f
J
/
n

m

3

. Remarkably, Sb2S3 is programmed into fine intermediate states by applying multiple identical pulses, providing controllable multilevel operations. Through dynamic pulse control, we achieve 5-bit (32 levels) operations, rendering 0.50 ± 0.16 dB per step. Using this multilevel behavior, we further trim random phase error in a balanced Mach-Zehnder interferometer.
Tunable coupling in magnetic thin film heterostructures with a magnetic phase transition
Authors: Stojak Repa Kristen , Kirby Brian J. , Miller Casey W. 
Published: June 2023

AbstractThe magnetic properties of permalloy-based trilayers of the form Py0.8Cu0.2/Py0.4Cu0.6/Py/IrMn were studied as the spacer layer undergoes a paramagnetic to ferromagnetic phase transition. We find the coupling between the free Py0.8Cu0.2 layer and the exchange bias pinned Py to be strongly temperature-dependent: there is negligible coupling above the Curie temperature of the Py0.4Cu0.6 spacer layer, strong ferromagnetic coupling below that temperature, and a tunable coupling between these extremes. Polarized neutron reflectometry was used to measure the depth profile of the magnetic order in the system, allowing us to correlate the order parameter with the coupling strength. The thickness dependence shows that these are interface effects with an inverse relationship to thickness, and that there is a magnetic proximity effect that enhances the Curie temperature of the spacer layer with characteristic length scale of about 7 nm. As a demonstration of potential functionality of such a system, the structure is shown to spontaneously flip from the antiparallel to parallel magnetic configuration once the spacer layer has developed long-range magnetic order.
Deforestation for oil palm increases microclimate suitability for the development of the disease vector Aedes albopictus
Authors: Saager E. S. , Iwamura T. , Jucker T. , Murray K. A. 
Published: June 2023

AbstractA major trade-off of land-use change is the potential for increased risk of infectious diseases, a.o. through impacting disease vector life-cycles. Evaluating the public health implications of land-use conversions requires spatially detailed modelling linking land-use to vector ecology. Here, we estimate the impact of deforestation for oil palm cultivation on the number of life-cycle completions ofAedes albopictusvia its impact on local microclimates. We apply a recently developed mechanistic phenology model to a fine-scaled (50-m resolution) microclimate dataset that includes daily temperature, rainfall and evaporation. Results of this combined model indicate that the conversion from lowland rainforest to plantations increases suitability forA. albopictusdevelopment by 10.8%, moderated to 4.7% with oil palm growth to maturity. Deforestation followed by typical plantation planting-maturation-clearance-replanting cycles is predicted to create pulses of high development suitability. Our results highlight the need to explore sustainable land-use scenarios that resolve conflicts between agricultural and human health objectives.
Prediction of microseismic events in rock burst mines based on MEA-BP neural network
Authors: Lan Tianwei , Guo Xutao , Zhang Zhijia , Liu Mingwei 
Published: June 2023

AbstractMicroseismic monitoring is an important tool for predicting and preventing rock burst incidents in mines, as it provides precursor information on rock burst. To improve the prediction accuracy of microseismic events in rock burst mines, the working face of the Hegang Junde coal mine is selected as the research object, and the research data will consist of the microseismic monitoring data from this working face over the past 4 years, adopts expert system and temporal energy data mining method to fuse and analyze the mine pressure manifestation regularity and microseismic data, and the "noise reduction" data model is established. By comparing the MEA-BP and traditional BP neural network models, the results of the study show that the prediction accuracy of the MEA-BP neural network model was higher than that of the BP neural network. The absolute and relative errors of the MEA-BP neural network were reduced by 247.24 J and 46.6%, respectively. Combined with the online monitoring data of the KJ550 rock burst, the MEA-BP neural network proved to be more effective in microseismic energy prediction and improved the accuracy of microseismic event prediction in rock burst mines.
Formalin-evoked pain triggers sex-specific behavior and spinal immune response
Authors: Pepino Lucie , Malapert Pascale , Saurin Andrew J. , Moqrich Aziz , Reynders Ana 
Published: June 2023

AbstractMounting evidence shows sex-related differences in the experience of pain with women suffering more from chronic pain than men. Yet, our understanding of the biological basis underlying those differences remains incomplete. Using an adapted model of formalin-induced chemical/inflammatory pain, we report here that in contrast to male mice, females distinctly display two types of nocifensive responses to formalin, distinguishable by the duration of the interphase. Females in proestrus and in metestrus exhibited respectively a short-lasting and a long-lasting interphase, underscoring the influence of the estrus cycle on the duration of the interphase, rather than the transcriptional content of the dorsal horn of the spinal cord (DHSC). Additionally, deep RNA-sequencing of DHSC showed that formalin-evoked pain was accompanied by a male-preponderant enrichment in genes associated with the immune modulation of pain, revealing an unanticipated contribution of neutrophils. Taking advantage of the male-enriched transcript encoding the neutrophil associated protein Lipocalin 2 (Lcn2) and using flow cytometry, we confirmed that formalin triggered the recruitment of LCN2-expressing neutrophils in the pia mater of spinal meninges, preferentially in males. Our data consolidate the contribution of female estrus cycle to pain perception and provide evidence supporting a sex-specific immune regulation of formalin-evoked pain.