bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and estimation of the intake of fermented foods and their contribution to energy and nutrients among Japanese adults
Authors: Fujihashi Hitomi , Sasaki Satoshi 
Published: February 2024

Abstract

Objective:
Few studies have reported intakes of fermented foods with their clear definitions. This study aimed to identify fermented foods and beverages consumed in Japan based on international definitions and to estimate their intake and contribution to energy and nutrients.

Design:
Data from a 16-d (four non-consecutive days within each season at 3-month intervals) semi-weighted dietary records (DR) were used. To identify ‘entirely fermented foods’ and ‘partially fermented foods’, a literature search on food processing and ingredients was conducted for all foods that appeared in the DR. For ‘partially fermented foods’, only the weight of the fermented food component was included in the estimation of total fermented food intake.

Setting:
Four regions in Japan: Osaka, Nagano, Tottori and Okinawa.

Participants:
Two-hundred forty-two apparently healthy Japanese adults aged 31–81 years.

Results:
Of the 1396 kinds of unique foods that appeared in the DR, 101 were ‘entirely fermented foods’ and 104 were ‘partially fermented foods’. The mean intake of fermented foods was 438 g/d per person (17 % of the total weight). They were mainly derived from beer, coffee, bread and yogurt. The mean contribution of fermented foods to the total energy intake was 18 %. For nutrients, the contribution to total intake was high to Na (46 %), Mg (22 %) and Ca (20 %).

Conclusions:
Fermented foods account for approximately one-fifth of the total weight and energy of dietary intake and are important contributors to some nutrients in Japanese adults.
Characterizing the Complexity of Subduction Zone Flow With an Ensemble of Multiscale Global Convection Models
Authors: Goldberg Samuel L. , Holt Adam F. 
Published: February 2024

AbstractSubduction zones are fundamental features of Earth's mantle convection and plate tectonics, but mantle flow and pressure around slabs are poorly understood because of the lack of direct observational constraints on subsurface flow. To characterize the linkages between slabs and mantle flow, we integrate high‐resolution representations of Earth's lithosphere and slabs into a suite of global mantle convection models to produce physically plausible present‐day flow fields for Earth's mantle. We find that subduction zones containing wide, thick, and long slabs dominate regional mantle flow in the neighboring regions and this flow conforms to patterns predicted by simpler regional subduction models. These subduction zones, such as Kuril‐Japan‐Izu‐Bonin‐Mariana, feature prismatic poloidal flow coupled to the downgoing slab that rotates toward toroidal slab‐parallel flow near the slab edge. However, other subduction zones, such as Sumatra, deviate from this pattern because of the competing influence of other slabs or longer‐wavelength mantle flow, showing that upper mantle flow can link separate subduction zones and how flow at subduction zones is influenced by broader scale mantle flow. We find that the non‐linear dislocation creep reduces the coupling between slab motion and asthenospheric flow and increases the occurrence of non‐ideal flow, in line with inferences derived from seismological constraints on mantle anisotropy.
Identifying Distinct Pre‐Eruptive Composition‐H2O‐Time Trends Using Plagioclase
Authors: Higgins Oliver , Sheldrake Tom 
Published: February 2024

AbstractMacrocrysts (large crystals) in magmas offer a premier record of pre‐eruptive magma storage conditions encoded in their chemistry and texture. Careful study of macrocryst zoning can deconvolve the conditions of crystal growth and the relative time a magma spends in a given physical‐chemical state prior to eruption. Importantly, identifying discrete macrocryst zones requires consideration of both chemistry and texture simultaneously. Here, we employ a novel image segmentation approach to characterize zoning from 2D chemical maps of plagioclase macrocrysts. We apply the method to 15 volcanic eruptions, across three stratigraphic sections, to track statistical differences in crystal zoning through relative time at an arc volcano (Mount Liamuiga, Saint Kitts). Plagioclase from the 15 eruptions are described by 7 unique textural‐chemical zoning populations, which we term “zoning groups,” each of which has a unique An# fingerprint. Two of the studied stratigraphic sections overwhelmingly record low‐An# zoning groups (ZGs), whereas the other section records mostly high‐An# ZGs, suggestive of two distinct storage conditions. Using observations from equilibrium experiments relevant to Saint Kitts bulk magma compositions, we show that differences in melt H2O are the primary drivers of the An# variability. Negative whole rock K2O versus predicted H2O trends are suggestive of ubiquitous H2O‐saturated conditions throughout the middle and upper crust, with a correlation between H2O‐saturated storage pressure (Psat) and eruptive dynamics; magmas stored in the upper‐crust (0.48 ± 0.28–1.08 ± 0.45 kbar) produce larger‐volume, pumice‐rich eruptions compared to magmas stored in the middle crust (3.29 ± 0.87–3.88 ± 1.05 kbar) which generally produce smaller‐volume, centimeter to decimeter‐thick fall deposits.
Archimedean Spiral Distribution of Energetic Particles in Earth's Inner Radiation Belt
Authors: Sun Weiqin , Yang Jian , Wang Wenrui , Cui Jun , Toffoletto Frank , Yue Chao , Gkioulidou Matina , Andrew Gerrard J. 
Published: February 2024

AbstractArchimedean spirals are common in various fields such as biology, engineering, astronomy, and space physics. Here we report the discovery of patterns resembling the general Archimedean spirals in particle distributions in the Earth radiation belt. Our analytic theory and numerical simulations demonstrate that electrons with initially asymmetric spatial distributions form such spirals in the inner magnetosphere, where particles at smaller radial distances move more slowly in angular velocity. These spirals result in time‐varying peaks and valleys in particle fluxes, referred to as “zebra stripes,” which are well consistent with Van Allen Probes measurements. Although the initial asymmetric distribution may be seeded by the electric field in the magnetosphere, the spiral formation does not require them. Furthermore, we show that, due to the same fundamental motion of charged particles in regions dominated by dipole fields, this spiral phenomenon may also appear in the proton distributions, as well as in planetary magnetospheres.
Non‐Linear Seismic Velocity Variations Observed During a Seismic Swarm in the Alto Tiberina Low Angle Normal Fault From Ambient Noise Correlation Measurements
Authors: Mikhael Nour , Poli Piero , Garambois Stéphane 
Published: February 2024

AbstractFrom seismic interferometry, we investigate the strain sensitivity to seismic velocity variations related to a seismic swarm activity that occurred in 2013 along the Alto Tiberina low angle normal fault. We compute daily auto‐correlation functions of ambient noise recorded at seismic stations located in the vicinity of the fault over the course of 10 years. Using the stretching technique, we compute daily velocity variations smoothed over a period of 100 days with a time lapse approach. Through the application of an optimization procedure based on synthetic modeling, we separate the non‐tectonic, thermoelastic and rain induced velocity variations, from the tectonic components. Consequently, we unravel a significant velocity drop of 0.033% coinciding with the swarm occurring at seismogenic depth (3–5 km). Additionally, the time evolution of the velocity changes shows a direct relationship with the strain rate rather than the strain indicating a non‐linear behavior of the crust induced by aseismic slip. The deduced strain sensitivity, exhibiting an order of magnitude comparable to that observed within volcanic settings, confirms this non‐linear behavior and suggests the presence of pressurized fluids at depth.
Protein phosphatase 1 regulatory subunit 15 A promotes translation initiation and induces G2M phase arrest during cuproptosis in cancers
Authors: Liu Chunyu , Chen Liang , Cong Yukun , Cheng Lulin , Shuai Yujun , Lv Fang , Chen Kang , Song Yarong , Xing Yifei 
Published: February 2024

AbstractCopper ions play a crucial role as cofactors for essential enzymes in cellular processes. However, when the intracellular concentration of copper ions exceeds the homeostatic threshold, they become toxic to cells. In our study, we demonstrated that elesclomol, as a carrier of copper ions, caused an upregulation of protein phosphatase 1 regulatory subunit 15 A (PPP1R15A), which plays a role in regulating substrate selectivity of protein phosphatase 1 during cuproptosis. Mechanistically, we investigated that PPP1R15A activated translation initiation by dephosphorylating eukaryotic translation initiation factor 2 subunit alpha at the S51 residue through protein phosphatase 1 and phosphorylating eukaryotic translation initiation factor 4E binding protein 1 at the T70 residue. In addition, PPP1R15A reduced H3K4 methylation by altering the phosphorylation of histone methyltransferases, which led to the silencing of MYC and G2M phase arrest.
Difficulty in chirality recognition for Transformer architectures learning chemical structures from string representations
Authors: Yoshikai Yasuhiro , Mizuno Tadahaya , Nemoto Shumpei , Kusuhara Hiroyuki 
Published: February 2024

AbstractRecent years have seen rapid development of descriptor generation based on representation learning of extremely diverse molecules, especially those that apply natural language processing (NLP) models to SMILES, a literal representation of molecular structure. However, little research has been done on how these models understand chemical structure. To address this black box, we investigated the relationship between the learning progress of SMILES and chemical structure using a representative NLP model, the Transformer. We show that while the Transformer learns partial structures of molecules quickly, it requires extended training to understand overall structures. Consistently, the accuracy of molecular property predictions using descriptors generated from models at different learning steps was similar from the beginning to the end of training. Furthermore, we found that the Transformer requires particularly long training to learn chirality and sometimes stagnates with low performance due to misunderstanding of enantiomers. These findings are expected to deepen the understanding of NLP models in chemistry.
Chiral active particles are sensitive reporters to environmental geometry
Authors: Chan Chung Wing , Wu Daihui , Qiao Kaiyao , Fong Kin Long , Yang Zhiyu , Han Yilong , Zhang Rui 
Published: February 2024

AbstractChiral active particles (CAPs) are self-propelling particles that break time-reversal symmetry by orbiting or spinning, leading to intriguing behaviors. Here, we examined the dynamics of CAPs moving in 2D lattices of disk obstacles through active Brownian dynamics simulations and granular experiments with grass seeds. We find that the effective diffusivity of the CAPs is sensitive to the structure of the obstacle lattice, a feature absent in achiral active particles. We further studied the transport of CAPs in obstacle arrays under an external field and found a reentrant directional locking effect, which can be used to sort CAPs with different activities. Finally, we demonstrated that parallelogram lattices of obstacles without mirror symmetry can separate clockwise and counter-clockwise CAPs. The mechanisms of the above three novel phenomena are qualitatively explained. As such, our work provides a basis for designing chirality-based tools for single-cell diagnosis and separation, and active particle-based environmental sensors.
Mosquito midgut stem cell cellular defense response limits Plasmodium parasite infection
Authors: Barletta Ana-Beatriz F. , Smith Jamie C. , Burkart Emily , Bondarenko Simon , Sharakhov Igor V. , Criscione Frank , O’Brochta David , Barillas-Mury Carolina 
Published: February 2024

AbstractA novel cellular response of midgut progenitors (stem cells and enteroblasts) to Plasmodium berghei infection was investigated in Anopheles stephensi. The presence of developing oocysts triggers proliferation of midgut progenitors that is modulated by the Jak/STAT pathway and is proportional to the number of oocysts on individual midguts. The percentage of parasites in direct contact with enteroblasts increases over time, as progenitors proliferate. Silencing components of key signaling pathways through RNA interference (RNAi) that enhance proliferation of progenitor cells significantly decreased oocyst numbers, while limiting proliferation of progenitors increased oocyst survival. Live imaging revealed that enteroblasts interact directly with oocysts and eliminate them. Midgut progenitors sense the presence of Plasmodium oocysts and mount a cellular defense response that involves extensive proliferation and tissue remodeling, followed by oocysts lysis and phagocytosis of parasite remnants by enteroblasts.
Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria
Authors: Maddamsetti Rohan , Yao Yi , Wang Teng , Gao Junheng , Huang Vincent T. , Hamrick Grayson S. , Son Hye-In , You Lingchong 
Published: February 2024

AbstractHorizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.
Facilitating alkaline hydrogen evolution reaction on the hetero-interfaced Ru/RuO2 through Pt single atoms doping
Authors: Zhu Yiming , Klingenhof Malte , Gao Chenlong , Koketsu Toshinari , Weiser Gregor , Pi Yecan , Liu Shangheng , Sui Lijun , Hou Jingrong , Li Jiayi , Jiang Haomin , Xu Limin , Huang Wei-Hsiang , Pao Chih-Wen , Yang Menghao , Hu Zhiwei , Strasser Peter , Ma Jiwei 
Published: February 2024

AbstractExploring an active and cost-effective electrocatalyst alternative to carbon-supported platinum nanoparticles for alkaline hydrogen evolution reaction (HER) have remained elusive to date. Here, we report a catalyst based on platinum single atoms (SAs) doped into the hetero-interfaced Ru/RuO2 support (referred to as Pt-Ru/RuO2), which features a low HER overpotential, an excellent stability and a distinctly enhanced cost-based activity compared to commercial Pt/C and Ru/C in 1 M KOH. Advanced physico-chemical characterizations disclose that the sluggish water dissociation is accelerated by RuO2 while Pt SAs and the metallic Ru facilitate the subsequent H* combination. Theoretical calculations correlate with the experimental findings. Furthermore, Pt-Ru/RuO2 only requires 1.90 V to reach 1 A cm−2 and delivers a high price activity in the anion exchange membrane water electrolyzer, outperforming the benchmark Pt/C. This research offers a feasible guidance for developing the noble metal-based catalysts with high performance and low cost toward practical H2 production.
Accessing ladder-shape azetidine-fused indoline pentacycles through intermolecular regiodivergent aza-Paternò–Büchi reactions
Authors: Huang Jianjian , Zhou Tai-Ping , Sun Ningning , Yu Huaibin , Yu Xixiang , Liao Rong-Zhen , Yao Weijun , Dai Zhifeng , Wu Guojiao , Zhong Fangrui 
Published: February 2024

AbstractSmall molecules with conformationally rigid, three-dimensional geometry are highly desirable in drug development, toward which a direct, simple-to-complexity synthetic logic is still of considerable challenges. Here, we report intermolecular aza-[2 + 2] photocycloaddition (the aza-Paternò–Büchi reaction) of indole that facilely assembles planar building blocks into ladder-shape azetidine-fused indoline pentacycles with contiguous quaternary carbons, divergent head-to-head/head-to-tail regioselectivity, and absolute exo stereoselectivity. These products exhibit marked three-dimensionality, many of which possess 3D score values distributed in the highest 0.5% region with reference to structures from DrugBank database. Mechanistic studies elucidated the origin of the observed regio- and stereoselectivities, which arise from distortion-controlled C-N coupling scenarios. This study expands the synthetic repertoire of energy transfer catalysis for accessing structurally intriguing architectures with high molecular complexity and underexplored topological chemical space.
A microfluidic platform integrating functional vascularized organoids-on-chip
Authors: Quintard Clément , Tubbs Emily , Jonsson Gustav , Jiao Jie , Wang Jun , Werschler Nicolas , Laporte Camille , Pitaval Amandine , Bah Thierno-Sidy , Pomeranz Gideon , Bissardon Caroline , Kaal Joris , Leopoldi Alexandra , Long David A. , Blandin Pierre , Achard Jean-Luc , Battail Christophe , Hagelkruys Astrid , Navarro Fabrice , Fouillet Yves , Penninger Josef M. , Gidrol Xavier 
Published: February 2024

AbstractThe development of vascular networks in microfluidic chips is crucial for the long-term culture of three-dimensional cell aggregates such as spheroids, organoids, tumoroids, or tissue explants. Despite rapid advancement in microvascular network systems and organoid technologies, vascularizing organoids-on-chips remains a challenge in tissue engineering. Most existing microfluidic devices poorly reflect the complexity of in vivo flows and require complex technical set-ups. Considering these constraints, we develop a platform to establish and monitor the formation of endothelial networks around mesenchymal and pancreatic islet spheroids, as well as blood vessel organoids generated from pluripotent stem cells, cultured for up to 30 days on-chip. We show that these networks establish functional connections with the endothelium-rich spheroids and vascular organoids, as they successfully provide intravascular perfusion to these structures. We find that organoid growth, maturation, and function are enhanced when cultured on-chip using our vascularization method. This microphysiological system represents a viable organ-on-chip model to vascularize diverse biological 3D tissues and sets the stage to establish organoid perfusions using advanced microfluidics.
Cellular hierarchy insights reveal leukemic stem-like cells and early death risk in acute promyelocytic leukemia
Authors: Jin Wen , Dai Yuting , Chen Li , Zhu Honghu , Dong Fangyi , Zhu Hongming , Meng Guoyu , Li Junmin , Chen Saijuan , Chen Zhu , Fang Hai , Wang Kankan 
Published: February 2024

AbstractAcute promyelocytic leukemia (APL) represents a paradigm for targeted differentiation therapy, with a minority of patients experiencing treatment failure and even early death. We here report a comprehensive single-cell analysis of 16 APL patients, uncovering cellular compositions and their impact on all-trans retinoic acid (ATRA) response in vivo and early death. We unveil a cellular differentiation hierarchy within APL blasts, rooted in leukemic stem-like cells. The oncogenic PML/RARα fusion protein exerts branch-specific regulation in the APL trajectory, including stem-like cells. APL cohort analysis establishes an association of leukemic stemness with elevated white blood cell counts and FLT3-ITD mutations. Furthermore, we construct an APL-specific stemness score, which proves effective in assessing early death risk. Finally, we show that ATRA induces differentiation of primitive blasts and patients with early death exhibit distinct stemness-associated transcriptional programs. Our work provides a thorough survey of APL cellular hierarchies, offering insights into cellular dynamics during targeted therapy.
Vascular network-inspired fluidic system (VasFluidics) with spatially functionalizable membranous walls
Authors: Yu Yafeng , Pan Yi , Shen Yanting , Tian Jingxuan , Zhang Ruotong , Guo Wei , Li Chang , Shum Ho Cheung 
Published: February 2024

AbstractIn vascular networks, the transport across different vessel walls regulates chemical compositions in blood over space and time. Replicating such trans-wall transport with spatial heterogeneity can empower synthetic fluidic systems to program fluid compositions spatiotemporally. However, it remains challenging as existing synthetic channel walls are typically impermeable or composed of homogeneous materials without functional heterogeneity. This work presents a vascular network-inspired fluidic system (VasFluidics), which is functionalizable for spatially different trans-wall transport. Facilitated by embedded three-dimensional (3D) printing, elastic, ultrathin, and semipermeable walls self-assemble electrostatically. Physicochemical reactions between fluids and walls are localized to vary the trans-wall molecules among separate regions, for instance, by confining solutions or locally immobilizing enzymes on the outside of channels. Therefore, fluid compositions can be regulated spatiotemporally, for example, to mimic blood changes during glucose absorption and metabolism. Our VasFluidics expands opportunities to replicate biofluid processing in nature, providing an alternative to traditional fluidics.
Integrating hydrogen utilization in CO2 electrolysis with reduced energy loss
Authors: Jiang Xiaoyi , Ke Le , Zhao Kai , Yan Xiaoyu , Wang Hongbo , Cao Xiaojuan , Liu Yuchen , Li Lingjiao , Sun Yifei , Wang Zhiping , Dang Dai , Yan Ning 
Published: February 2024

AbstractElectrochemical carbon dioxide reduction reaction using sustainable energy is a promising approach of synthesizing chemicals and fuels, yet is highly energy intensive. The oxygen evolution reaction is particularly problematic, which is kinetically sluggish and causes anodic carbon loss. In this context, we couple CO2 electrolysis with hydrogen oxidation reaction in a single electrochemical cell. A Ni(OH)2/NiOOH mediator is used to fully suppress the anodic carbon loss and hydrogen oxidation catalyst poisoning by migrated reaction products. This cell is highly flexible in producing either gaseous (CO) or soluble (formate) products with high selectivity (up to 95.3%) and stability (>100 h) at voltages below 0.9 V (50 mA cm−2). Importantly, thanks to the “transferred” oxygen evolution reaction to a water electrolyzer with thermodynamically and kinetically favored reaction conditions, the total polarization loss and energy consumption of our H2-integrated CO2 reduction reaction, including those for hydrogen generation, are reduced up to 22% and 42%, respectively. This work demonstrates the opportunity of combining CO2 electrolysis with the hydrogen economy, paving the way to the possible integration of various emerging energy conversion and storage approaches for improved energy/cost effectiveness.