bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Clear‐Sky 3D Sub‐Grid Terrain Solar Radiative Effect Parameterization Scheme Based on the Mountain Radiation Theory
Authors: Huang Anning , Gu Chunlei , Zhang Yaocun , Li Weiping , Zhang Lujun , Wu Yang , Zhang Xindan , Cai Shuxin 
Published: July 2022

AbstractTerrains strongly affect the surface solar radiation (SSR) and energy balance, and further greatly modulate the weather and climate in rugged areas. In this study, we have developed a clear‐sky 3‐dimensional sub‐grid terrain solar radiative effect (3DSTSRE) parameterization scheme based on the mountain radiation theory with full consideration of the influences of 3‐dimensional configuration of terrains. Results show that the 3DSTSRE scheme achieves the equivalent effect of the downward SSR flux at the model grids derived from those explicitly calculated at the sub‐grids without reducing the calculating efficiency of numerical models. It performs well at model grids with different horizontal resolutions. The instant downward SSR flux calculated by the 3DSTSRE scheme at 76.8%, 84.8%, 88.7%, 91.6%, 93.0%, and 87.1% model grids with the horizontal resolution of 0.025°, 0.05°, 0.1°, 0.2°, 0.4°, and 0.8° in the areas featured by complex terrains shows relative errors within ±1.0% against those derived from the explicit calculations at sub‐grids, respectively. The normalized mean absolute errors of the instant downward SSR flux calculated by the 3DSTSRE scheme are below 1% (2%) throughout the day and the year for the model grids with resolutions ranging from 0.05° to 0.8° (of 0.025°). Although the performance of 3DSTSRE scheme decreases slightly under the conditions with much lower solar zenith angle and finer model horizontal resolution, the 3DSTSRE scheme developed in current study shows broad application prospects in various numerical models with the advantages of a solid physical foundation, high accuracy, strong portability and flexibility.
Roles of Relative Humidity and Particle Size on Chemical Aging of Tropical Peatland Burning Particles: Potential Influence of Phase State and Implications for Hygroscopic Property
Authors: Chen Jing , Budisulistiorini Sri Hapsari , Itoh Masayuki , Kuwata Mikinori 
Published: July 2022

AbstractPeatland fires in Southeast Asia are an important source of primary organic aerosol (POA). Chemical aging of POA in the atmosphere produces oxygenated POA (OPOA). The OPOA production influences optical and hygroscopic properties, modulating the regional climate. However, the roles of environmental parameters such as relative humidity (RH) on chemical aging of peatland burning particles have rarely been investigated. Utilizing the potential aerosol mass (PAM) reactor, we conducted laboratory experiments for POA aging of particles generated from smoldering combustions of surface peat, fern, and Acacia leaves. The corresponding experiments for secondary organic aerosol formation were also separately conducted. Properties and chemical compositions of the resulting particle were quantified by both the hygroscopic tandem differential mobility analyzer and time‐of‐flight aerosol chemical speciation monitor (ToF‐ACSM). Conversion of peat combustion from POA to OPOA was pronounced when RH in the PAM reactor was higher. Considering that previous electromicroscopic observations demonstrated that peat combustion POA is likely (semi)solid, we postulate that oxidation of fresh peatland burning particles is faster at an elevated RH due to reduced viscosity following hygroscopic growth. Hygroscopicity parameter (κ) of aged POA particles linearly correlated with the mass fraction of OPOA that was quantified by the ToF‐ACSM. The above results highlight the importance of simultaneously measuring the chemical aging and particle phase state of peatland burning POA for quantifying their climatic impacts.
Thermophysical Properties of Lunar Irregular Mare Patches From LRO Diviner Radiometer Data
Authors: Byron B. D. , Elder C. M. , Williams J.‐P. , Ghent R. R. , Gallinger C. L. , Hayne P. O. , Paige D. A. 
Published: July 2022

AbstractIrregular mare patches (IMPs) are enigmatic features in the lunar maria that are characterized as having smooth mounds surrounded by uneven or blocky terrain. The IMPs appear anomalously young compared to surrounding maria, with crater counting methods estimating IMPs to be <100 Myr old and established measures of maturity showing that IMPs are relatively immature. Some studies propose that IMPs are the result of recent basaltic volcanism or episodic outgassing of volatiles, while others propose that the IMPs are of a similar age to the surrounding maria and appear geologically young due to unique physical properties resulting from late‐stage eruption dynamics. Here we present observations from the Lunar Reconnaissance Orbiter Diviner Lunar Radiometer Experiment for eight of the largest IMPs. We find that IMPs are slightly rockier than typical mare surfaces, and the fines components of a number of IMPs have relatively low thermal inertia. The IMP Ina has noticeably lower thermal inertia than the other IMPs. We suggest that the other IMPs (which in many cases are smaller and have ambiguous or gradational contacts with the surrounding maria) could contain similarly low thermal inertia material as Ina, but that it is not fully resolvable with Diviner. We interpret lower‐thermal inertia material as being less‐consolidated or containing fewer small rocks than typical regolith. This would be consistent with elements of a number of proposed formation hypotheses; however, higher spatial resolution is needed for a full comparison of the thermophysical properties of the different IMPs and different terrains within each IMP.
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis
Authors: Green Anna G. , Yoon Chang Ho , Chen Michael L. , Ektefaie Yasha , Fina Mack , Freschi Luca , Gröschel Matthias I. , Kohane Isaac , Beam Andrew , Farhat Maha 
Published: July 2022

AbstractLong diagnostic wait times hinder international efforts to address antibiotic resistance inM. tuberculosis. Pathogen whole genome sequencing, coupled with statistical and machine learning models, offers a promising solution. However, generalizability and clinical adoption have been limited by a lack of interpretability, especially in deep learning methods. Here, we present two deep convolutional neural networks that predict antibiotic resistance phenotypes ofM. tuberculosisisolates: a multi-drug CNN (MD-CNN), that predicts resistance to 13 antibiotics based on 18 genomic loci, with AUCs 82.6-99.5% and higher sensitivity than state-of-the-art methods; and a set of 13 single-drug CNNs (SD-CNN) with AUCs 80.1-97.1% and higher specificity than the previous state-of-the-art. Using saliency methods to evaluate the contribution of input sequence features to the SD-CNN predictions, we identify 18 sites in the genome not previously associated with resistance. The CNN models permit functional variant discovery, biologically meaningful interpretation, and clinical applicability.
Humidity response in Drosophila olfactory sensory neurons requires the mechanosensitive channel TMEM63
Authors: Li Songling , Li Bingxue , Gao Li , Wang Jingwen , Yan Zhiqiang 
Published: July 2022

AbstractBirds, reptiles and insects have the ability to discriminate humidity levels that influence their survival and geographic distribution. Insects are particularly susceptible to humidity changes due to high surface area to volume ratios, but it remains unclear how humidity sensors transduce humidity signals. Here we identified Or42b-expressing olfactory sensory neurons, which are required for moisture attraction in Drosophila. The sensilla housing Or42b neurons show cuticular deformations upon moist air stimuli, indicating a conversion of humidity into mechanical force. Accordingly, we found Or42b neurons directly respond to humidity changes and rely on the mechanosensitive ion channel TMEM63 to mediate humidity sensing (hygrosensation). Expressing human TMEM63B in Tmem63 mutant flies rescued their defective phenotype in moisture attraction, demonstrating functional conservation. Thus, our results reveal a role of Tmem63 in hygrosensation and support the strategy to detect humidity by transforming it into a mechanical stimulus, which is unique in sensory transduction.
Photo-tailored heterocrystalline covalent organic framework membranes for organics separation
Authors: Yuan Jinqiu , You Xinda , Khan Niaz Ali , Li Runlai , Zhang Runnan , Shen Jianliang , Cao Li , Long Mengying , Liu Yanan , Xu Zijian , Wu Hong , Jiang Zhongyi 
Published: July 2022

AbstractOrganics separation for purifying and recycling environment-detrimental solvents is essential to sustainable chemical industries. Covalent organic framework (COF) membranes hold great promise in affording precise and fast organics separation. Nonetheless, how to well coordinate facile processing—high crystalline structure—high separation performance remains a critical issue and a grand challenge. Herein, we propose a concept of heterocrystalline membrane which comprises high-crystalline regions and low-crystalline regions. The heterocrystalline COF membranes are fabricated by a two-step procedure, i.e., dark reaction for the construction of high-crystalline regions followed by photo reaction for the construction of low-crystalline regions, thus linking the high-crystalline regions tightly and flexibly, blocking the defect in high-crystalline regions. Accordingly, the COF membrane exhibits sharp molecular sieving properties with high organic solvent permeance up to 44-times higher than the state-of-the-art membranes.
Endosomal LC3C-pathway selectively targets plasma membrane cargo for autophagic degradation
Authors: Coelho Paula P. , Hesketh Geoffrey G. , Pedersen Annika , Kuzmin Elena , Fortier Anne-Marie N. , Bell Emily S. , Ratcliffe Colin D. H. , Gingras Anne-Claude , Park Morag 
Published: July 2022

AbstractAutophagy selectively targets cargo for degradation, yet mechanistic understanding remains incomplete. The ATG8-family plays key roles in autophagic cargo recruitment. Here by mapping the proximal interactome of ATG8-paralogs, LC3B and LC3C, we uncover a LC3C-Endocytic-Associated-Pathway (LEAP) that selectively recruits plasma-membrane (PM) cargo to autophagosomes. We show that LC3C localizes to peripheral endosomes and engages proteins that traffic between PM, endosomes and autophagosomes, including the SNARE-VAMP3 and ATG9, a transmembrane protein essential for autophagy. We establish that endocytic LC3C binds cargo internalized from the PM, including the Met receptor tyrosine kinase and transferrin receptor, and is necessary for their recruitment into ATG9 vesicles targeted to sites of autophagosome initiation. Structure-function analysis identified that LC3C-endocytic localization and engagement with PM-cargo requires the extended carboxy-tail unique to LC3C, the TBK1 kinase, and TBK1-phosphosites on LC3C. These findings identify LEAP as an unexpected LC3C-dependent pathway, providing new understanding of selective coupling of PM signalling with autophagic degradation.
Unveiling the S=3/2 Kitaev honeycomb spin liquids
Authors: Jin Hui-Ke , Natori W. M. H. , Pollmann F. , Knolle J. 
Published: July 2022

AbstractThe S=3/2 Kitaev honeycomb model (KHM) is a quantum spin liquid (QSL) state coupled to a static Z2 gauge field. Employing an SO(6) Majorana representation of spin3/2’s, we find an exact representation of the conserved plaquette fluxes in terms of static Z2 gauge fields akin to the S=1/2 KHM which enables us to treat the remaining interacting matter fermion sector in a parton mean-field theory. We uncover a ground-state phase diagram consisting of gapped and gapless QSLs. Our parton description is in quantitative agreement with numerical simulations, and is furthermore corroborated by the addition of a [001] single ion anisotropy (SIA) which continuously connects the gapless Dirac QSL of our model with that of the S=1/2 KHM. In the presence of a weak [111] SIA, we discuss an emergent chiral QSL within a perturbation theory.
Adenine oligomer directed synthesis of chiral gold nanoparticles
Authors: Cho Nam Heon , Kim Young Bi , Lee Yoon Young , Im Sang Won , Kim Ryeong Myeong , Kim Jeong Won , Namgung Seok Daniel , Lee Hye-Eun , Kim Hyeohn , Han Jeong Hyun , Chung Hye Won , Lee Yoon Ho , Han Jeong Woo , Nam Ki Tae 
Published: July 2022

AbstractPrecise control of morphology and optical response of 3-dimensional chiral nanoparticles remain as a significant challenge. This work demonstrates chiral gold nanoparticle synthesis using single-stranded oligonucleotide as a chiral shape modifier. The homo-oligonucleotide composed of Adenine nucleobase specifically show a distinct chirality development with a dissymmetric factor up to g ~ 0.04 at visible wavelength, whereas other nucleobases show no development of chirality. The synthesized nanoparticle shows a counter-clockwise rotation of generated chiral arms with approximately 200 nm edge length. The molecular dynamics and density functional theory simulations reveal that Adenine shows the highest enantioselective interaction with Au(321)R/S facet in terms of binding orientation and affinity. This is attributed to the formation of sequence-specific intra-strand hydrogen bonding between nucleobases. We also found that different sequence programming of Adenine-and Cytosine-based oligomers result in chiral gold nanoparticles’ morphological and optical change. These results extend our understanding of the biomolecule-directed synthesis of chiral gold nanoparticles to sequence programmable deoxyribonucleic acid and provides a foundation for programmable synthesis of chiral gold nanoparticles.
Acceptor engineering for NIR-II dyes with high photochemical and biomedical performance
Authors: Ji Aiyan , Lou Hongyue , Qu Chunrong , Lu Wanglong , Hao Yifan , Li Jiafeng , Wu Yuyang , Chang Tonghang , Chen Hao , Cheng Zhen 
Published: July 2022

AbstractIt is highly important and challenging to develop donor-acceptor-donor structured small-molecule second near-infrared window (NIR-II) dyes with excellent properties such as water-solubility and chem/photostability. Here, we discovery an electron acceptor, 6,7-di(thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-g]quinoxaline (TQT) with highest stability in alkaline conditions, compared with conventional NIR-II building block benzobisthiadiazole (BBT) and 6,7-diphenyl-[1,2,5] thiadiazolo[3,4-g]quinoxaline (PTQ). The sulfonated hydrophilic dye, FT-TQT, is further synthesized with 2.13-fold increased quantum yield than its counterpart FT-BBT with BBT as acceptor. FT-TQT complexed with FBS is also prepared and displays a 16-fold increase in fluorescence intensity compared to FT-TQT alone. It demonstrates real-time cerebral and tumor vessel imaging capability with µm-scale resolution. Dynamic monitoring of tumor vascular disruption after drug treatment is achieved by NIR-II fluorescent imaging. Overall, TQT is an efficient electron acceptor for designing innovative NIR-II dyes. The acceptor engineering strategy provides a promising approach to design next generation of NIR-II fluorophores which open new biomedical applications.
Structure induced laminar vortices control anomalous dispersion in porous media
Authors: Bordoloi Ankur Deep , Scheidweiler David , Dentz Marco , Bouabdellaoui Mohammed , Abbarchi Marco , de Anna Pietro 
Published: July 2022

AbstractNatural porous systems, such as soil, membranes, and biological tissues comprise disordered structures characterized by dead-end pores connected to a network of percolating channels. The release and dispersion of particles, solutes, and microorganisms from such features is key for a broad range of environmental and medical applications including soil remediation, filtration and drug delivery. Yet, owing to the stagnant and opaque nature of these disordered systems, the role of microscopic structure and flow on the dispersion of particles and solutes remains poorly understood. Here, we use a microfluidic model system that features a pore structure characterized by distributed dead-ends to determine how particles are transported, retained and dispersed. We observe strong tailing of arrival time distributions at the outlet of the medium characterized by power-law decay with an exponent of 2/3. Using numerical simulations and an analytical model, we link this behavior to particles initially located within dead-end pores, and explain the tailing exponent with a hopping across and rolling along the streamlines of vortices within dead-end pores. We quantify such anomalous dispersal by a stochastic model that predicts the full evolution of arrival times. Our results demonstrate how microscopic flow structures can impact macroscopic particle transport.
Olfactory modulation of barrel cortex activity during active whisking and passive whisker stimulation
Authors: Renard Anthony , Harrell Evan R. , Bathellier Brice 
Published: July 2022

AbstractRodents depend on olfaction and touch to meet many of their fundamental needs. However, the impact of simultaneous olfactory and tactile inputs on sensory representations in the cortex remains elusive. To study these interactions, we recorded large populations of barrel cortex neurons using 2-photon calcium imaging in head-fixed mice during olfactory and tactile stimulation. Here we show that odors bidirectionally alter activity in a small but significant population of barrel cortex neurons through at least two mechanisms, first by enhancing whisking, and second by a central mechanism that persists after whisking is abolished by facial nerve sectioning. Odor responses have little impact on tactile information, and they are sufficient for decoding odor identity, while behavioral parameters like whisking, sniffing, and facial movements are not odor identity-specific. Thus, barrel cortex activity encodes specific olfactory information that is not linked with odor-induced changes in behavior.
Metabolomics-guided discovery of cytochrome P450s involved in pseudotropine-dependent biosynthesis of modified tropane alkaloids
Authors: Sadre Radin , Anthony Thilani M. , Grabar Josh M. , Bedewitz Matthew A. , Jones A. Daniel , Barry Cornelius S. 
Published: July 2022

AbstractPlant alkaloids constitute an important class of bioactive chemicals with applications in medicine and agriculture. However, the knowledge gap of the diversity and biosynthesis of phytoalkaloids prevents systematic advances in biotechnology for engineered production of these high-value compounds. In particular, the identification of cytochrome P450s driving the structural diversity of phytoalkaloids has remained challenging. Here, we use a combination of reverse genetics with discovery metabolomics and multivariate statistical analysis followed by in planta transient assays to investigate alkaloid diversity and functionally characterize two candidate cytochrome P450s genes from Atropa belladonna without a priori knowledge of their functions or information regarding the identities of key pathway intermediates. This approach uncovered a largely unexplored root localized alkaloid sub-network that relies on pseudotropine as precursor. The two cytochrome P450s catalyze N-demethylation and ring-hydroxylation reactions within the early steps in the biosynthesis of diverse N-demethylated modified tropane alkaloids.
A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model
Authors: Yildiz Soner , Mazel-Sanchez Beryl , Bonifacio Joao P. P. , Schmolke Mirco 
Published: July 2022

AbstractIn adult animals, acute viral infections only temporarily alter the composition of both respiratory and intestinal commensal microbiota, potentially due to the intrinsic stability of this microbial ecosystem. In stark contrast, commensal bacterial communities are rather vulnerable to perturbation in infancy. Animal models proved that disruption of a balanced microbiota development e.g., by antibiotics treatment early in life, increases the probability for metabolic disorders in adults. Importantly, infancy is also a phase in life with high incidence of acute infections. We postulated that acute viral infections in early life might pose a similarly severe perturbation and permanently shape microbiota composition with long-term physiological consequences for the adult host. As a proof of concept, we infected infant mice with a sub-lethal dose of influenza A virus. We determined microbiota composition up to early adulthood (63 days) from small intestine by 16S rRNA gene-specific next-generation sequencing. Infected mice underwent long-lasting changes in microbiota composition, associated with increase in fat mass. High-fat-high-glucose diet promoted this effect while co-housing with mock-treated animals overwrote the weight gain. Our data suggest that in the critical phase of infancy even a single silent viral infection could cast a long shadow and cause long-term microbiota perturbations, affecting adult host physiology.
PSHG-TISS: A collection of polarization-resolved second harmonic generation microscopy images of fixed tissues
Authors: Hristu Radu , Stanciu Stefan G. , Dumitru Adrian , Eftimie Lucian G. , Paun Bogdan , Tranca Denis E. , Gheorghita Pavel , Costache Mariana , Stanciu George A. 
Published: July 2022

AbstractSecond harmonic generation (SHG) microscopy is acknowledged as an established imaging technique capable to provide information on the collagen architecture in tissues that is highly valuable for the diagnostics of various pathologies. The polarization-resolved extension of SHG (PSHG) microscopy, together with associated image processing methods, retrieves extensive image sets under different input polarization settings, which are not fully exploited in clinical settings. To facilitate this, we introduce PSHG-TISS, a collection of PSHG images, accompanied by additional computationally generated images which can be used to complement the subjective qualitative analysis of SHG images. These latter have been calculated using the single-axis molecule model for collagen and provide 2D representations of different specific PSHG parameters known to account for the collagen structure and distribution. PSHG-TISS can aid refining existing PSHG image analysis methods, while also supporting the development of novel image processing and analysis methods capable to extract meaningful quantitative data from the raw PSHG image sets. PSHG-TISS can facilitate the breadth and widespread of PSHG applications in tissue analysis and diagnostics.