bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glacier‐Derived Particles as a Regional Control on Marine Dissolved Pb Concentrations
Authors: Krause Jana , Zhu Xunchi , Höfer Juan , Achterberg Eric P. , Engel Anja , Meire Lorenz , Stuart‐Lee Alice E. , Hopwood Mark J. 
Published: September 2023

AbstractHigher than expected concentrations of dissolved lead (dPb) have been consistently observed along glaciated coastlines and it is widely hypothesized that there is a net release of dPb from glacier‐derived sediments. Here we further corroborate that dPb concentrations in diverse locations around west Greenland (3.2–252 pM) and the Western Antarctic Peninsula (7.7–107 pM) appear to be generally higher than can be explained by addition of dPb from glacier‐derived freshwater. The distribution of dPb across the salinity gradient is unlike any other commonly studied trace element (e.g., Fe, Co, Ni, Cu, Mn, and Al) implying a dynamic, reversible exchange between dissolved and labile particulate Pb. Incubating a selection of glacier‐derived particles from SW Greenland (Ameralik and Nuup Kangerlua) and Svalbard (Kongsfjorden), with a range of labile particulate Pb (LpPb) content (11–113 nmol g−1), the equivalent of 2–46% LpPb was released as dPb within 24 hr of addition to Atlantic seawater. Over longer time periods, the majority of this dPb was typically readsorbed. Sediment loading was the dominant factor influencing the net release of dPb into seawater, with a pronounced decline in net dPb release efficiency when sediment load increased from 20 to 500 mg L−1. Yet temperature also had some effect with 68 ± 22% higher dPb release at 11°C compared to 4°C. Future regional changes in dPb dynamics may therefore be more sensitive to short‐term suspended sediment dynamics, and potentially temperature changes, than to changing interannual runoff volume.
Enhanced YOLOv5 network-based object detection (BALFilter Reader) promotes PERFECT filter-enabled liquid biopsy of lung cancer from bronchoalveolar lavage fluid (BALF)
Authors: Liu Zheng , Zhang Jixin , Wang Ningyu , Feng Yun’ai , Tang Fei , Li Tingyu , Lv Liping , Li Haichao , Wang Wei , Liu Yaoping 
Published: September 2023

AbstractLiquid biopsy of cancers, detecting tumor-related information from liquid samples, has attracted wide attentions as an emerging technology. Our previously reported large-area PERFECT (Precise-Efficient-Robust-Flexible-Easy-Controllable-Thin) filter has demonstrated competitive sensitivity in recovering rare tumor cells from clinical samples. However, it is time-consuming and easily biased to manually inspect rare target cells among numerous background cells distributed in a large area (Φ ≥ 13 mm). This puts forward an urgent demand for rapid and bias-free inspection. Hereby, this paper implemented deep learning-based object detection for the inspection of rare tumor cells from large-field images of PERFECT filters with hematoxylin-eosin (HE)-stained cells recovered from bronchoalveolar lavage fluid (BALF). CenterNet, EfficientDet, and YOLOv5 were trained and validated with 240 and 60 image blocks containing tumor and/or background cells, respectively. YOLOv5 was selected as the basic network given the highest mAP@0.5 of 92.1%, compared to those of CenterNet and EfficientDet at 85.2% and 91.6%, respectively. Then, tricks including CIoU loss, image flip, mosaic, HSV augmentation and TTA were applied to enhance the performance of the YOLOv5 network, improving mAP@0.5 to 96.2%. This enhanced YOLOv5 network-based object detection, named as BALFilter Reader, was tested and cross-validated on 24 clinical cases. The overall diagnosis performance (~2 min) with sensitivity@66.7% ± 16.7%, specificity@100.0% ± 0.0% and accuracy@75.0% ± 12.5% was superior to that from two experienced pathologists (10–30 min) with sensitivity@61.1%, specificity@16.7% and accuracy@50.0%, with the histopathological result as the gold standard. The AUC of the BALFilter Reader is 0.84 ± 0.08. Moreover, a customized Web was developed for a user-friendly interface and the promotion of wide applications. The current results revealed that the developed BALFilter Reader is a rapid, bias-free and easily accessible AI-enabled tool to promote the transplantation of the BALFilter technique. This work can easily expand to other cytopathological diagnoses and improve the application value of micro/nanotechnology-based liquid biopsy in the era of intelligent pathology.
Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation
Authors: Wang Xia , Teng Ying , Wang Xiaomi , Xu Yongfeng , Li Ran , Sun Yi , Dai Shixiang , Hu Wenbo , Wang Hongzhe , Li Yanning , Fang Yan , Luo Yongming 
Published: September 2023

Abstract
Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS − 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.
Organic cation transporter 2 contributes to SSRI antidepressant efficacy by controlling tryptophan availability in the brain
Authors: Orrico-Sanchez Alejandro , Guiard Bruno P. , Manta Stella , Callebert Jacques , Launay Jean-Marie , Louis Franck , Paccard Antoine , Gruszczynski Carole , Betancur Catalina , Vialou Vincent , Gautron Sophie 
Published: September 2023

AbstractSelective serotonin reuptake inhibitors (SSRI) are common first-line treatments for major depression. However, a significant number of depressed patients do not respond adequately to these pharmacological treatments. In the present preclinical study, we demonstrate that organic cation transporter 2 (OCT2), an atypical monoamine transporter, contributes to the effects of SSRI by regulating the routing of the essential amino acid tryptophan to the brain. Contrarily to wild-type mice, OCT2-invalidated mice failed to respond to prolonged fluoxetine treatment in a chronic depression model induced by corticosterone exposure recapitulating core symptoms of depression, i.e., anhedonia, social withdrawal, anxiety, and memory impairment. After corticosterone and fluoxetine treatment, the levels of tryptophan and its metabolites serotonin and kynurenine were decreased in the brain of OCT2 mutant mice compared to wild-type mice and reciprocally tryptophan and kynurenine levels were increased in mutants’ plasma. OCT2 was detected by immunofluorescence in several structures at the blood-cerebrospinal fluid (CSF) or brain-CSF interface. Tryptophan supplementation during fluoxetine treatment increased brain concentrations of tryptophan and, more discreetly, of 5-HT in wild-type and OCT2 mutant mice. Importantly, tryptophan supplementation improved the sensitivity to fluoxetine treatment of OCT2 mutant mice, impacting chiefly anhedonia and short-term memory. Western blot analysis showed that glycogen synthase kinase-3β (GSK3β) and mammalian/mechanistic target of rapamycin (mTOR) intracellular signaling was impaired in OCT2 mutant mice brain after corticosterone and fluoxetine treatment and, conversely, tryptophan supplementation recruited selectively the mTOR protein complex 2. This study provides the first evidence of the physiological relevance of OCT2-mediated tryptophan transport, and its biological consequences on serotonin homeostasis in the brain and SSRI efficacy.
Formation of binary magnon polaron in a two-dimensional artificial magneto-elastic crystal
Authors: Majumder Sudip , Drobitch J. L. , Bandyopadhyay Supriyo , Barman Anjan 
Published: September 2023

AbstractWe observed strong tripartite magnon-phonon-magnon coupling in a two-dimensional periodic array of magnetostrictive nanomagnets deposited on a piezoelectric substrate, forming a 2D magnetoelastic “crystal”; the coupling occurred between two Kittel-type spin wave (magnon) modes and a (non-Kittel) magnetoelastic spin wave mode caused by a surface acoustic wave (SAW) (phonons). The strongest coupling occurred when the frequencies and wavevectors of the three modes matched, leading to perfect phase matching. We achieved this condition by carefully engineering the frequency of the SAW, the nanomagnet dimensions and the bias magnetic field that determined the frequencies of the two Kittel-type modes. The strong coupling (cooperativity factor exceeding unity) led to the formation of a new quasi-particle, called a binary magnon-polaron, accompanied by nearly complete (~100%) transfer of energy from the magnetoelastic mode to the two Kittel-type modes. This coupling phenomenon exhibited significant anisotropy since the array did not have rotational symmetry in space. The experimental observations were in good agreement with the theoretical simulations.
Reducing risks of antibiotics to crop production requires land system intensification within thresholds
Authors: Zhao Fangkai , Yang Lei , Yen Haw , Feng Qingyu , Li Min , Chen Liding 
Published: September 2023

AbstractLand system intensification has substantially enhanced crop production; however, it has also created soil antibiotic pollution, undermining crop production. Here, we projected soil antibiotic pollution risks to crop production at multiple geographical scales in China and linked them to land system intensification (including arable land expansion and input increase). Our projections suggest that crop production will substantially decrease when the soil antibiotic pollution risk quotient exceeds 8.30–9.98. Land systems explain most of the variability in antibiotic pollution risks (21–66%) across spatial scales. The convex nonlinearities in tradeoffs between antibiotic pollution risk and crop production indicate that vegetable and wheat production have higher thresholds of land system intensification at which the risk–yield tradeoffs will peak than do maize and rice production. Our study suggests that land system intensification below the minimum thresholds at multiple scales is required for acceptable antibiotic pollution risks related to crop yield reduction.
A Lagrangian model for drifting ecosystems reveals heterogeneity-driven enhancement of marine plankton blooms
Authors: Ser-Giacomi Enrico , Martinez-Garcia Ricardo , Dutkiewicz Stephanie , Follows Michael J. 
Published: September 2023

AbstractMarine plankton play a crucial role in carbon storage, global climate, and ecosystem function. Planktonic ecosystems are embedded in patches of water that are continuously moving, stretching, and diluting. These processes drive inhomegeneities on a range of scales, with implications for the integrated ecosystem properties, but are hard to characterize. We present a theoretical framework that accounts for all these aspects; tracking the water patch hosting a drifting ecosystem along with its physical, environmental, and biochemical features. The theory resolves patch dilution and internal physical mixing as a function of oceanic strain and diffusion. Ecological dynamics are parameterized by an idealized nutrient and phytoplankton population and we specifically capture the time evolution of the biochemical spatial variances to represent within-patch heterogeneity. We find that, depending only on the physical processes to which the water patch is subjected, the plankton biomass response to a resource perturbation can vary in size up to six times. This work indicates that we must account for these processes when interpreting and modeling marine ecosystems and provides a framework with which to do so.
Iron oxide nanozymes stabilize stannous fluoride for targeted biofilm killing and synergistic oral disease prevention
Authors: Huang Yue , Liu Yuan , Pandey Nil Kanatha , Shah Shrey , Simon-Soro Aurea , Hsu Jessica C. , Ren Zhi , Xiang Zhenting , Kim Dongyeop , Ito Tatsuro , Oh Min Jun , Buckley Christine , Alawi Faizan , Li Yong , Smeets Paul J. M. , Boyer Sarah , Zhao Xingchen , Joester Derk , Zero Domenick T. , Cormode David P. , Koo Hyun 
Published: September 2023

AbstractDental caries is the most common human disease caused by oral biofilms despite the widespread use of fluoride as the primary anticaries agent. Recently, an FDA-approved iron oxide nanoparticle (ferumoxytol, Fer) has shown to kill and degrade caries-causing biofilms through catalytic activation of hydrogen peroxide. However, Fer cannot interfere with enamel acid demineralization. Here, we show notable synergy when Fer is combined with stannous fluoride (SnF2), markedly inhibiting both biofilm accumulation and enamel damage more effectively than either alone. Unexpectedly, we discover that the stability of SnF2 is enhanced when mixed with Fer in aqueous solutions while increasing catalytic activity of Fer without any additives. Notably, Fer in combination with SnF2 is exceptionally effective in controlling dental caries in vivo, even at four times lower concentrations, without adverse effects on host tissues or oral microbiome. Our results reveal a potent therapeutic synergism using approved agents while providing facile SnF2 stabilization, to prevent a widespread oral disease with reduced fluoride exposure.
Mild replication stress causes premature centriole disengagement via a sub-critical Plk1 activity under the control of ATR-Chk1
Authors: Dwivedi Devashish , Harry Daniela , Meraldi Patrick 
Published: September 2023

AbstractA tight synchrony between the DNA and centrosome cycle is essential for genomic integrity. Centriole disengagement, which licenses centrosomes for duplication, occurs normally during mitotic exit. We recently demonstrated that mild DNA replication stress typically seen in cancer cells causes premature centriole disengagement in untransformed mitotic human cells, leading to transient multipolar spindles that favour chromosome missegregation. How mild replication stress accelerates the centrosome cycle at the molecular level remained, however, unclear. Using ultrastructure expansion microscopy, we show that mild replication stress induces premature centriole disengagement already in G2 via the ATR-Chk1 axis of the DNA damage repair pathway. This results in a sub-critical Plk1 kinase activity that primes the pericentriolar matrix for Separase-dependent disassembly but is insufficient for rapid mitotic entry, causing premature centriole disengagement in G2. We postulate that the differential requirement of Plk1 activity for the DNA and centrosome cycles explains how mild replication stress disrupts the synchrony between both processes and contributes to genomic instability.
Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system
Authors: Zhong Zhaohui , Liu Guanqing , Tang Zhongjie , Xiang Shuyue , Yang Liang , Huang Lan , He Yao , Fan Tingting , Liu Shishi , Zheng Xuelian , Zhang Tao , Qi Yiping , Huang Jian , Zhang Yong 
Published: September 2023

AbstractAmong CRISPR-Cas genome editing systems, Streptococcus pyogenes Cas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probiotic Lactobacillus rhamnosus. We have confirmed the predicted 5’-NGAAA-3’ PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9’s A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.
TMEM135 links peroxisomes to the regulation of brown fat mitochondrial fission and energy homeostasis
Authors: Hu Donghua , Tan Min , Lu Dongliang , Kleiboeker Brian , Liu Xuejing , Park Hongsuk , Kravitz Alexxai V. , Shoghi Kooresh I. , Tseng Yu-Hua , Razani Babak , Ikeda Akihiro , Lodhi Irfan J. 
Published: September 2023

AbstractMitochondrial morphology, which is controlled by mitochondrial fission and fusion, is an important regulator of the thermogenic capacity of brown adipocytes. Adipose-specific peroxisome deficiency impairs thermogenesis by inhibiting cold-induced mitochondrial fission due to decreased mitochondrial membrane content of the peroxisome-derived lipids called plasmalogens. Here, we identify TMEM135 as a critical mediator of the peroxisomal regulation of mitochondrial fission and thermogenesis. Adipose-specific TMEM135 knockout in mice blocks mitochondrial fission, impairs thermogenesis, and increases diet-induced obesity and insulin resistance. Conversely, TMEM135 overexpression promotes mitochondrial division, counteracts obesity and insulin resistance, and rescues thermogenesis in peroxisome-deficient mice. Mechanistically, thermogenic stimuli promote association between peroxisomes and mitochondria and plasmalogen-dependent localization of TMEM135 in mitochondria, where it mediates PKA-dependent phosphorylation and mitochondrial retention of the fission factor Drp1. Together, these results reveal a previously unrecognized inter-organelle communication regulating mitochondrial fission and energy homeostasis and identify TMEM135 as a potential target for therapeutic activation of BAT.
CNOT circuits need little help to implement arbitrary Hadamard-free Clifford transformations they generate
Authors: Maslov Dmitri , Yang Willers 
Published: September 2023

AbstractA Hadamard-free Clifford transformation is a circuit composed of quantum Phase (P), CZ, and CNOT gates. It is known that such a circuit can be written as a three-stage computation, -P-CZ-CNOT-, where each stage consists only of gates of the specified type. In this paper, we focus on the minimization of circuit depth by entangling gates, corresponding to the important time-to-solution metric and the reduction of noise due to decoherence. We consider two popular connectivity maps: Linear Nearest Neighbor (LNN) and all-to-all. First, we show that a Hadamard-free Clifford operation can be implemented over LNN in depth 5n, i.e., in the same depth as the -CNOT- stage alone. This allows us to implement arbitrary Clifford transformation over LNN in depth no more than 7n − 4, improving the best previous upper bound of 9n. Second, we report heuristic evidence that on average a random uniformly distributed Hadamard-free Clifford transformation over n > 6 qubits can be implemented with only a tiny additive overhead over all-to-all connected architecture compared to the best-known depth-optimized implementation of the -CNOT- stage alone. This suggests the reduction of the depth of Clifford circuits from $$2n\,+\,O({\log }^{2}(n))$$

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to $$1.5n\,+\,O({\log }^{2}(n))$$

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over unrestricted architectures.
Oblique stagnation point flow of magnetized Maxwell fluid over a stretchable Riga plate with Cattaneo-Christov heat flux and convective conditions
Authors: Baig Mirza Naveed Jahangeer , Salamat Nadeem , Akhtar Salman , Nadeem Sohail 
Published: September 2023

AbstractThe current work deals with the oblique stagnation point flow phenomenon of a rate-type Maxwell fluid with the significance of the Cattaneo-Christov double diffusion theory. The Cattaneo-Christov theory is illustrated through the modified form of Fourier’s and Fick’s laws. The steady magnetized flow mechanism is observed in two dimensions through a stretchable convective Riga plate. In the mass and heat transfer analysis, the consequences of chemical reactions and thermal radiation are also incorporated. With the contribution of relevant dimensionless quantities, the setup of dimensionless equations is acquired which further takes the form of nonlinear equations. The physical significance of the numerous parameters on different features of the flow phenomenon is graphically exhibited. The interesting physical quantities are computed and numerically evaluated relative to the pertinent parameters. This study reveals that the thermal relaxation time parameter lowers the rate of heat transfer, and the thermal Biot number enhances the rate of heat transport. Moreover, the Deborah number minimizes the flow field of both tangential and axial velocities.
Multi-structural molecular docking (MOD) combined with molecular dynamics reveal the structural requirements of designing broad-spectrum inhibitors of SARS-CoV-2 entry to host cells
Authors: Da Anqi , Wu-Lu Meritxell , Dragelj Jovan , Mroginski Maria Andrea , Ebrahimi Kourosh H. 
Published: September 2023

AbstractNew variants of SARS-CoV-2 that can escape immune response continue to emerge. Consequently, there is an urgent demand to design small molecule therapeutics inhibiting viral entry to host cells to reduce infectivity rate. Despite numerous in silico and in situ studies, the structural requirement of designing viral-entry inhibitors effective against multiple variants of SARS-CoV-2 has yet to be described. Here we systematically screened the binding of various natural products (NPs) to six different SARS-CoV-2 receptor-binding domain (RBD) structures. We demonstrate that Multi-structural Molecular Docking (MOD) combined with molecular dynamics calculations allowed us to predict a vulnerable site of RBD and the structural requirement of ligands binding to this vulnerable site. We expect that our findings lay the foundation for in silico screening and identification of lead molecules to guide drug discovery into designing new broad-spectrum lead molecules to counter the threat of future variants of SARS-CoV-2.