bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of Synoptic Patterns and Meteorological Factors on Distribution Trends of Ozone in Southeast China During 2015–2020
Authors: Ji Xiaoting , Hong Youwei , Lin Yiling , Xu Ke , Chen Gaojie , Liu Taotao , Xu Lingling , Li Mengren , Fan Xiaolong , Wang Hong , Zhang Hongliang , Chen Yuping , Yang Chen , Lin Ziyi , Chen Jinsheng 
Published: July 2023

AbstractSurface ozone (O3) pollution under global climate change has become one of the top environmental issues. In this study, we focused on the coastal region in Southeast China with relatively low O3 precursor's emissions and complicated synoptic conditions, where the O3 trends and meteorological contributions remain unclear. An increasing trend of O3 concentrations in the cities (0.3–4.6 μg m−3 yr−1) from 2015 to 2020 was observed. Twenty‐three synoptic patterns were clustered based on weather typing method, in which cyclone‐related types and southwesterly type were generally associated with low O3 concentrations, and high O3 levels occurred with anticyclone‐related types. Considering both frequency and intensity of synoptic patterns, reconstructed O3 series captured 46.0%–58.3% of the observed variability. Using Kolmogorov‐Zurbenko filter, an increasing trend of long‐term O3 was found. By implementing the multiple linear regression model between O3 concentrations and meteorological factors, the meteorological contributions to O3 variabilities (44.7%–66.1%) were quantified. The results indicated the meteorological conditions were particularly important in O3 pollution with the reductions of O3 precursor's emissions, among which relative humidity, boundary layer height, solar radiation along with low cloud cover were proved to play important roles. The weakening southwest winds along with more anti‐cyclone systems under climate change could increase surface O3. This study elucidated the crucial meteorological drivers on the O3 variability in relatively clean areas and implied the challenges for local governments to mitigate O3 pollution under global climate change.
Where should siRNAs go: applicable organs for siRNA drugs
Authors: Ahn Insook , Kang Chanhee S. , Han Jinju 
Published: July 2023

AbstractRNA interference mediated by small interfering RNAs (siRNAs) has been exploited for the development of therapeutics. siRNAs can be a powerful therapeutic tool because the working mechanisms of siRNAs are straightforward. siRNAs determine targets based on their sequence and specifically regulate the gene expression of the target gene. However, efficient delivery of siRNAs to the target organ has long been an issue that needs to be solved. Tremendous efforts regarding siRNA delivery have led to significant progress in siRNA drug development, and from 2018 to 2022, a total of five siRNA drugs were approved for the treatment of patients. Although all FDA-approved siRNA drugs target the hepatocytes of the liver, siRNA-based drugs targeting different organs are in clinical trials. In this review, we introduce siRNA drugs in the market and siRNA drug candidates in clinical trials that target cells in multiple organs. The liver, eye, and skin are the preferred organs targeted by siRNAs. Three or more siRNA drug candidates are in phase 2 or 3 clinical trials to suppress gene expression in these preferred organs. On the other hand, the lungs, kidneys, and brain are challenging organs with relatively few clinical trials. We discuss the characteristics of each organ related to the advantages and disadvantages of siRNA drug targeting and strategies to overcome the barriers in delivering siRNAs based on organ-specific siRNA drugs that have progressed to clinical trials.
Emerging roles of tRNA-derived small RNAs in cancer biology
Authors: Lee Saebyeol , Kim Jungeun , Valdmanis Paul N. , Kim Hak Kyun 
Published: July 2023

AbstractTransfer RNAs (tRNAs) play an essential role in mRNA translation by delivering amino acids to growing polypeptide chains. Recent data demonstrate that tRNAs can be cleaved by ribonucleases, and the resultant cleavage products, tRNA-derived small RNAs (tsRNAs), have crucial roles in physiological and pathological conditions. They are classified into more than six types according to their size and cleavage positions. Since the initial discovery of the physiological functions of tsRNAs more than a decade ago, accumulating data have demonstrated that tsRNAs play critical roles in gene regulation and tumorigenesis. These tRNA-derived molecules have various regulatory functions at the transcriptional, post-transcriptional, and translational levels. More than a hundred types of modifications are found on tRNAs, affecting the biogenesis, stability, function, and biochemical properties of tsRNA. Both oncogenic and tumor suppressor functions have been reported for tsRNAs, which play important roles in the development and progression of various cancers. Abnormal expression patterns and modification of tsRNAs are associated with various diseases, including cancer and neurological disorders. In this review, we will describe the biogenesis, versatile gene regulation mechanisms, and modification-mediated regulation mechanisms of tsRNA as well as the expression patterns and potential therapeutic roles of tsRNAs in various cancers.
Gas-assisted microfluidic step-emulsification for generating micron- and submicron-sized droplets
Authors: Huang Biao , Ge Xinjin , Rubinstein Boris Y. , Chen Xianchun , Wang Lu , Xie Huiying , Leshansky Alexander M. , Li Zhenzhen 
Published: July 2023

AbstractMicron- and submicron-sized droplets have extensive applications in biomedical diagnosis and drug delivery. Moreover, accurate high-throughput analysis requires a uniform droplet size distribution and high production rates. Although the previously reported microfluidic coflow step-emulsification method can be used to generate highly monodispersed droplets, the droplet diameter (d) is constrained by the microchannel height (b), $$d\gtrsim 3b$$

d
≳
3
b

, while the production rate is limited by the maximum capillary number of the step-emulsification regime, impeding emulsification of highly viscous liquids. In this paper, we report a novel, gas-assisted coflow step-emulsification method, where air serves as the innermost phase of a precursor hollow-core air/oil/water emulsion. Air gradually diffuses out, producing oil droplets. The size of the hollow-core droplets and the ultrathin oil layer thickness both follow the scaling laws of triphasic step-emulsification. The minimal droplet size attains $$d\approx 1.7b$$

d
≈
1.7
b

, inaccessible in standard all-liquid biphasic step-emulsification. The production rate per single channel is an order-of-magnitude higher than that in the standard all-liquid biphasic step-emulsification and is also superior to alternative emulsification methods. Due to low gas viscosity, the method can also be used to generate micron- and submicron-sized droplets of high-viscosity fluids, while the inert nature of the auxiliary gas offers high versatility.
Roles of macrophages in tumor development: a spatiotemporal perspective
Authors: Bied Mathilde , Ho William W. , Ginhoux Florent , Blériot Camille 
Published: July 2023

AbstractMacrophages are critical regulators of tissue homeostasis but are also abundant in the tumor microenvironment (TME). In both primary tumors and metastases, such tumor-associated macrophages (TAMs) seem to support tumor development. While we know that TAMs are the dominant immune cells in the TME, their vast heterogeneity and associated functions are only just being unraveled. In this review, we outline the various known TAM populations found thus far and delineate their specialized roles associated with the main stages of cancer progression. We discuss how macrophages may prime the premetastatic niche to enable the growth of a metastasis and then how subsequent metastasis-associated macrophages can support secondary tumor growth. Finally, we speculate on the challenges that remain to be overcome in TAM research.
Quantum simulation of exact electron dynamics can be more efficient than classical mean-field methods
Authors: Babbush Ryan , Huggins William J. , Berry Dominic W. , Ung Shu Fay , Zhao Andrew , Reichman David R. , Neven Hartmut , Baczewski Andrew D. , Lee Joonho 
Published: July 2023

AbstractQuantum algorithms for simulating electronic ground states are slower than popular classical mean-field algorithms such as Hartree–Fock and density functional theory but offer higher accuracy. Accordingly, quantum computers have been predominantly regarded as competitors to only the most accurate and costly classical methods for treating electron correlation. However, here we tighten bounds showing that certain first-quantized quantum algorithms enable exact time evolution of electronic systems with exponentially less space and polynomially fewer operations in basis set size than conventional real-time time-dependent Hartree–Fock and density functional theory. Although the need to sample observables in the quantum algorithm reduces the speedup, we show that one can estimate all elements of the k-particle reduced density matrix with a number of samples scaling only polylogarithmically in basis set size. We also introduce a more efficient quantum algorithm for first-quantized mean-field state preparation that is likely cheaper than the cost of time evolution. We conclude that quantum speedup is most pronounced for finite-temperature simulations and suggest several practically important electron dynamics problems with potential quantum advantage.
Fluid-assisted grain size reduction leads to strain localization in oceanic transform faults
Authors: Bickert Manon , Kaczmarek Mary-Alix , Brunelli Daniele , Maia Marcia , Campos Thomas F. C. , Sichel Susanna E. 
Published: July 2023

AbstractOceanic Transform Faults are major plate boundaries representing the most seismogenic part of the mid ocean ridge system. Nonetheless, their structure and deformation mechanisms at depth are largely unknown due to rare exposures of deep sections. Here we study the mineral fabric of deformed mantle peridotites - ultramafic mylonites - collected from the transpressive Atobá ridge, along the northern fault of the St. Paul transform system in the Equatorial Atlantic Ocean. We show that, at pressure and temperature conditions of the lower oceanic lithosphere, the dominant deformation mechanism is fluid-assisted dissolution-precipitation creep. Grain size reduction during deformation is enhanced by dissolution of coarser pyroxene grains in presence of fluid and contextual precipitation of small interstitial ones, leading to strain localization at lower stresses than dislocation creep. This mechanism potentially represents the dominant weakening factor in the oceanic lithosphere and a main driver for the onset and maintenance of oceanic transform faults.
Observation of flat band, Dirac nodal lines and topological surface states in Kagome superconductor CsTi3Bi5
Authors: Yang Jiangang , Yi Xinwei , Zhao Zhen , Xie Yuyang , Miao Taimin , Luo Hailan , Chen Hao , Liang Bo , Zhu Wenpei , Ye Yuhan , You Jing-Yang , Gu Bo , Zhang Shenjin , Zhang Fengfeng , Yang Feng , Wang Zhimin , Peng Qinjun , Mao Hanqing , Liu Guodong , Xu Zuyan , Chen Hui , Yang Haitao , Su Gang , Gao Hongjun , Zhao Lin , Zhou X. J. 
Published: July 2023

AbstractKagome lattices of various transition metals are versatile platforms for achieving anomalous Hall effects, unconventional charge-density wave orders and quantum spin liquid phenomena due to the strong correlations, spin-orbit coupling and/or magnetic interactions involved in such a lattice. Here, we use laser-based angle-resolved photoemission spectroscopy in combination with density functional theory calculations to investigate the electronic structure of the newly discovered kagome superconductor CsTi3Bi5, which is isostructural to the AV3Sb5(A = K, Rb or Cs) kagome superconductor family and possesses a two-dimensional kagome network of titanium. We directly observe a striking flat band derived from the local destructive interference of Bloch wave functions within the kagome lattice. In agreement with calculations, we identify type-II and type-III Dirac nodal lines and their momentum distribution in CsTi3Bi5from the measured electronic structures. In addition, around the Brillouin zone centre,$${{\mathbb{Z}}}_{2}$$Z2nontrivial topological surface states are also observed due to band inversion mediated by strong spin-orbit coupling.
nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes
Authors: Weber Lukas M. , Saha Arkajyoti , Datta Abhirup , Hansen Kasper D. , Hicks Stephanie C. 
Published: July 2023

AbstractFeature selection to identify spatially variable genes or other biologically informative genes is a key step during analyses of spatially-resolved transcriptomics data. Here, we propose nnSVG, a scalable approach to identify spatially variable genes based on nearest-neighbor Gaussian processes. Our method (i) identifies genes that vary in expression continuously across the entire tissue or within a priori defined spatial domains, (ii) uses gene-specific estimates of length scale parameters within the Gaussian process models, and (iii) scales linearly with the number of spatial locations. We demonstrate the performance of our method using experimental data from several technological platforms and simulations. A software implementation is available athttps://bioconductor.org/packages/nnSVG.
Oxidation kinetics and non-Marcusian charge transfer in dimensionally confined semiconductors
Authors: Xu Ning , Shi Li , Pei Xudong , Zhang Weiyang , Chen Jian , Han Zheng , Samorì Paolo , Wang Jinlan , Wang Peng , Shi Yi , Li Songlin 
Published: July 2023

AbstractElectrochemical reactions represent essential processes in fundamental chemistry that foster a wide range of applications. Although most electrochemical reactions in bulk substances can be well described by the classical Marcus-Gerischer charge transfer theory, the realistic reaction character and mechanism in dimensionally confined systems remain unknown. Here, we report the multiparametric survey on the kinetics of lateral photooxidation in structurally identical WS2and MoS2monolayers, where electrochemical oxidation occurs at the atomically thin monolayer edges. The oxidation rate is correlated quantitatively with various crystallographic and environmental parameters, including the density of reactive sites, humidity, temperature, and illumination fluence. In particular, we observe distinctive reaction barriers of 1.4 and 0.9 eV for the two structurally identical semiconductors and uncover an unusual non-Marcusian charge transfer mechanism in these dimensionally confined monolayers due to the limit in reactant supplies. A scenario of band bending is proposed to explain the discrepancy in reaction barriers. These results add important knowledge into the fundamental electrochemical reaction theory in low-dimensional systems.
Molecular conformation of polyelectrolytes inside Layer-by-Layer assembled films
Authors: Gutfreund Philipp , Higy Christophe , Fragneto Giovanna , Tschopp Michel , Felix Olivier , Decher Gero 
Published: July 2023

AbstractAmong all methods available for the preparation of multifunctional nanostructured composite materials with remarkable functional properties, Layer-by-Layer (LbL) assembly is currently one of the most widely used techniques due to its environmental friendliness, its ease of use and its versatility in combining a plethora of available colloids and macromolecules into finely tuned multicomponent architectures with nanometer scale control. Despite the importance of these systems in emerging technologies, their nanoscopic 3D structure, and thus the ability to predict and understand the device performance, is still largely unknown. In this article, we use neutron scattering to determine the average conformation of individual deuterated polyelectrolyte chains inside LbL assembled films. In particular, we determine that in LbL-films composed of poly(sodium 4-styrenesulfonate) (PSS) and poly(allylamine hydrochloride) (PAH) multilayers prepared from 2 M sodium chloride solutions the PSS chains exhibit a flattened coil conformation with an asymmetry factor of around seven. Albeit this highly non-equilibrium state of the polymer chain, its density profiles follow Gaussian distributions occupying roughly the same volume as in the bulk complex.
Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential
Authors: Wang Jing , Pan Yuan-fei , Yang Li-fen , Yang Wei-hong , Lv Kexin , Luo Chu-ming , Wang Juan , Kuang Guo-peng , Wu Wei-chen , Gou Qin-yu , Xin Gen-yang , Li Bo , Luo Huan-le , Chen Shoudeng , Shu Yue-long , Guo Deyin , Gao Zi-Hou , Liang Guodong , Li Jun , Chen Yao-qing , Holmes Edward C. , Feng Yun , Shi Mang 
Published: July 2023

AbstractBats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.
ARIH1 activates STING-mediated T-cell activation and sensitizes tumors to immune checkpoint blockade
Authors: Liu Xiaolan , Cen Xufeng , Wu Ronghai , Chen Ziyan , Xie Yanqi , Wang Fengqi , Shan Bing , Zeng Linghui , Zhou Jichun , Xie Bojian , Cai Yangjun , Huang Jinyan , Liang Yingjiqiong , Wu Youqian , Zhang Chao , Wang Dongrui , Xia Hongguang 
Published: July 2023

AbstractDespite advances in cancer treatment, immune checkpoint blockade (ICB) only achieves complete response in some patients, illustrating the need to identify resistance mechanisms. Using an ICB-insensitive tumor model, here we discover cisplatin enhances the anti-tumor effect of PD-L1 blockade and upregulates the expression of Ariadne RBR E3 ubiquitin-protein ligase 1 (ARIH1) in tumors. Arih1 overexpression promotes cytotoxic T cell infiltration, inhibits tumor growth, and potentiates PD-L1 blockade. ARIH1 mediates ubiquitination and degradation of DNA-PKcs to trigger activation of the STING pathway, which is blocked by the phospho-mimetic mutant T68E/S213D of cGAS protein. Using a high-throughput drug screen, we further identify that ACY738, less cytotoxic than cisplatin, effectively upregulates ARIH1 and activates STING signaling, sensitizing tumors to PD-L1 blockade. Our findings delineate a mechanism that tumors mediate ICB resistance through the loss of ARIH1 and ARIH1-DNA-PKcs-STING signaling and indicate that activating ARIH1 is an effective strategy to improve the efficacy of cancer immunotherapy.
Macrophage-based therapy for intervertebral disc herniation: preclinical proof-of-concept
Authors: Ribeiro-Machado Cláudia , Santos Susana G. , Amaral Inês A. , Caldeira Joana , Pereira Paulo , Barbosa Mário A. , Cunha Carla 
Published: July 2023

AbstractIntervertebral disc (IVD) degeneration and herniation is a leading cause of disability globally and a large unmet clinical need. No efficient non-surgical therapy is available, and there is an urgency for minimally invasive therapies capable of restoring tissue function. IVD spontaneous hernia regression following conservative treatment is a clinically relevant phenomenon that has been linked to an inflammatory response. This study establishes the central role of macrophages in IVD spontaneous hernia regression and provides the first preclinical demonstration of a macrophage-based therapy for IVD herniation. A rat model of IVD herniation was used to test complementary experimental setups: (1) macrophage systemic depletion via intravenous administration of clodronate liposomes (Group CLP2w: depletion between 0 and 2 weeks post-lesion; Group CLP6w: depletion between 2 and 6 weeks post-lesion), and (2) administration of bone marrow-derived macrophages into the herniated IVD, 2 weeks post-lesion (Group Mac6w). Herniated animals without treatment were used as controls. The herniated area was quantified by histology in consecutive proteoglycan/collagen IVD sections at 2 and 6 weeks post-lesion. Clodronate-mediated macrophage systemic depletion was confirmed by flow cytometry and resulted in increased hernia sizes. Bone marrow-derived macrophages were successfully administered into rat IVD hernias resulting in a 44% decrease in hernia size. No relevant systemic immune reaction was identified by flow cytometry, cytokine, or proteomic analysis. Furthermore, a possible mechanism for macrophage-induced hernia regression and tissue repair was unveiled through IL4, IL17a, IL18, LIX, and RANTES increase. This study represents the first preclinical proof-of-concept of macrophage-based immunotherapy for IVD herniation.
Manifestation of depression in speech overlaps with characteristics used to represent and recognize speaker identity
Authors: Dumpala Sri Harsha , Dikaios Katerina , Rodriguez Sebastian , Langley Ross , Rempel Sheri , Uher Rudolf , Oore Sageev 
Published: July 2023

AbstractThe sound of a person’s voice is commonly used to identify the speaker. The sound of speech is also starting to be used to detect medical conditions, such as depression. It is not known whether the manifestations of depression in speech overlap with those used to identify the speaker. In this paper, we test the hypothesis that the representations of personal identity in speech, known as speaker embeddings, improve the detection of depression and estimation of depressive symptoms severity. We further examine whether changes in depression severity interfere with the recognition of speaker’s identity. We extract speaker embeddings from models pre-trained on a large sample of speakers from the general population without information on depression diagnosis. We test these speaker embeddings for severity estimation in independent datasets consisting of clinical interviews (DAIC-WOZ), spontaneous speech (VocalMind), and longitudinal data (VocalMind). We also use the severity estimates to predict presence of depression. Speaker embeddings, combined with established acoustic features (OpenSMILE), predicted severity with root mean square error (RMSE) values of 6.01 and 6.28 in DAIC-WOZ and VocalMind datasets, respectively, lower than acoustic features alone or speaker embeddings alone. When used to detect depression, speaker embeddings showed higher balanced accuracy (BAc) and surpassed previous state-of-the-art performance in depression detection from speech, with BAc values of 66% and 64% in DAIC-WOZ and VocalMind datasets, respectively. Results from a subset of participants with repeated speech samples show that the speaker identification is affected by changes in depression severity. These results suggest that depression overlaps with personal identity in the acoustic space. While speaker embeddings improve depression detection and severity estimation, deterioration or improvement in mood may interfere with speaker verification.