bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regionally sourced bioaerosols drive high-temperature ice nucleating particles in the Arctic
Authors: Pereira Freitas Gabriel , Adachi Kouji , Conen Franz , Heslin-Rees Dominic , Krejci Radovan , Tobo Yutaka , Yttri Karl Espen , Zieger Paul 
Published: September 2023

AbstractPrimary biological aerosol particles (PBAP) play an important role in the climate system, facilitating the formation of ice within clouds, consequently PBAP may be important in understanding the rapidly changing Arctic. Within this work, we use single-particle fluorescence spectroscopy to identify and quantify PBAP at an Arctic mountain site, with transmission electronic microscopy analysis supporting the presence of PBAP. We find that PBAP concentrations range between 10−3–10−1 L−1 and peak in summer. Evidences suggest that the terrestrial Arctic biosphere is an important regional source of PBAP, given the high correlation to air temperature, surface albedo, surface vegetation and PBAP tracers. PBAP clearly correlate with high-temperature ice nucleating particles (INP) (>-15 °C), of which a high a fraction (>90%) are proteinaceous in summer, implying biological origin. These findings will contribute to an improved understanding of sources and characteristics of Arctic PBAP and their links to INP.
Estrogen receptor beta in astrocytes modulates cognitive function in mid-age female mice
Authors: Itoh Noriko , Itoh Yuichiro , Meyer Cassandra E. , Suen Timothy Takazo , Cortez-Delgado Diego , Rivera Lomeli Michelle , Wendin Sophia , Somepalli Sri Sanjana , Golden Lisa C. , MacKenzie-Graham Allan , Voskuhl Rhonda R. 
Published: September 2023

AbstractMenopause is associated with cognitive deficits and brain atrophy, but the brain region and cell-specific mechanisms are not fully understood. Here, we identify a sex hormone by age interaction whereby loss of ovarian hormones in female mice at midlife, but not young age, induced hippocampal-dependent cognitive impairment, dorsal hippocampal atrophy, and astrocyte and microglia activation with synaptic loss. Selective deletion of estrogen receptor beta (ERβ) in astrocytes, but not neurons, in gonadally intact female mice induced the same brain effects. RNA sequencing and pathway analyses of gene expression in hippocampal astrocytes from midlife female astrocyte-ERβ conditional knock out (cKO) mice revealed Gluconeogenesis I and Glycolysis I as the most differentially expressed pathways. Enolase 1 gene expression was increased in hippocampi from both astrocyte-ERβ cKO female mice at midlife and from postmenopausal women. Gain of function studies showed that ERβ ligand treatment of midlife female mice reversed dorsal hippocampal neuropathology.
A common human MLKL polymorphism confers resistance to negative regulation by phosphorylation
Authors: Garnish Sarah E. , Martin Katherine R. , Kauppi Maria , Jackson Victoria E. , Ambrose Rebecca , Eng Vik Ven , Chiou Shene , Meng Yanxiang , Frank Daniel , Tovey Crutchfield Emma C. , Patel Komal M. , Jacobsen Annette V. , Atkin-Smith Georgia K. , Di Rago Ladina , Doerflinger Marcel , Horne Christopher R. , Hall Cathrine , Young Samuel N. , Cook Matthew , Athanasopoulos Vicki , Vinuesa Carola G. , Lawlor Kate E. , Wicks Ian P. , Ebert Gregor , Ng Ashley P. , Slade Charlotte A. , Pearson Jaclyn S. , Samson André L. , Silke John , Murphy James M. , Hildebrand Joanne M. 
Published: September 2023

AbstractAcross the globe, 2-3% of humans carry the p.Ser132Pro single nucleotide polymorphism in MLKL, the terminal effector protein of the inflammatory form of programmed cell death, necroptosis. Here we show that this substitution confers a gain in necroptotic function in human cells, with more rapid accumulation of activated MLKLS132P in biological membranes and MLKLS132P overriding pharmacological and endogenous inhibition of MLKL. In mouse cells, the equivalent Mlkl S131P mutation confers a gene dosage dependent reduction in sensitivity to TNF-induced necroptosis in both hematopoietic and non-hematopoietic cells, but enhanced sensitivity to IFN-β induced death in non-hematopoietic cells. In vivo, MlklS131P homozygosity reduces the capacity to clear Salmonella from major organs and retards recovery of hematopoietic stem cells. Thus, by dysregulating necroptosis, the S131P substitution impairs the return to homeostasis after systemic challenge. Present day carriers of the MLKL S132P polymorphism may be the key to understanding how MLKL and necroptosis modulate the progression of complex polygenic human disease.
Differential phase-diversity electrooptic modulator for cancellation of fiber dispersion and laser noise
Authors: Ordouie Ehsan , Jiang Tianwei , Zhou Tingyi , A. Juneghani Farzaneh , Eshaghi Mahdi , G. Vazimali Milad , Fathpour Sasan , Jalali Bahram 
Published: September 2023

AbstractBandwidth and noise are fundamental considerations in all communication and signal processing systems. The group-velocity dispersion of optical fibers creates nulls in their frequency response, limiting the bandwidth and hence the temporal response of communication and signal processing systems. Intensity noise is often the dominant optical noise source for semiconductor lasers in data communication. In this paper, we propose and demonstrate a class of electrooptic modulators that is capable of mitigating both of these problems. The modulator, fabricated in thin-film lithium niobate, simultaneously achieves phase diversity and differential operations. The former compensates for the fiber’s dispersion penalty, while the latter overcomes intensity noise and other common mode fluctuations. Applications of the so-called four-phase electrooptic modulator in time-stretch data acquisition and in optical communication are demonstrated.
Acetylation reprograms MITF target selectivity and residence time
Authors: Louphrasitthiphol Pakavarin , Loffreda Alessia , Pogenberg Vivian , Picaud Sarah , Schepsky Alexander , Friedrichsen Hans , Zeng Zhiqiang , Lashgari Anahita , Thomas Benjamin , Patton E. Elizabeth , Wilmanns Matthias , Filippakopoulos Panagis , Lambert Jean-Philippe , Steingrímsson Eiríkur , Mazza Davide , Goding Colin R. 
Published: September 2023

AbstractThe ability of transcription factors to discriminate between different classes of binding sites associated with specific biological functions underpins effective gene regulation in development and homeostasis. How this is achieved is poorly understood. The microphthalmia-associated transcription factor MITF is a lineage-survival oncogene that plays a crucial role in melanocyte development and melanoma. MITF suppresses invasion, reprograms metabolism and promotes both proliferation and differentiation. How MITF distinguishes between differentiation and proliferation-associated targets is unknown. Here we show that compared to many transcription factors MITF exhibits a very long residence time which is reduced by p300/CBP-mediated MITF acetylation at K206. While K206 acetylation also decreases genome-wide MITF DNA-binding affinity, it preferentially directs DNA binding away from differentiation-associated CATGTG motifs toward CACGTG elements. The results reveal an acetylation-mediated switch that suppresses differentiation and provides a mechanistic explanation of why a human K206Q MITF mutation is associated with Waardenburg syndrome.
Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes
Authors: Cerezer Felipe O. , Dambros Cristian S. , Coelho Marco T. P. , Cassemiro Fernanda A. S. , Barreto Elisa , Albert James S. , Wüest Rafael O. , Graham Catherine H. 
Published: September 2023

AbstractSpeciation rates vary greatly among taxa and regions and are shaped by both biotic and abiotic factors. However, the relative importance and interactions of these factors are not well understood. Here we investigate the potential drivers of speciation rates in South American freshwater fishes, the most diverse continental vertebrate fauna, by examining the roles of multiple biotic and abiotic factors. We integrate a dataset on species geographic distribution, phylogenetic, morphological, climatic, and habitat data. We find that Late Neogene-Quaternary speciation events are strongly associated with body-size evolution, particularly in lineages with small body sizes that inhabit higher elevations near the continental periphery. Conversely, the effects of temperature, area, and diversity-dependence, often thought to facilitate speciation, are negligible. By evaluating multiple factors simultaneously, we demonstrate that habitat characteristics associated with elevation, as well as body size evolution, correlate with rapid speciation in South American freshwater fishes. Our study emphasizes the importance of integrative approaches that consider the interplay of biotic and abiotic factors in generating macroecological patterns of species diversity.
Revealing the aging process of solid electrolyte interphase on SiOx anode
Authors: Qian Guoyu , Li Yiwei , Chen Haibiao , Xie Lin , Liu Tongchao , Yang Ni , Song Yongli , Lin Cong , Cheng Junfang , Nakashima Naotoshi , Zhang Meng , Li Zikun , Zhao Wenguang , Yang Xiangjie , Lin Hai , Lu Xia , Yang Luyi , Li Hong , Amine Khalil , Chen Liquan , Pan Feng 
Published: September 2023

AbstractAs one of the most promising alternatives to graphite negative electrodes, silicon oxide (SiOx) has been hindered by its fast capacity fading. Solid electrolyte interphase (SEI) aging on silicon SiOx has been recognized as the most critical yet least understood facet. Herein, leveraging 3D focused ion beam-scanning electron microscopy (FIB-SEM) tomographic imaging, we reveal an exceptionally characteristic SEI microstructure with an incompact inner region and a dense outer region, which overturns the prevailing belief that SEIs are homogeneous structure and reveals the SEI evolution process. Through combining nanoprobe and electron energy loss spectroscopy (EELS), it is also discovered that the electronic conductivity of thick SEI relies on the percolation network within composed of conductive agents (e.g., carbon black particles), which are embedded into the SEI upon its growth. Therefore, the free growth of SEI will gradually attenuate this electron percolation network, thereby causing capacity decay of SiOx. Based on these findings, a proof-of-concept strategy is adopted to mechanically restrict the SEI growth via applying a confining layer on top of the electrode. Through shedding light on the fundamental understanding of SEI aging for SiOx anodes, this work could potentially inspire viable improving strategies in the future.
Deep learning-driven adaptive optics for single-molecule localization microscopy
Authors: Zhang Peiyi , Ma Donghan , Cheng Xi , Tsai Andy P. , Tang Yu , Gao Hao-Cheng , Fang Li , Bi Cheng , Landreth Gary E. , Chubykin Alexander A. , Huang Fang 
Published: September 2023

AbstractThe inhomogeneous refractive indices of biological tissues blur and distort single-molecule emission patterns generating image artifacts and decreasing the achievable resolution of single-molecule localization microscopy (SMLM). Conventional sensorless adaptive optics methods rely on iterative mirror changes and image-quality metrics. However, these metrics result in inconsistent metric responses and thus fundamentally limit their efficacy for aberration correction in tissues. To bypass iterative trial-then-evaluate processes, we developed deep learning-driven adaptive optics for SMLM to allow direct inference of wavefront distortion and near real-time compensation. Our trained deep neural network monitors the individual emission patterns from single-molecule experiments, infers their shared wavefront distortion, feeds the estimates through a dynamic filter and drives a deformable mirror to compensate sample-induced aberrations. We demonstrated that our method simultaneously estimates and compensates 28 wavefront deformation shapes and improves the resolution and fidelity of three-dimensional SMLM through >130-µm-thick brain tissue specimens.
A chromosome-level reference genome of an aromatic medicinal plant Adenosma buchneroides
Authors: Huang Hui , Wang Chen , Pei Shengji , Wang Yuhua 
Published: September 2023

AbstractAdenosma buchneroides Bonati, belonging to the genus Adenosum (Plantaginaceae), is an aromatic medicinal plant and utilized in traditional Chinese medicine. It has been widely used as plant-based repellents to prevent vector-borne diseases. However, the lack of a reference genome limits the study of conservation management and molecular biology of A. buchneroides. Here, we generated a chromosome-level de novo genome assembly of A. buchneroides which is a high-quality chromosome-scale assembly of aromatic medicinal plant in Plantaginaceae. The genome has a total length of 442.84 Mb with scaffold N50 of 27.98 Mb and 95.55% of the genome assigned to 14 chromosomes. BUSCO assessment yielded a completeness score of 97.2%. Furthermore, we predicted 24,367 protein-coding genes, and 95.79% of them was functionally annotated. The chromosome-scale genome of A. buchneroides will be a significant resource for understanding the genetic basis and evolution of active components biosynthesis, which will facilitate further study and exploit of A. buchneroides.
Computer simulation of scavenging by hominins and giant hyenas in the late Early Pleistocene
Authors: Rodríguez Jesús , Hölzchen Ericson , Caso-Alonso Ana Isabel , Berndt Jan Ole , Hertler Christine , Timm Ingo J. , Mateos Ana 
Published: September 2023

AbstractConsumption of animal-sourced food is an important factor in broadening the diet of early hominins, promoting brain and body growth, and increasing behavioural complexity. However, whether early hominins obtained animal food by scavenging or hunting large mammals remains debated. Sabre-toothed felids have been proposed to facilitate the expansion of early Homo out of Africa into Europe 1.4–0.8 Ma by creating a niche for scavengers in Eurasia as the carcasses abandoned by these felids still contained abundant edible resources. In contrast, it has been argued that the niche for a large scavenger was already occupied in Eurasia by the giant hyena, preventing hominins from utilising this resource. This study shows that sabre-toothed felids generated carcasses rich in edible resources and that hominins were capable of competing with giant hyenas for this resource. The simulation experiments showed that maintaining an optimum group size is essential for the success of the hominin scavenging strategy. Early hominins could outcompete giant hyenas only if they could successfully dispute carcasses with them. Thus, in the presence of a strong competitor, passive scavenging is essentially the same as confrontational scavenging.
Crystal structures and molecular dynamics simulations of a humanised antibody fragment at acidic to basic pH
Authors: Tang Jiazhi , Zhang Cheng , Castillo Nuria Codina , Lalaurie Christophe J. , Gao Xin , Dalby Paul A. , Kozielski Frank 
Published: September 2023

AbstractAntibody-fragment (Fab) therapy development has the potential to be accelerated by computational modelling and simulations that predict their target binding, stability, formulation, manufacturability, and the impact of further protein engineering. Such approaches are currently predicated on starting with good crystal structures that closely represent those found under the solution conditions to be simulated. A33 Fab, is an undeveloped immunotherapeutic antibody candidate that was targeted to the human A33 antigen homogeneously expressed in 95% cases of primary and metastatic colorectal cancers. It is now used as a very well characterised testing ground for developing analytics, formulation and protein engineering strategies, and to gain a deeper understanding of mechanisms of destabilisation, representative of the wider therapeutic Fab platform. In this article, we report the structure of A33 Fab in two different crystal forms obtained at acidic and basic pH. The structures overlapped with RMSD of 1.33 Å overall, yet only 0.5 Å and 0.76 Å for the variable- and constant regions alone. While most of the differences were within experimental error, the switch linker between the variable and the constant regions showed some small differences between the two pHs. The two structures then enabled a direct evaluation of the impact of initial crystal structure selection on the outcomes of molecular dynamics simulations under different conditions, and their subsequent use for determining best fit solution structures using previously obtained small-angle x-ray scattering (SAXS) data. The differences in the two structures did not have a major impact on MD simulations regardless of the pH, other than a slight persistence of structure affecting the solvent accessibility of one of the predicted APR regions of A33 Fab. Interestingly, despite being obtained at pH 4 and pH 9, the two crystal structures were more similar to the SAXS solution structures obtained at pH 7, than to those at pH 4 or pH 9. Furthermore, the P65 crystal structure from pH 4 was also a better representation of the solution structures at any other pH, than was the P1 structure obtained at pH 9. Thus, while obtained at different pH, the two crystal structures may represent highly (P65) and lesser (P1) populated species that both exist at pH 7 in solution. These results now lay the foundation for confident MD simulations of A33 Fab that rationalise or predict behaviours in a range of conditions.
Fibroblast growth factors induce hepatic tumorigenesis post radiofrequency ablation
Authors: Markezana Aurelia , Paldor Mor , Liao Haixing , Ahmed Muneeb , Zorde-Khvalevsky Elina , Rozenblum Nir , Stechele Matthias , Salvermoser Lukas , Laville Flinn , Goldmann Salome , Rosenberg Nofar , Andrasina Tomas , Ricke Jens , Galun Eithan , Goldberg Shraga Nahum 
Published: September 2023

AbstractImage-guided radiofrequency ablation (RFA) is used to treat focal tumors in the liver and other organs. Despite potential advantages over surgery, hepatic RFA can promote local and distant tumor growth by activating pro-tumorigenic growth factor and cytokines. Thus, strategies to identify and suppress pro-oncogenic effects of RFA are urgently required to further improve the therapeutic effect. Here, the proliferative effect of plasma of Hepatocellular carcinoma or colorectal carcinoma patients 90 min post-RFA was tested on HCC cell lines, demonstrating significant cellular proliferation compared to baseline plasma. Multiplex ELISA screening demonstrated increased plasma pro-tumorigenic growth factors and cytokines including the FGF protein family which uniquely and selectively activated HepG2. Primary mouse and immortalized human hepatocytes were then subjected to moderate hyperthermia in-vitro, mimicking thermal stress induced during ablation in the peri-ablational normal tissue. Resultant culture medium induced proliferation of multiple cancer cell lines. Subsequent non-biased protein array revealed that these hepatocytes subjected to moderate hyperthermia also excrete a similar wide spectrum of growth factors. Recombinant FGF-2 activated multiple cell lines. FGFR inhibitor significantly reduced liver tumor load post-RFA in MDR2-KO inflammation-induced HCC mouse model. Thus, Liver RFA can induce tumorigenesis via the FGF signaling pathway, and its inhibition suppresses HCC development.
An additive manufacturing approach based on electrohydrodynamic printing to fabricate P3HT:PCBM thin films
Authors: Esa Zulfikre , Nauman Malik Muhammad , Jin Lei , Khalid Muhammad Usman , Hj Zaini Juliana , Iqbal Asif , Ali Kamran , Aïssa Brahim , Rosei Federico 
Published: September 2023

AbstractAdditive manufacturing (AM) enables the production of high value and high performance components with applications from aerospace to biomedical fields. We report here on the fabrication of poly(3-hexylthiophene): phenyl-C61-butyric acid methyl ester (P3HT:PCBM) thin films through the electrohydrodynamic atomization (EHDA) process and its integration as absorber layer for organic solar cells. Prior to the film fabrication, the optimization of the process was carried out by developing the operating envelope for the P3HT:PCBM ink to determine the optimal flow rate and the appropriate applied voltage to achieve a stable-cone deposition mode. The EHDA printed thin-film’s topography, morphology and optical properties were systematically analyzed. The root-mean-square roughness was found to vary significantly with the annealing temperature and the flow rate and ranged from 1.938 to 3.345 nm. The estimated film mass and thickness were found between 3.235 and 23.471 mg and 597.5 nm to 1.60 µm, respectively. The films exhibited a broad visible absorption spectrum ranging from ~ 340 to ~ 600 nm, with a maximum peak λmax located at ~ 500 nm. As the annealing temperature and the flow rate were increased, discernible alterations in the PCBM clusters were consequently observed in the blends of the film and the size of the PCBM clusters has decreased by 3% while the distance between them was highly reduced by as much as 82%.
Research on land cover classification of multi-source remote sensing data based on improved U-net network
Authors: Zhang Guanjin , Roslan Siti Nur Aliaa binti , Wang Ci , Quan Ling 
Published: September 2023

AbstractIn recent years, remote sensing images of various types have found widespread applications in resource exploration, environmental protection, and land cover classification. However, relying solely on a single optical or synthetic aperture radar (SAR) image as the data source for land cover classification studies may not suffice to achieve the desired accuracy in ground information monitoring. One widely employed neural network for remote sensing image land cover classification is the U-Net network, which is a classical semantic segmentation network. Nonetheless, the U-Net network has limitations such as poor classification accuracy, misclassification and omission of small-area terrains, and a large number of network parameters. To address these challenges, this research paper proposes an improved approach that combines both optical and SAR images in bands for land cover classification and enhances the U-Net network. The approach incorporates several modifications to the network architecture. Firstly, the encoder-decoder framework serves as the backbone terrain-extraction network. Additionally, a convolutional block attention mechanism is introduced in the terrain extraction stage. Instead of pooling layers, convolutions with a step size of 2 are utilized, and the Leaky ReLU function is employed as the network's activation function. This design offers several advantages: it enhances the network's ability to capture terrain characteristics from both spatial and channel dimensions, resolves the loss of terrain map information while reducing network parameters, and ensures non-zero gradients during the training process. The effectiveness of the proposed method is evaluated through land cover classification experiments conducted on optical, SAR, and combined optical and SAR datasets. The results demonstrate that our method achieves classification accuracies of 0.8905, 0.8609, and 0.908 on the three datasets, respectively, with corresponding mIoU values of 0.8104, 0.7804, and 0.8667. Compared to the traditional U-Net network, our method exhibits improvements in both classification accuracy and mIoU to a certain extent.