bluuebunny/crossref_metadata_2025_split huggingface dataset:
USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication
Authors: Mackay Hannah L. , Stone Helen R. , Ronson George E. , Ellis Katherine , Lanz Alexander , Aghabi Yara , Walker Alexandra K. , Starowicz Katarzyna , Garvin Alexander J. , Van Eijk Patrick , Koestler Stefan A. , Anthony Elizabeth J. , Piberger Ann Liza , Chauhan Anoop S. , Conway-Thomas Poppy , Vaitsiankova Alina , Vijayendran Sobana , Beesley James F. , Petermann Eva , Brown Eric J. , Densham Ruth M. , Reed Simon H. , Dobbs Felix , Saponaro Marco , Morris Joanna R. 
Published: September 2024

AbstractMammalian DNA replication relies on various DNA helicase and nuclease activities to ensure accurate genetic duplication, but how different helicase and nuclease activities are properly directed remains unclear. Here, we identify the ubiquitin-specific protease, USP50, as a chromatin-associated protein required to promote ongoing replication, fork restart, telomere maintenance, cellular survival following hydroxyurea or pyridostatin treatment, and suppression of DNA breaks near GC-rich sequences. We find that USP50 supports proper WRN-FEN1 localisation at or near stalled replication forks. Nascent DNA in cells lacking USP50 shows increased association of the DNA2 nuclease and RECQL4 and RECQL5 helicases and replication defects in cells lacking USP50, or FEN1 are driven by these proteins. Consequently, suppression of DNA2 or RECQL4/5 improves USP50-depleted cell resistance to agents inducing replicative stress and restores telomere stability. These data define an unexpected regulatory protein that promotes the balance of helicase and nuclease use at ongoing and stalled replication forks.
Gesture recognition with Brownian reservoir computing using geometrically confined skyrmion dynamics
Authors: Beneke Grischa , Winkler Thomas Brian , Raab Klaus , Brems Maarten A. , Kammerbauer Fabian , Gerhards Pascal , Knobloch Klaus , Krishnia Sachin , Mentink Johan H. , Kläui Mathias 
Published: September 2024

AbstractPhysical reservoir computing leverages the dynamical properties of complex physical systems to process information efficiently, significantly reducing training efforts and energy consumption. Magnetic skyrmions, topological spin textures, are promising candidates for reservoir computing systems due to their enhanced stability, non-linear interactions and low-power manipulation. Traditional spin-based reservoir computing has been limited to quasi-static detection or real-world data must be rescaled to the intrinsic timescale of the reservoir. We address this challenge by time-multiplexed skyrmion reservoir computing, that allows for aligning the reservoir’s intrinsic timescales to real-world temporal patterns. Using millisecond-scale hand gestures recorded with Range-Doppler radar, we feed voltage excitations directly into our device and detect the skyrmion trajectory evolution. This method scales down to the nanometer level and demonstrates competitive or superior performance compared to energy-intensive software-based neural networks. Our hardware approach’s key advantage is its ability to integrate sensor data in real-time without temporal rescaling, enabling numerous applications.
Erythropoietin regulates energy metabolism through EPO-EpoR-RUNX1 axis
Authors: Yin Weiqin , Rajvanshi Praveen Kumar , Rogers Heather M. , Yoshida Teruhiko , Kopp Jeffrey B. , An Xiuli , Gassmann Max , Noguchi Constance T. 
Published: September 2024

AbstractErythropoietin (EPO) plays a key role in energy metabolism, with EPO receptor (EpoR) expression in white adipose tissue (WAT) mediating its metabolic activity. Here, we show that male mice lacking EpoR in adipose tissue exhibit increased fat mass and susceptibility to diet-induced obesity. Our findings indicate that EpoR is present in WAT, brown adipose tissue, and skeletal muscle. Elevated EPO in male mice improves glucose tolerance and insulin sensitivity while reducing expression of lipogenic-associated genes in WAT, which is linked to an increase in transcription factor RUNX1 that directly inhibits lipogenic genes expression. EPO treatment in wild-type male mice decreases fat mass and lipogenic gene expression and increase in RUNX1 protein in adipose tissue which is not observed in adipose tissue EpoR ablation mice. EPO treatment decreases WAT ubiquitin ligase FBXW7 expression and increases RUNX1 stability, providing evidence that EPO regulates energy metabolism in male mice through the EPO-EpoR-RUNX1 axis.
Extending the defect tolerance of halide perovskite nanocrystals to hot carrier cooling dynamics
Authors: Ye Junzhi , Mondal Navendu , Carwithen Ben P. , Zhang Yunwei , Dai Linjie , Fan Xiang-Bing , Mao Jian , Cui Zhiqiang , Ghosh Pratyush , Otero‐Martínez Clara , van Turnhout Lars , Huang Yi-Teng , Yu Zhongzheng , Chen Ziming , Greenham Neil C. , Stranks Samuel D. , Polavarapu Lakshminarayana , Bakulin Artem , Rao Akshay , Hoye Robert L. Z. 
Published: September 2024

AbstractDefect tolerance is a critical enabling factor for efficient lead-halide perovskite materials, but the current understanding is primarily on band-edge (cold) carriers, with significant debate over whether hot carriers can also exhibit defect tolerance. Here, this important gap in the field is addressed by investigating how intentionally-introduced traps affect hot carrier relaxation in CsPbX3 nanocrystals (X = Br, I, or mixture). Using femtosecond interband and intraband spectroscopy, along with energy-dependent photoluminescence measurements and kinetic modelling, it is found that hot carriers are not universally defect tolerant in CsPbX3, but are strongly correlated to the defect tolerance of cold carriers, requiring shallow traps to be present (as in CsPbI3). It is found that hot carriers are directly captured by traps, instead of going through an intermediate cold carrier, and deeper traps cause faster hot carrier cooling, reducing the effects of the hot phonon bottleneck and Auger reheating. This work provides important insights into how defects influence hot carriers, which will be important for designing materials for hot carrier solar cells, multiexciton generation, and optical gain media.
Post-transcriptional reprogramming by thousands of mRNA untranslated regions in trypanosomes
Authors: Trenaman Anna , Tinti Michele , Wall Richard J. , Horn David 
Published: September 2024

AbstractAlthough genome-wide polycistronic transcription places major emphasis on post-transcriptional controls in trypanosomatids, messenger RNA cis-regulatory untranslated regions (UTRs) have remained largely uncharacterised. Here, we describe a genome-scale massive parallel reporter assay coupled with 3’-UTR-seq profiling in the African trypanosome and identify thousands of regulatory UTRs. Increased translation efficiency was associated with dosage of adenine-rich poly-purine tracts (pPuTs). An independent assessment of native UTRs using machine learning based predictions confirmed the robust correspondence between pPuTs and positive control, as did an assessment of synthetic UTRs. Those 3’-UTRs associated with upregulated expression in bloodstream-stage cells were also enriched in uracil-rich poly-pyrimidine tracts, suggesting a mechanism for developmental activation through pPuT ‘unmasking’. Thus, we describe a cis-regulatory UTR sequence ‘code’ that underpins gene expression control in the context of a constitutively transcribed genome. We conclude that thousands of UTRs post-transcriptionally reprogram gene expression profiles in trypanosomes.
Characterizing the structural complexity of the Earth’s forests with spaceborne lidar
Authors: de Conto Tiago , Armston John , Dubayah Ralph 
Published: September 2024

AbstractForest structural complexity is a key element of ecosystem functioning, impacting light environments, nutrient cycling, biodiversity, and habitat quality. Addressing the need for a comprehensive global assessment of actual forest structural complexity, we derive a near-global map of 3D canopy complexity using data from the GEDI spaceborne lidar mission. These data show that tropical forests harbor most of the high complexity observations, while less than 20% of temperate forests reached median levels of tropical complexity. Structural complexity in tropical forests is more strongly related to canopy attributes from lower and middle waveform layers, whereas in temperate forests upper and middle layers are more influential. Globally, forests exhibit robust scaling relationships between complexity and canopy height, but these vary geographically and by biome. Our results offer insights into the spatial distribution of forest structural complexity and emphasize the importance of considering biome-specific and fine-scale variations for ecological research and management applications. The GEDI Waveform Structural Complexity Index data product, derived from our analyses, provides researchers and conservationists with a single, easily interpretable metric by combining various aspects of canopy structure.
Neuroanatomical changes observed over the course of a human pregnancy
Authors: Pritschet Laura , Taylor Caitlin M. , Cossio Daniela , Faskowitz Joshua , Santander Tyler , Handwerker Daniel A. , Grotzinger Hannah , Layher Evan , Chrastil Elizabeth R. , Jacobs Emily G. 
Published: September 2024

AbstractPregnancy is a period of profound hormonal and physiological changes experienced by millions of women annually, yet the neural changes unfolding in the maternal brain throughout gestation are not well studied in humans. Leveraging precision imaging, we mapped neuroanatomical changes in an individual from preconception through 2 years postpartum. Pronounced decreases in gray matter volume and cortical thickness were evident across the brain, standing in contrast to increases in white matter microstructural integrity, ventricle volume and cerebrospinal fluid, with few regions untouched by the transition to motherhood. This dataset serves as a comprehensive map of the human brain across gestation, providing an open-access resource for the brain imaging community to further explore and understand the maternal brain.
Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses
Authors: Steindorff Andrei S. , Aguilar-Pontes Maria Victoria , Robinson Aaron J. , Andreopoulos Bill , LaButti Kurt , Kuo Alan , Mondo Stephen , Riley Robert , Otillar Robert , Haridas Sajeet , Lipzen Anna , Grimwood Jane , Schmutz Jeremy , Clum Alicia , Reid Ian D. , Moisan Marie-Claude , Butler Gregory , Nguyen Thi Truc Minh , Dewar Ken , Conant Gavin , Drula Elodie , Henrissat Bernard , Hansel Colleen , Singer Steven , Hutchinson Miriam I. , de Vries Ronald P. , Natvig Donald O. , Powell Amy J. , Tsang Adrian , Grigoriev Igor V. 
Published: September 2024

AbstractThermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.
ER-phagy restrains inflammatory responses through its receptor UBAC2
Authors: He Xing , He Haowei , Hou Zitong , Wang Zheyu , Shi Qinglin , Zhou Tao , Wu Yaoxing , Qin Yunfei , Wang Jun , Cai Zhe , Cui Jun , Jin Shouheng 
Published: September 2024

AbstractER-phagy, a selective form of autophagic degradation of endoplasmic reticulum (ER) fragments, plays an essential role in governing ER homeostasis. Dysregulation of ER-phagy is associated with the unfolded protein response (UPR), which is a major clue for evoking inflammatory diseases. However, the molecular mechanism underpinning the connection between ER-phagy and disease remains poorly defined. Here, we identified ubiquitin-associated domain-containing protein 2 (UBAC2) as a receptor for ER-phagy, while at the same time being a negative regulator of inflammatory responses. UBAC2 harbors a canonical LC3-interacting region (LIR) in its cytoplasmic domain, which binds to autophagosomal GABARAP. Upon ER-stress or autophagy activation, microtubule affinity-regulating kinase 2 (MARK2) phosphorylates UBAC2 at serine (S) 223, promoting its dimerization. Dimerized UBAC2 interacts more strongly with GABARAP, thus facilitating selective degradation of the ER. Moreover, by affecting ER-phagy, UBAC2 restrains inflammatory responses and acute ulcerative colitis (UC) in mice. Our findings indicate that ER-phagy directed by a MARK2-UBAC2 axis may provide targets for the treatment of inflammatory disease.
Non-cell-autonomous regulation of germline proteostasis by insulin/IGF-1 signaling-induced dietary peptide uptake via PEPT-1
Authors: Muhammad Tahir , Edwards Stacey L , Morphis Allison C , Johnson Mary V , Oliveira Vitor De , Chamera Tomasz , Liu Siyan , Nguyen Ngoc Gia Tuong , Li Jian 
Published: September 2024

AbstractGametogenesis involves active protein synthesis and is proposed to rely on proteostasis. Our previous work in C. elegans indicates that germline development requires coordinated activities of insulin/IGF-1 signaling (IIS) and HSF-1, the central regulator of the heat shock response. However, the downstream mechanisms were not identified. Here, we show that depletion of HSF-1 from germ cells impairs chaperone gene expression, causing protein degradation and aggregation and, consequently, reduced fecundity and gamete quality. Conversely, reduced IIS confers germ cell resilience to HSF-1 depletion-induced protein folding defects and various proteotoxic stresses. Surprisingly, this effect was not mediated by an enhanced stress response, which underlies longevity in low IIS conditions, but by reduced ribosome biogenesis and translation rate. We found that IIS activates the expression of intestinal peptide transporter PEPT-1 by alleviating its repression by FOXO/DAF-16, allowing dietary proteins to be efficiently incorporated into an amino acid pool that fuels germline protein synthesis. Our data suggest this non-cell-autonomous pathway is critical for proteostasis regulation during gametogenesis.
RNF144B negatively regulates antiviral immunity by targeting MDA5 for autophagic degradation
Authors: Li Guoxiu , Zhang Jing , Zhao Zhixun , Wang Jian , Li Jiaoyang , Xu Weihong , Cui Zhanding , Sun Pu , Yuan Hong , Wang Tao , Li Kun , Bai Xingwen , Ma Xueqing , Li Pinghua , Fu Yuanfang , Cao Yimei , Bao Huifang , Li Dong , Liu Zaixin , Zhu Ning , Tang Lijie , Lu Zengjun 
Published: September 2024

AbstractAs a RIG-I-like receptor, MDA5 plays a critical role in antiviral innate immunity by acting as a cytoplasmic double-stranded RNA sensor capable of initiating type I interferon pathways. Here, we show that RNF144B specifically interacts with MDA5 and promotes K27/K33-linked polyubiquitination of MDA5 at lysine 23 and lysine 43, which promotes autophagic degradation of MDA5 by p62. Rnf144b deficiency greatly promotes IFN production and inhibits EMCV replication in vivo. Importantly, Rnf144b−/− mice has a significantly higher overall survival rate than wild-type mice upon EMCV infection. Collectively, our results identify RNF144B as a negative regulator of innate antiviral response by targeting CARDs of MDA5 and mediating autophagic degradation of MDA5.
Long-stable lithium metal batteries with a high-performance dual-salt solid polymer electrolyte
Authors: Gan Ling , Liang Yufeng , Feng Tingting , Li Huilan , Wu Mengqiang 
Published: September 2024

A high-performance dual-salt solid polymer electrolyte, consisting of cross-linked NPGDA-VEC copolymer interpenetrated in a PVDF-HFP nanofiber matrix, with LiTFSI and LiBOB as Li+ sources, was prepared for lithium metal battery applications.
The development of a low-temperature terahertz scanning tunneling microscope based on a cryogen-free scheme
Authors: Zhang Huaiyu , Tian Dacheng , Zhan Yang , Liu Zijia , Ma Chen , Zhang Yuwu , Hu Jianwei , He Xiaoyue , Feng Baojie , Zhang Yiqi , Chen Lan , Cheng Peng , Wu Kehui 
Published: September 2024

We have developed a cryogen-free, low-temperature terahertz scanning tunneling microscope (THz-STM). This system utilizes a continuous-flow cryogen-free cooler to achieve low temperatures of ∼25 K. Meanwhile, an ultra-small ultra-high vacuum chamber results in the reduction of the distance from sample to viewport to only 4 cm. NA = 0.6 can be achieved while placing the entire optical component, including a large parabolic mirror, outside the vacuum chamber. Thus, the convenience of optical coupling is much improved without compromising the performance of STM. Based on this, we introduced THz pulses into the tunnel junction and constructed the THz-STM, achieving atomic-level spatial resolution in THz-driven current imaging and sub-picosecond (sub-ps) time resolution in autocorrelation signals during pump–probe measurements. Experimental data from various representative samples are presented to showcase the performance of the instrument, establishing it as an ideal platform for studying non-equilibrium dynamic processes at nanoscale.
High temperature setup for measurement of Hall coefficient and electrical conductivity of thermoelectric materials
Authors: Agrawal B. , Choudhary S. , Sahu P. K. , Dasgupta T. 
Published: September 2024

An experimental setup has been developed for the simultaneous measurement of the Hall coefficient (RH) and electrical conductivity (σ) of thermoelectric (TE) specimens in the temperature range of 300–700 K. The van der Pauw geometry is utilized for the RH and σ measurements. The sample holder geometry has been designed for diverse TE specimen dimensions and easy sample mounting. A special feature of the holder geometry is that the same sample can be used for other relevant thermoelectric measurements such as the Seebeck coefficient and thermal diffusivity. This minimizes measurement errors associated with compositional or doping inhomogeneities. In the absence of high temperature standard reference materials for Hall coefficient measurements, silicon samples with different doping concentrations have been used to verify the accuracy of the instrument. Additionally, the electrical conductivity data have been validated by measurements on the same samples in a calibrated setup. Repeat measurements indicate a maximum standard deviation of ±3% and ±0.5% for the RH and σ data in the studied temperature range. Furthermore, comparisons with the calibrated setup indicate deviations within ±3% for the σ data. The suitability of the measurement setup for TE specimens has been demonstrated using measurements on n-type (Mg2Sn) and p-type (Mg3Sb2) specimens with carrier concentrations in the range of 1019–1020 cm−3.
Ex situ calibration of the scattered-light time-history diagnostic on the National Ignition Facility
Authors: Kostick S. , Filkins T. , Rosenberg M. J. , Katz J. , Theobald W. , Lemos N. , Tubman E. , Sommers R. , Hernandez J. E. , Swadling G. , Ross J. S. , Radha P. B. , Grullon F. , Heinmiller J. M. , Fornes J. , Hillyard P. , McCumber J. , Ceurvorst L. , Regan S. P. 
Published: September 2024

The scattered-light time-history diagnostic (SLTD) suite measures time-resolved scattered light in three wavelength bands: stimulated Brillouin scattering (350–352 nm), stimulated Raman scattering (430–760 nm), and plasma emission at half the laser frequency (695–735 nm), at 15 locations around the National Ignition Facility (NIF) target chamber. The SLTD, along with the full-aperture backscatter station (FABS), collects scattered light from direct- and indirect-drive inertial confinement fusion experiments. The SLTD calibration was revisited after a discrepancy between FABS and SLTD measurements was observed on NIF polar direct-drive [Skupsky et al., Phys. Plasmas 11, 2763 (2004)] experiments. An integrated calibration of the SLTD was performed for the first time, and individual components were also calibrated for the wavelengths of 351, 527, and 532 nm. The optical transmission of the instrument was measured to be (1.12 ± 0.04) × 10−7 and (1.96 ± 0.11) × 10−7 for the wavelengths of 351 and 532 nm, respectively. The revised calibration at 351 nm brings the SLTD measured scattered energy in agreement with the FABS measured scattered energy after additionally accounting for the degradation of an optical element in FABS. This decreased the inferred absorption by 7% for a representative experiment. However, discrepancies remain between FABS and SLTD measurements in the SRS band (532 nm).
Density functional theory (DFT) study of water autoionization in solvated clusters
Authors: Kolasinski Kurt W. , Salkowski Alexa M. 
Published: September 2024

We have implemented a cluster-continuum method using density functional theory to model water clusters and various charged species derived from water. The two aims of this study are to determine the minimal basis required for proper modeling of water autoionization and to determine the minimum number of explicit water molecules required to properly model the energetics of solvation. The thermodynamics of water autoionization converge following a modified power law to deliver chemically accurate values of the Gibbs energy change for autoionization with tractably small clusters. Convergence is slower and not exponential as assumed in previous work. We identify the n = 21 set of clusters as the first effectively bulk water like clusters that can capture the energetic influence of both the first and second solvation shells. In this cluster, a water molecule is encapsulated in the center of a closed shell of other water molecules that hydrogen bond to form five-membered rings. The total energy change for clusters with n ≥ 21 calculated using both the RPBE-D3 and ωB97X-D exchange–correlation functionals with the 6-311+G** basis set is shown to deliver good approximations to the free energy change at 298 K. This is true even though neither functional models the individual enthalpy or entropy contributions particularly well.