bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized superconductivity in the vicinity of a nematic quantum critical point in the kagome superconductor Cs(V1-xTix)3Sb5
Authors: Sur Yeahan , Kim Kwang-Tak , Kim Sukho , Kim Kee Hoon 
Published: July 2023

AbstractCsV3Sb5 exhibits superconductivity at Tc = 3.2 K after undergoing intriguing two high-temperature transitions: charge density wave order at ~98 K and electronic nematic order at Tnem ~ 35 K. Here, we investigate nematic susceptibility in single crystals of Cs(V1-xTix)3Sb5 (x = 0.00-0.06) where double-dome-shaped superconducting phase diagram is realized. The nematic susceptibility typically exhibits the Curie‒Weiss behaviour above Tnem, which is monotonically decreased with x. Moreover, the Curie‒Weiss temperature is systematically suppressed from ~30 K for x = 0 to ~4 K for x = 0.0075, resulting in a sign change at x = ~0.009. Furthermore, the Curie constant reaches a maximum at x = 0.01, suggesting drastically enhanced nematic susceptibility near a putative nematic quantum critical point (NQCP) at x = ~0.009. Strikingly, Tc is enhanced up to ~4.1 K with full Meissner shielding realized at x = ~0.0075-0.01, forming the first superconducting dome near the NQCP. Our findings directly point to a vital role of nematic fluctuations in enhancing the superconducting properties of Cs(V1-xTix)3Sb5.
TET2 and TET3 loss disrupts small intestine differentiation and homeostasis
Authors: Ansari Ihab , Solé-Boldo Llorenç , Ridnik Meshi , Gutekunst Julian , Gilliam Oliver , Korshko Maria , Liwinski Timur , Jickeli Birgit , Weinberg-Corem Noa , Shoshkes-Carmel Michal , Pikarsky Eli , Elinav Eran , Lyko Frank , Bergman Yehudit 
Published: July 2023

AbstractTET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
SpatialDM for rapid identification of spatially co-expressed ligand–receptor and revealing cell–cell communication patterns
Authors: Li Zhuoxuan , Wang Tianjie , Liu Pentao , Huang Yuanhua 
Published: July 2023

AbstractCell-cell communication is a key aspect of dissecting the complex cellular microenvironment. Existing single-cell and spatial transcriptomics-based methods primarily focus on identifying cell-type pairs for a specific interaction, while less attention has been paid to the prioritisation of interaction features or the identification of interaction spots in the spatial context. Here, we introduce SpatialDM, a statistical model and toolbox leveraging a bivariant Moran’s statistic to detect spatially co-expressed ligand and receptor pairs, their local interacting spots (single-spot resolution), and communication patterns. By deriving an analytical null distribution, this method is scalable to millions of spots and shows accurate and robust performance in various simulations. On multiple datasets including melanoma, Ventricular-Subventricular Zone, and intestine, SpatialDM reveals promising communication patterns and identifies differential interactions between conditions, hence enabling the discovery of context-specific cell cooperation and signalling.
Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase
Authors: Li Zhong , Zhang Lilan , Xu Kangwei , Jiang Yuanyuan , Du Jieke , Zhang Xingwang , Meng Ling-Hong , Wu Qile , Du Lei , Li Xiaoju , Hu Yuechan , Xie Zhenzhen , Jiang Xukai , Tang Ya-Jie , Wu Ruibo , Guo Rey-Ting , Li Shengying 
Published: July 2023

AbstractDiterpene synthase VenA is responsible for assembling venezuelaene A with a unique 5-5-6-7 tetracyclic skeleton from geranylgeranyl pyrophosphate. VenA also demonstrates substrate promiscuity by accepting geranyl pyrophosphate and farnesyl pyrophosphate as alternative substrates. Herein, we report the crystal structures of VenA in bothapoform andholoform in complex with a trinuclear magnesium cluster and pyrophosphate group. Functional and structural investigations on the atypical115DSFVSD120motif of VenA,versusthe canonical Asp-rich motif of DDXX(X)D/E, reveal that the absent second Asp of canonical motif is functionally replaced by Ser116 and Gln83, together with bioinformatics analysis identifying a hidden subclass of type I microbial terpene synthases. Further structural analysis, multiscale computational simulations, and structure-directed mutagenesis provide significant mechanistic insights into the substrate selectivity and catalytic promiscuity of VenA. Finally, VenA is semi-rationally engineered into a sesterterpene synthase to recognize the larger substrate geranylfarnesyl pyrophosphate.
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms
Authors: Erdem Cemal , Gross Sean M. , Heiser Laura M. , Birtwistle Marc R. 
Published: July 2023

AbstractRobust identification of context-specific network features that control cellular phenotypes remains a challenge. We here introduce MOBILE (Multi-Omics Binary Integration via Lasso Ensembles) to nominate molecular features associated with cellular phenotypes and pathways. First, we use MOBILE to nominate mechanisms of interferon-γ (IFNγ) regulated PD-L1 expression. Our analyses suggest that IFNγ-controlled PD-L1 expression involvesBST2,CLIC2,FAM83D,ACSL5, andHIST2H2AA3genes, which were supported by prior literature. We also compare networks activated by related family members transforming growth factor-beta 1 (TGFβ1) and bone morphogenetic protein 2 (BMP2) and find that differences in ligand-induced changes in cell size and clustering properties are related to differences in laminin/collagen pathway activity. Finally, we demonstrate the broad applicability and adaptability of MOBILE by analyzing publicly available molecular datasets to investigate breast cancer subtype specific networks. Given the ever-growing availability of multi-omics datasets, we envision that MOBILE will be broadly useful for identification of context-specific molecular features and pathways.
Natural statistics support a rational account of confidence biases
Authors: Webb Taylor W. , Miyoshi Kiyofumi , So Tsz Yan , Rajananda Sivananda , Lau Hakwan 
Published: July 2023

AbstractPrevious work has sought to understand decision confidence as a prediction of the probability that a decision will be correct, leading to debate over whether these predictions are optimal, and whether they rely on the same decision variable as decisions themselves. This work has generally relied on idealized, low-dimensional models, necessitating strong assumptions about the representations over which confidence is computed. To address this, we used deep neural networks to develop a model of decision confidence that operates directly over high-dimensional, naturalistic stimuli. The model accounts for a number of puzzling dissociations between decisions and confidence, reveals a rational explanation of these dissociations in terms of optimization for the statistics of sensory inputs, and makes the surprising prediction that, despite these dissociations, decisions and confidence depend on a common decision variable.
Deep quantum neural networks on a superconducting processor
Authors: Pan Xiaoxuan , Lu Zhide , Wang Weiting , Hua Ziyue , Xu Yifang , Li Weikang , Cai Weizhou , Li Xuegang , Wang Haiyan , Song Yi-Pu , Zou Chang-Ling , Deng Dong-Ling , Sun Luyan 
Published: July 2023

AbstractDeep learning and quantum computing have achieved dramatic progresses in recent years. The interplay between these two fast-growing fields gives rise to a new research frontier of quantum machine learning. In this work, we report an experimental demonstration of training deep quantum neural networks via the backpropagation algorithm with a six-qubit programmable superconducting processor. We experimentally perform the forward process of the backpropagation algorithm and classically simulate the backward process. In particular, we show that three-layer deep quantum neural networks can be trained efficiently to learn two-qubit quantum channels with a mean fidelity up to 96.0% and the ground state energy of molecular hydrogen with an accuracy up to 93.3% compared to the theoretical value. In addition, six-layer deep quantum neural networks can be trained in a similar fashion to achieve a mean fidelity up to 94.8% for learning single-qubit quantum channels. Our experimental results indicate that the number of coherent qubits required to maintain does not scale with the depth of the deep quantum neural network, thus providing a valuable guide for quantum machine learning applications with both near-term and future quantum devices.
Tumor collagens predict genetic features and patient outcomes
Authors: Guo Kevin S. , Brodsky Alexander S. 
Published: July 2023

AbstractThe extracellular matrix (ECM) is a critical determinant of tumor fate that reflects the output from myriad cell types in the tumor. Collagens constitute the principal components of the tumor ECM. The changing collagen composition in tumors along with their impact on patient outcomes and possible biomarkers remains largely unknown. The RNA expression of the 43 collagen genes from solid tumors in The Cancer Genome Atlas (TCGA) was clustered to classify tumors. PanCancer analysis revealed how collagens by themselves can identify the tissue of origin. Clustering by collagens in each cancer type demonstrated strong associations with survival, specific immunoenvironments, somatic gene mutations, copy number variations, and aneuploidy. We developed a machine learning classifier that predicts aneuploidy, and chromosome arm copy number alteration (CNA) status based on collagen expression alone with high accuracy in many cancer types with somatic mutations, suggesting a strong relationship between the collagen ECM context and specific molecular alterations. These findings have broad implications in defining the relationship between cancer-related genetic defects and the tumor microenvironment to improve prognosis and therapeutic targeting for patient care, opening new avenues of investigation to define tumor ecosystems.
Sensitivity of Arctic CH4 emissions to landscape wetness diminished by atmospheric feedbacks
Authors: de Vrese Philipp , Beckebanze Lutz , Galera Leonardo de Aro , Holl David , Kleinen Thomas , Kutzbach Lars , Rehder Zoé , Brovkin Victor 
Published: July 2023

AbstractSimulations using land surface models suggest future increases in Arctic methane emissions to be limited by the thaw-induced drying of permafrost landscapes. Here we use the Max Planck Institute Earth System Model to show that this constraint may be weaker than previously thought owing to compensatory atmospheric feedbacks. In two sets of extreme scenario simulations, a modification of the permafrost hydrology resulted in diverging hydroclimatic trajectories that, however, led to comparable methane fluxes. While a wet Arctic showed almost twice the wetland area compared with an increasingly dry Arctic, the latter featured greater substrate availability due to higher temperatures resulting from reduced evaporation, diminished cloudiness and more surface solar radiation. Given the limitations of present-day models and the potential model dependence of the atmospheric response, our results provide merely a qualitative estimation of these effects, but they suggest that atmospheric feedbacks play an important role in shaping future Arctic methane emissions.
Groundwater springs formed during glacial retreat are a large source of methane in the high Arctic
Authors: Kleber Gabrielle E. , Hodson Andrew J. , Magerl Leonard , Mannerfelt Erik Schytt , Bradbury Harold J. , Zhu Yizhu , Trimmer Mark , Turchyn Alexandra V. 
Published: July 2023

AbstractPermafrost and glaciers in the high Arctic form an impermeable ‘cryospheric cap’ that traps a large reservoir of subsurface methane, preventing it from reaching the atmosphere. Cryospheric vulnerability to climate warming is making releases of this methane possible. On Svalbard, where air temperatures are rising more than two times faster than the average for the Arctic, glaciers are retreating and leaving behind exposed forefields that enable rapid methane escape. Here we document how methane-rich groundwater springs have formed in recently revealed forefields of 78 land-terminating glaciers across central Svalbard, bringing deep-seated methane gas to the surface. Waters collected from these springs during February–May of 2021 and 2022 are supersaturated with methane up to 600,000 times greater than atmospheric equilibration. Spatial sampling reveals a geological dependency on the extent of methane supersaturation, with isotopic evidence of a thermogenic source. We estimate annual methane emissions from proglacial groundwaters to be up to 2.31 kt across the Svalbard archipelago. Further investigations into marine-terminating glaciers indicate future methane emission sources as these glaciers transition into fully land-based systems. Our findings reveal that climate-driven glacial retreat facilitates widespread release of methane, a positive feedback loop that is probably prevalent across other regions of the rapidly warming Arctic.
A panel dataset of COVID-19 vaccination policies in 185 countries
Authors: Cameron-Blake Emily , Tatlow Helen , Andretti Bernardo , Boby Thomas , Green Kaitlyn , Hale Thomas , Petherick Anna , Phillips Toby , Pott Annalena , Wade Adam , Zha Hao 
Published: July 2023

AbstractWe present a panel dataset of COVID-19 vaccine policies, with data from 01 January 2020 for 185 countries and a number of subnational jurisdictions, reporting on vaccination prioritization plans, eligibility and availability, cost to the individual and mandatory vaccination policies. For each of these indicators, we recorded who is targeted by a policy using 52 standardized categories. These indicators document a detailed picture of the unprecedented scale of international COVID-19 vaccination rollout and strategy, indicating which countries prioritized and vaccinated which groups, when and in what order. We highlight key descriptive findings from these data to demonstrate uses for the data and to encourage researchers and policymakers in future research and vaccination planning. Numerous patterns and trends begin to emerge. For example: ‘eliminator’ countries (those that aimed to prevent virus entry into the country and community transmission) tended to prioritize border workers and economic sectors, while ‘mitigator’ countries (those that aimed to reduce the impact of community transmission) tended to prioritize the elderly and healthcare sectors for the first COVID-19 vaccinations; high-income countries published prioritization plans and began vaccinations earlier than low- and middle-income countries. Fifty-five countries were found to have implemented at least one policy of mandatory vaccination. We also demonstrate the value of combining this data with vaccination uptake rates, vaccine supply and demand data, and with further COVID-19 epidemiological data.
A beginner’s guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration
Authors: Gomes Moreira Diana , Jan Asad 
Published: July 2023

AbstractThe discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this “beginner’s guide” will benefit the research community in NDDs, and would serve as a useful educational tool.
Chromosome-level genome assembly of the Asian aspen Populus davidiana Dode
Authors: Bae Eun-Kyung , Kang Min-Jeong , Lee Seung-Jae , Park Eung-Jun , Kim Ki-Tae 
Published: July 2023

AbstractThe genome ofPopulus davidiana, a keystone aspen species, has been sequenced to improve our understanding of the evolutionary and functional genomics of thePopulusgenus. The Hi-C scaffolding genome assembly resulted in a 408.1 Mb genome with 19 pseudochromosomes. The BUSCO assessment revealed that 98.3% of the genome matched the embryophytes dataset. A total of 31,862 protein-coding sequences were predicted, of which 31,619 were functionally annotated. The assembled genome was composed of 44.9% transposable elements. These findings provide new knowledge about the characteristics of theP. davidianagenome and will facilitate comparative genomics and evolutionary research on the genusPopulus.
Wildfire immediately reduces nest and adult survival of greater sage-grouse
Authors: Tyrrell Emmy A. , Coates Peter S. , Prochazka Brian G. , Brussee Brianne E. , Espinosa Shawn P. , Hull Joshua M. 
Published: July 2023

AbstractWildfire events are becoming more frequent and severe on a global scale. Rising temperatures, prolonged drought, and the presence of pyrophytic invasive grasses are contributing to the degradation of native vegetation communities. Within the Great Basin region of the western U.S., increasing wildfire frequency is transforming the ecosystem toward a higher degree of homogeneity, one dominated by invasive annual grasses and declining landscape productivity. Greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) are a species of conservation concern that rely on large tracts of structurally and functionally diverse sagebrush (Artemisia spp.) communities. Using a 12-year (2008–2019) telemetry dataset, we documented immediate impacts of wildfire on demographic rates of a population of sage-grouse that were exposed to two large wildfire events (Virginia Mountains Fire Complex—2016; Long Valley Fire—2017) near the border of California and Nevada. Spatiotemporal heterogeneity in demographic rates were accounted for using a Before-After Control-Impact Paired Series (BACIPS) study design. Results revealed a 40% reduction in adult survival and a 79% reduction in nest survival within areas impacted by wildfires. Our results indicate that wildfire has strong and immediate impacts to two key life stages of a sagebrush indicator species and underscores the importance of fire suppression and immediate restoration following wildfire events.
Relationship between radioactivity and toxicity in some medicinal plants
Authors: Abdelfadeel Eman H. , El-Halim E. S. Abd , Hegazy T. M. , Ghany H. A. Abdel 
Published: July 2023

AbstractPlants absorb water, nutrients and minerals from the soil through their root. Also, minerals, the radionuclides present in the growing media also are absorbed by plant parts following the same pathway. Consequently, it is important to determine the concentrations of these radionuclides in edible plants to access the associated risk to human health. In the present work, the levels of natural radioactivity and the level of some toxic elements in 17 medicinal plants, commonly used in Egypt, were measured using high-purity germanium gamma spectrometry and atomic absorption, respectively. The investigated plants were sub-grouped according to the edible parts into leave samples (n = 8), roots (n = 3), and seeds (n = 6). Also, the specific activity of both radon and thoron was measured by using alpha emitters registration which is emitted from radon and thoron gases in CR-39 nuclear track detectors. Additionally, the concentration of some toxic elements (Cu, Zn, Cd and, Pb) in six samples of medicinal plants was determined by atomic absorption spectrometry.
Boosting the thermal management performance of a PCM-based module using novel metallic pin fin geometries: Numerical study
Authors: Elshaer Abdelrahman M. , Soliman A. M. A. , Kassab M. , Hawwash A. A. 
Published: July 2023

AbstractSatellite avionics and electronic components are getting compact and have high power density. Thermal management systems are essential for their optimal operational performance and survival. Thermal management systems keep the electronic components within a safe temperature range. Phase change materials (PCMs) have high thermal capacity, so they are promising for thermal control applications. This work adopted a PCM-integrated thermal control device (TCD) to manage the small satellite subsystems under zero gravity conditions thermally. The TCD's outer dimensions were selected upon a typical small satellite subsystem. The PCM adopted was the organic PCM of RT 35. Pin fins with different geometries were adopted to boost the lower thermal conductivity of the PCM. Six-pin fins geometries were used. First, the conventional geometries were square, circular, and triangular. Second, the novel geometries were cross-shaped, I-shaped, and V-shaped fins. The fins were designed at two-volume fractions of 20% and 50%. The electronic subsystem was assumed to be "ON" for 10 min releasing 20 W of heat, and "OFF" for 80 min. The findings show a remarkable decrease in the TCD's base plate temperature by 5.7 ℃ as the fins' number changed from 15 to 80 for square fins. The results also show that the novel cross-shaped, I-shaped, and V-shaped pin fins could significantly enhance thermal performance. The cross-shaped, I-shaped, and V-shaped reported a decrease in the temperature by about 1.6%, 2.6%, and 6.6%, respectively, relative to the circular fin geometry. V-shaped fins could also increase the PCM melt fraction by 32.3%.