bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of T cells in liver metastasis
Authors: Wu Kejia , Zhang Guozhu , Shen Changbing , Zhu Li , Yu Chongyuan , Sartorius Kurt , Ding Wei , Jiang Yong , Lu Yunjie 
Published: May 2024

AbstractThe liver is a major metastatic site (organ) for gastrointestinal cancers (such as colorectal, gastric, and pancreatic cancers) as well as non-gastrointestinal cancers (such as lung, breast, and melanoma cancers). Due to the innate anatomical position of the liver, the apoptosis of T cells in the liver, the unique metabolic regulation of hepatocytes and other potential mechanisms, the liver tends to form an immunosuppressive microenvironment and subsequently form a pre-metastatic niche (PMN), which can promote metastasis and colonization by various tumor cells(TCs). As a result, the critical role of immunoresponse in liver based metastasis has become increasingly appreciated. T cells, a centrally important member of adaptive immune response, play a significant role in liver based metastases and clarifying the different roles of the various T cells subsets is important to guide future clinical treatment. In this review, we first introduce the predisposing factors and related mechanisms of liver metastasis (LM) before introducing the PMN and its transition to LM. Finally, we detail the role of different subsets of T cells in LM and advances in the management of LM in order to identify potential therapeutic targets for patients with LM.
Squeezed light from an oscillator measured at the rate of oscillation
Authors: Bærentsen Christian , Fedorov Sergey A. , Østfeldt Christoffer , Balabas Mikhail V. , Zeuthen Emil , Polzik Eugene S. 
Published: May 2024

AbstractSufficiently fast continuous measurements of the position of an oscillator approach measurements projective on position eigenstates. We evidence the transition into the projective regime for a spin oscillator within an ensemble of 2 × 1010 room-temperature atoms by observing correlations between the quadratures of the meter light field. These correlations squeeze the fluctuations of one light quadrature below the vacuum level. When the measurement is slower than the oscillation, we generate $$11.{5}_{-1.5}^{+2.5}\,{{{{{{{\rm{dB}}}}}}}}$$
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and detect $$8.{5}_{-0.1}^{+0.1}\,{{{{{{{\rm{dB}}}}}}}}$$
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of squeezing in a tunable band that is a fraction of the resonance frequency. When the measurement is as fast as the oscillation, we detect 4.7 dB of squeezing that spans more than one decade of frequencies below the resonance. Our results demonstrate a new regime of continuous quantum measurements on material oscillators, and set a new benchmark for the performance of a linear quantum sensor.
Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers
Authors: Deyell Rebecca J. , Shen Yaoqing , Titmuss Emma , Dixon Katherine , Williamson Laura M. , Pleasance Erin , Nelson Jessica M. T. , Abbasi Sanna , Krzywinski Martin , Armstrong Linlea , Bonakdar Melika , Ch’ng Carolyn , Chuah Eric , Dunham Chris , Fok Alexandra , Jones Martin , Lee Anna F. , Ma Yussanne , Moore Richard A. , Mungall Andrew J. , Mungall Karen L. , Rogers Paul C. , Schrader Kasmintan A. , Virani Alice , Wee Kathleen , Young Sean S. , Zhao Yongjun , Jones Steven J. M. , Laskin Janessa , Marra Marco A. , Rassekh Shahrad R. 
Published: May 2024

AbstractThe role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.
Structure, mechanism, and evolution of the last step in vitamin C biosynthesis
Authors: Boverio Alessandro , Jamil Neelam , Mannucci Barbara , Mascotti Maria Laura , Fraaije Marco W. , Mattevi Andrea 
Published: May 2024

AbstractPhotosynthetic organisms, fungi, and animals comprise distinct pathways for vitamin C biosynthesis. Besides this diversity, the final biosynthetic step consistently involves an oxidation reaction carried out by the aldonolactone oxidoreductases. Here, we study the origin and evolution of the diversified activities and substrate preferences featured by these flavoenzymes using molecular phylogeny, kinetics, mutagenesis, and crystallographic experiments. We find clear evidence that they share a common ancestor. A flavin-interacting amino acid modulates the reactivity with the electron acceptors, including oxygen, and determines whether an enzyme functions as an oxidase or a dehydrogenase. We show that a few side chains in the catalytic cavity impart the reaction stereoselectivity. Ancestral sequence reconstruction outlines how these critical positions were affixed to specific amino acids along the evolution of the major eukaryotic clades. During Eukarya evolution, the aldonolactone oxidoreductases adapted to the varying metabolic demands while retaining their overarching vitamin C-generating function.
Carbon pricing and system reliability impacts on pathways to universal electricity access in Africa
Authors: Beath Hamish , Mittal Shivika , Few Sheridan , Winchester Benedict , Sandwell Philip , Markides Christos N. , Nelson Jenny , Gambhir Ajay 
Published: May 2024

AbstractOff-grid photovoltaic systems have been proposed as a panacea for economies with poor electricity access, offering a lower-cost “leapfrog” over grid infrastructure used in higher-income economies. Previous research examining pathways to electricity access may understate the role of off-grid photovoltaics as it has not considered reliability and carbon pricing impacts. We perform high-resolution geospatial analysis on universal household electricity access in Sub-Saharan Africa that includes these aspects via least-cost pathways at different electricity demand levels. Under our “Tier 3" demand reference scenario, 24% of our study’s 470 million people obtaining electricity access by 2030 do so via off-grid photovoltaics. Including a unit cost for unmet demand of 0.50 US dollars ($)/kWh, to penalise poor system reliability increases this share to 41%. Applying a carbon price (around $80/tonne CO2-eq) increases it to 38%. Our results indicate considerable diversity in the level of policy intervention needed between countries and suggest several regions where lower levels of policy intervention may be effective.
Benchmarking of methods for DNA methylome deconvolution
Authors: De Ridder Kobe , Che Huiwen , Leroy Kaat , Thienpont Bernard 
Published: May 2024

AbstractDefining the number and abundance of different cell types in tissues is important for understanding disease mechanisms as well as for diagnostic and prognostic purposes. Typically, this is achieved by immunohistological analyses, cell sorting, or single-cell RNA-sequencing. Alternatively, cell-specific DNA methylome information can be leveraged to deconvolve cell fractions from a bulk DNA mixture. However, comprehensive benchmarking of deconvolution methods and modalities was not yet performed. Here we evaluate 16 deconvolution algorithms, developed either specifically for DNA methylome data or more generically. We assess the performance of these algorithms, and the effect of normalization methods, while modeling variables that impact deconvolution performance, including cell abundance, cell type similarity, reference panel size, method for methylome profiling (array or sequencing), and technical variation. We observe differences in algorithm performance depending on each these variables, emphasizing the need for tailoring deconvolution analyses. The complexity of the reference, marker selection method, number of marker loci and, for sequencing-based assays, sequencing depth have a marked influence on performance. By developing handles to select the optimal analysis configuration, we provide a valuable source of information for studies aiming to deconvolve array- or sequencing-based methylation data.
Dual-phase nano-glass-hydrides overcome the strength-ductility trade-off and magnetocaloric bottlenecks of rare earth based amorphous alloys
Authors: Shao Liliang , Luo Qiang , Zhang Mingjie , Xue Lin , Cui Jingxian , Yang Qianzi , Ke Haibo , Zhang Yao , Shen Baolong , Wang Weihua 
Published: May 2024

AbstractMetal-hydrogen systems have attracted intense interest for diverse energy-related applications. However, metals usually reduce their ductility after hydrogenation. Here, we show that hydrogen can take the form of nano-sized ordered hydrides (NOH) homogeneously dispersed in a stable glassy shell, leading to remarkable enhancement in both strength and ductility. The yield strength is enhanced by 44% and the plastic strain is substantially improved from almost zero to over 70%, which is attributed to the created NOH and their interplay with the glassy shell. Moreover, the hydride-glass composite GdCoAlH possesses a giant magnetic entropy change (−ΔSM) of 18.7 J kg−1K−1 under a field change of 5 T, which is 105.5% larger than the hydrogen-free sample and is the largest value among amorphous alloys and related composites. The prominent ΔSM-ductility combination overcomes the bottlenecks of amorphous alloys as magnetic refrigerants. These results provide a promising strategy for property breakthrough of structural-functional alloys.
Sustainable thermal regulation improves stability and efficiency in all-perovskite tandem solar cells
Authors: Tan Shuchen , Li Chongwen , Peng Cheng , Yan Wenjian , Bu Hongkai , Jiang Haokun , Yue Fang , Zhang Linbao , Gao Hongtao , Zhou Zhongmin 
Published: May 2024

AbstractMixed Sn-Pb perovskites have emerged as promising photovoltaic materials for both single- and multi-junction solar cells. However, achieving their scale-up and practical application requires further enhancement in stability. We identify that their poor thermal conductivity results in insufficient thermal transfer, leading to heat accumulation within the absorber layer that accelerates thermal degradation. A thermal regulation strategy by incorporating carboranes into perovskites is developed; these are electron-delocalized carbon-boron molecules known for their efficient heat transfer capability. We specifically select ortho-carborane due to its low thermal hysteresis. We observe its existence through the perovskite layer showing a decreasing trend from the buried interface to the top surface, effectively transferring heat and lowering the surface temperature by around 5 °C under illumination. o-CB also facilitates hole extraction at the perovskite/PEDOT:PSS interface and reduces charge recombination. These enable mixed Sn-Pb cells to exhibit improved thermal stability, retaining 80% of their initial efficiencies after aging at 85 °C for 1080 hours. When integrated into monolithic all-perovskite tandems, we achieve efficiencies of over 27%. A tandem cell maintains 87% of its initial PCE after 704 h of continuous operation under illumination.
On the potential of vehicle-to-grid and second-life batteries to provide energy and material security
Authors: Aguilar Lopez Fernando , Lauinger Dirk , Vuille François , Müller Daniel B. 
Published: May 2024

AbstractThe global energy transition relies increasingly on lithium-ion batteries for electric transportation and renewable energy integration. Given the highly concentrated supply chain of battery materials, importing regions have a strategic imperative to reduce their reliance on battery material imports through, e.g., battery recycling or reuse. We investigate the potential of vehicle-to-grid and second-life batteries to reduce resource use by displacing new stationary batteries dedicated to grid storage. Based on dynamic material flow analysis, we show that equipping around 50% of electric vehicles with vehicle-to-grid or reusing 40% of electric vehicle batteries for second life each have the potential to fully cover the European Union’s need for stationary storage by 2040. This could reduce total primary material demand from 2020–2050 by up to 7.5% and 1.5%, respectively, which could ease geopolitical risks and increase the European Union’s energy and material security. Any surplus capacity could be used as a strategic reserve to increase resilience in the face of emergencies such as blackouts or adverse geo-political events.
CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair
Authors: Hassan Dalia , Chen Jichao 
Published: May 2024

AbstractCell plasticity theoretically extends to all possible cell types, but naturally decreases as cells differentiate, whereas injury-repair re-engages the developmental plasticity. Here we show that the lung alveolar type 2 (AT2)-specific transcription factor (TF), CEBPA, restricts AT2 cell plasticity in the mouse lung. AT2 cells undergo transcriptional and epigenetic maturation postnatally. Without CEBPA, both neonatal and mature AT2 cells reduce the AT2 program, but only the former reactivate the SOX9 progenitor program. Sendai virus infection bestows mature AT2 cells with neonatal plasticity whereCebpamutant, but not wild type, AT2 cells express SOX9, as well as more readily proliferate and form KRT8/CLDN4+ transitional cells. CEBPA promotes the AT2 program by recruiting the lung lineage TF NKX2-1. The temporal change in CEBPA-dependent plasticity reflects AT2 cell developmental history. The ontogeny of AT2 cell plasticity and its transcriptional and epigenetic mechanisms have implications in lung regeneration and cancer.
A baseline structure inventory with critical attribution for the US and its territories
Authors: Yang Hsiuhan Lexie , Laverdiere Melanie , Hauser Taylor , Swan Benjamin , Schmidt Erik , Moehl Jessica , Reith Andrew , Adams Daniel , Morris Bennett , McKee Jacob , Whitehead Matthew , Tuttle Mark 
Published: May 2024

AbstractLeveraging high performance computing, remote sensing, geographic data science, machine learning, and computer vision, Oak Ridge National Laboratory has partnered with Federal Emergency Management Agency (FEMA) to build a baseline structure inventory covering the US and its territories to support disaster preparedness, response, and recovery. The dataset contains more than 125 million structures with critical attribution, and is ready to be used by federal agencies, local government and first responders to accelerate on-the-ground response to disasters, further identify vulnerable areas, and develop strategies to enhance the resilience of critical structures and communities. Data can be freely and openly accessed through Figshare data repository, ESRI’s Living Atlas or FEMA’s Geodata platform.
Cloud micro- and macrophysical properties from ground-based remote sensing during the MOSAiC drift experiment
Authors: Griesche Hannes J. , Seifert Patric , Engelmann Ronny , Radenz Martin , Hofer Julian , Althausen Dietrich , Walbröl Andreas , Barrientos-Velasco Carola , Baars Holger , Dahlke Sandro , Tukiainen Simo , Macke Andreas 
Published: May 2024

AbstractIn the framework of the Multidisciplinary drifting Observatory for the Study of Arctic Climate Polarstern expedition, the Leibniz Institute for Tropospheric Research, Leipzig, Germany, operated the shipborne OCEANET-Atmosphere facility for cloud and aerosol observations throughout the whole year. OCEANET-Atmosphere comprises, amongst others, a multiwavelength Raman lidar, a microwave radiometer, and an optical disdrometer. A cloud radar was operated aboard Polarstern by the US Atmospheric Radiation Measurement program. These measurements were processed by applying the so-called Cloudnet methodology to derive cloud properties. To gain a comprehensive view of the clouds, lidar and cloud radar capabilities for low- and high-altitude observations were combined. Cloudnet offers a variety of products with a spatiotemporal resolution of 30 s and 30 m, such as the target classification, and liquid and ice microphysical properties. Additionally, a lidar-based low-level stratus retrieval was applied for cloud detection below the lowest range gate of the cloud radar. Based on the presented dataset, e.g., studies on cloud formation processes and their radiative impact, and model evaluation studies can be conducted.
Evaluation of precipitated CaCO3 produced from locally available limestone as a reinforcement filler for PVC pipe
Authors: Jembere Addis Lemessa , Genet Melkamu Birlie , Sintayehu Bantelay 
Published: May 2024

AbstractThe current experimental work aimed at developing PCC through two major process steps: dissolution and precipitation, using raw materials domestically available as SL, which are intensively used in construction inputs. The pH level was the decisive parameter used to determine the time required to complete the dissolution and carbonation processes during precipitation. The optimal pH levels were found to be 13 for dissolution and 7.1 for precipitation, respectively. The produced PCC was characterized based on chemical analysis, crystallinity, and morphology, showing an increment of CaCO3 content exceeding 99%, sharper crystal peaks, and predominantly calcite PCC. The compatibility of the PCC was assessed by incorporating 25%, 50%, 75%, and 100% of PCC with commercial filler, followed by selected mechanical tests, such as stress at yield, density, and elongation at break. The results indicated that mixing ratios of 25%, 50%, and 75% of PCC with the commercial filler met the standards, with stress at a yield above 45 MPa and density within the range of 1.35 to 1.46 g/cm3. However, complete substitution slightly lowered these properties. Nevertheless, the elongation at break was acceptable at all treatment levels.
System-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution
Authors: Ozisik Ozan , Gorokhova Svetlana , Cerino Mathieu , Bartoli Marc , Baudot Anaïs 
Published: May 2024

AbstractMuscular dystrophies (MDs) are inherited genetic diseases causing weakness and degeneration of muscles. The distribution of muscle weakness differs between MDs, involving distal muscles or proximal muscles. While the mutations in most of the MD-associated genes lead to either distal or proximal onset, there are also genes whose mutations can cause both types of onsets. We hypothesized that the genes associated with different MD onsets code proteins with distinct cellular functions. To investigate this, we collected the MD-associated genes and assigned them to three onset groups: genes mutated only in distal onset dystrophies, genes mutated only in proximal onset dystrophies, and genes mutated in both types of onsets. We then systematically evaluated the cellular functions of these gene sets with computational strategies based on functional enrichment analysis and biological network analysis. Our analyses demonstrate that genes mutated in either distal or proximal onset MDs code proteins linked with two distinct sets of cellular processes. Interestingly, these two sets of cellular processes are relevant for the genes that are associated with both onsets. Moreover, the genes associated with both onsets display high centrality and connectivity in the network of muscular dystrophy genes. Our findings support the hypothesis that the proteins associated with distal or proximal onsets have distinct functional characteristics, whereas the proteins associated with both onsets are multifunctional.
Effect of emergent vegetation on riverbank erosion with sediment mining
Authors: Arora Sukhjeet , Kumar Bimlesh 
Published: May 2024

AbstractThe present work investigates the combined effects of the upstream sediment mining pit and vegetation on the riverbank using emergent rigid vegetation beyond the toe on the flow structure and morphological changes due to fluvial erosion. A steep gradient of streamwise velocity and other turbulence parameters such as Reynolds shear stress (RSS), transverse RSS, and turbulent kinetic energy (TKE) at the interface of the vegetated and unvegetated part of the test segment was observed. The cross-sectional analysis showed that vegetation increased the velocity of the unvegetated main channel, and the sandpit increased even the near-bed velocity with a similar trend in its longitudinal variation at the center line of the main channel. The abrupt variation in RSS and transverse RSS at the location of the berm induces instability and erodes the berm present at the toe of the riverbank. The combination of the vegetation and sandpit led to increased TKE of the flow at the near-bed and berm locations. The morphological analysis showed complete riverbank erosion in both cases of the unvegetated riverbank, i.e., without or with an upstream pit. The installed stems of rigid vegetation on the riverbank helped decrease the fluvial erosion of the riverbank, and its profile observed minimal changes over the length of the test segment. However, the main channel erosion was amplified due to the vegetation (in no-pit case) at the beginning of the test segment, which eroded the bed of the main channel by about 67% of the bed thickness. Also, in the vegetated riverbank cases, the upstream pit caused an increase in erosion by 7.66% at the center of the main channel. The study helps establish the hypothesis of negating the effects of sediment mining on bank erosion by using the rigid vegetation on the riverbank beyond its toe location, which performed well by maintaining the riverbank profile.