bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability
Authors: Takasawa Ken , Asada Ken , Kaneko Syuzo , Shiraishi Kouya , Machino Hidenori , Takahashi Satoshi , Shinkai Norio , Kouno Nobuji , Kobayashi Kazuma , Komatsu Masaaki , Mizuno Takaaki , Okubo Yu , Mukai Masami , Yoshida Tatsuya , Yoshida Yukihiro , Horinouchi Hidehito , Watanabe Shun-Ichi , Ohe Yuichiro , Yatabe Yasushi , Kohno Takashi , Hamamoto Ryuji 
Published: March 2024

AbstractDNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. While tools for DNA methylation analysis have been developed, most of them have focused on intergroup comparative analysis within a dataset; therefore, it is difficult to conduct cross-dataset studies, such as rare disease studies or cross-institutional studies. This study describes a novel method for DNA methylation analysis, namely, methPLIER, which enables interdataset comparative analyses. methPLIER combines Pathway Level Information Extractor (PLIER), which is a non-negative matrix factorization (NMF) method, with regularization by a knowledge matrix and transfer learning. methPLIER can be used to perform intersample and interdataset comparative analysis based on latent feature matrices, which are obtained via matrix factorization of large-scale data, and factor-loading matrices, which are obtained through matrix factorization of the data to be analyzed. We used methPLIER to analyze a lung cancer dataset and confirmed that the data decomposition reflected sample characteristics for recurrence-free survival. Moreover, methPLIER can analyze data obtained via different preprocessing methods, thereby reducing distributional bias among datasets due to preprocessing. Furthermore, methPLIER can be employed for comparative analyses of methylation data obtained from different platforms, thereby reducing bias in data distribution due to platform differences. methPLIER is expected to facilitate cross-sectional DNA methylation data analysis and enhance DNA methylation data resources.
Targeted knockdown of PGAM5 in synovial macrophages efficiently alleviates osteoarthritis
Authors: Liu Yuhang , Hao Ruihan , Lv Jia , Yuan Jie , Wang Xuelei , Xu Churong , Ma Ding , Duan Zhouyi , Zhang Bingjun , Dai Liming , Cheng Yiyun , Lu Wei , Zhang Xiaoling 
Published: March 2024

AbstractOsteoarthritis (OA) is a common degenerative disease worldwide and new therapeutics that target inflammation and the crosstalk between immunocytes and chondrocytes are being developed to prevent and treat OA. These attempts involve repolarizing pro-inflammatory M1 macrophages into the anti-inflammatory M2 phenotype in synovium. In this study, we found that phosphoglycerate mutase 5 (PGAM5) significantly increased in macrophages in OA synovium compared to controls based on histology of human samples and single-cell RNA sequencing results of mice models. To address the role of PGAM5 in macrophages in OA, we found conditional knockout of PGAM5 in macrophages greatly alleviated OA symptoms and promoted anabolic metabolism of chondrocytes in vitro and in vivo. Mechanistically, we found that PGAM5 enhanced M1 polarization via AKT-mTOR/p38/ERK pathways, whereas inhibited M2 polarization via STAT6-PPARγ pathway in murine bone marrow-derived macrophages. Furthermore, we found that PGAM5 directly dephosphorylated Dishevelled Segment Polarity Protein 2 (DVL2) which resulted in the inhibition of β-catenin and repolarization of M2 macrophages into M1 macrophages. Conditional knockout of both PGAM5 and β-catenin in macrophages significantly exacerbated osteoarthritis compared to PGAM5-deficient mice. Motivated by these findings, we successfully designed mannose modified fluoropolymers combined with siPGAM5 to inhibit PGAM5 specifically in synovial macrophages via intra-articular injection, which possessed desired targeting abilities of synovial macrophages and greatly attenuated murine osteoarthritis. Collectively, these findings defined a key role for PGAM5 in orchestrating macrophage polarization and provides insights into novel macrophage-targeted strategy for treating OA.
Association between stopping renin-angiotensin system inhibitors immediately before hemodialysis initiation and subsequent cardiovascular events
Authors: Nakamura Yoshihiro , Inaguma Daijo , Imaizumi Takahiro , Kurasawa Shimon , Hishida Manabu , Okazaki Masaki , Fujishima Yuki , Nishibori Nobuhiro , Suzuki Katsuhiko , Takeda Yuki , Maruyama Shoichi 
Published: March 2024

AbstractIt is controversial whether renin-angiotensin system inhibitors (RASIs) should be stopped in patients with advanced chronic kidney disease (CKD). Recently, it was reported that stopping RASIs in advanced CKD was associated with increased mortality and cardiovascular (CV) events; however, it remains unclear whether stopping RASIs before dialysis initiation affects clinical outcomes after dialysis, which this study aimed to evaluate. In this multicenter prospective cohort study in Japan, we included 717 patients (mean age, 67 years; 68% male) who had a nephrology care duration ≥90 days, initiated hemodialysis, and used RASIs 3 months before hemodialysis initiation. The multivariable adjusted Cox models were used to compare mortality and CV event risk between 650 (91%) patients who continued RASIs until hemodialysis initiation and 67 (9.3%) patients who stopped RASIs. During a median follow-up period of 3.5 years, 170 (24%) patients died and 228 (32%) experienced CV events. Compared with continuing RASIs, stopping RASIs was unassociated with mortality (adjusted hazard ratio [aHR]: 0.82; 95% confidence interval [CI]: 0.50–1.34) but was associated with higher CV events (aHR: 1.59; 95% CI: 1.06–2.38). Subgroup analyses showed that the risk of stopping RASIs for CV events was particularly high in patients aged <75 years, with a significant interaction between stopping RASIs and age. This study revealed that patients who stopped RASIs immediately before dialysis initiation were associated with subsequent higher CV events. Active screening for CV disease may be especially beneficial for these patients.
A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution
Authors: Nardone Stefano , De Luca Roberto , Zito Antonino , Klymko Nataliya , Nicoloutsopoulos Dimitris , Amsalem Oren , Brannigan Cory , Resch Jon M. , Jacobs Christopher L. , Pant Deepti , Veregge Molly , Srinivasan Harini , Grippo Ryan M. , Yang Zongfang , Zeidel Mark L. , Andermann Mark L. , Harris Kenneth D. , Tsai Linus T. , Arrigoni Elda , Verstegen Anne M. J. , Saper Clifford B. , Lowell Bradford B. 
Published: March 2024

AbstractThe “dorsal pons”, or “dorsal pontine tegmentum” (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed the unique marker genes of many neuronal subtypes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study’s translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.
Full-waveform tomography reveals iron spin crossover in Earth’s lower mantle
Authors: Cobden Laura , Zhuang Jingyi , Lei Wenjie , Wentzcovitch Renata , Trampert Jeannot , Tromp Jeroen 
Published: March 2024

AbstractThree-dimensional models of Earth’s seismic structure can be used to identify temperature-dependent phenomena, including mineralogical phase and spin transformations, that are obscured in 1-D spherical averages. Full-waveform tomography maps seismic wave-speeds inside the Earth in three dimensions, at a higher resolution than classical methods. By providing absolute wave speeds (rather than perturbations) and simultaneously constraining bulk and shear wave speeds over the same frequency range, it becomes feasible to distinguish variations in temperature from changes in composition or spin state. We present a quantitative joint interpretation of bulk and shear wave speeds in the lower mantle, using a recently published full-waveform tomography model. At all depths the diversity of wave speeds cannot be explained by an isochemical mantle. Between 1000 and 2500 km depth, hypothetical mantle models containing an electronic spin crossover in ferropericlase provide a significantly better fit to the wave-speed distributions, as well as more realistic temperatures and silica contents, than models without a spin crossover. Below 2500 km, wave speed distributions are explained by an enrichment in silica towards the core-mantle boundary. This silica enrichment may represent the fractionated remains of an ancient basal magma ocean.
Extensive DNA methylome rearrangement during early lamprey embryogenesis
Authors: Angeloni Allegra , Fissette Skye , Kaya Deniz , Hammond Jillian M. , Gamaarachchi Hasindu , Deveson Ira W. , Klose Robert J. , Li Weiming , Zhang Xiaotian , Bogdanovic Ozren 
Published: March 2024

AbstractDNA methylation (5mC) is a repressive gene regulatory mark widespread in vertebrate genomes, yet the developmental dynamics in which 5mC patterns are established vary across species. While mammals undergo two rounds of global 5mC erasure, teleosts, for example, exhibit localized maternal-to-paternal 5mC remodeling. Here, we studied 5mC dynamics during the embryonic development of sea lamprey, a jawless vertebrate which occupies a critical phylogenetic position as the sister group of the jawed vertebrates. We employed 5mC quantification in lamprey embryos and tissues, and discovered large-scale maternal-to-paternal epigenome remodeling that affects ~30% of the embryonic genome and is predominantly associated with partially methylated domains. We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in diverse developmental strategies.
Dynamic chloride ion adsorption on single iridium atom boosts seawater oxidation catalysis
Authors: Duan Xinxuan , Sha Qihao , Li Pengsong , Li Tianshui , Yang Guotao , Liu Wei , Yu Ende , Zhou Daojin , Fang Jinjie , Chen Wenxing , Chen Yizhen , Zheng Lirong , Liao Jiangwen , Wang Zeyu , Li Yaping , Yang Hongbin , Zhang Guoxin , Zhuang Zhongbin , Hung Sung-Fu , Jing Changfei , Luo Jun , Bai Lu , Dong Juncai , Xiao Hai , Liu Wen , Kuang Yun , Liu Bin , Sun Xiaoming 
Published: March 2024

AbstractSeawater electrolysis offers a renewable, scalable, and economic means for green hydrogen production. However, anode corrosion by Cl- pose great challenges for its commercialization. Herein, different from conventional catalysts designed to repel Cl- adsorption, we develop an atomic Ir catalyst on cobalt iron layered double hydroxide (Ir/CoFe-LDH) to tailor Cl- adsorption and modulate the electronic structure of the Ir active center, thereby establishing a unique Ir-OH/Cl coordination for alkaline seawater electrolysis. Operando characterizations and theoretical calculations unveil the pivotal role of this coordination state to lower OER activation energy by a factor of 1.93. The Ir/CoFe-LDH exhibits a remarkable oxygen evolution reaction activity (202 mV overpotential and TOF = 7.46 O2 s−1) in 6 M NaOH+2.8 M NaCl, superior over Cl--free 6 M NaOH electrolyte (236 mV overpotential and TOF = 1.05 O2 s−1), with 100% catalytic selectivity and stability at high current densities (400-800 mA cm−2) for more than 1,000 h.
Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis
Authors: Hua Xuanwen , Han Keyi , Mandracchia Biagio , Radmand Afsane , Liu Wenhao , Kim Hyejin , Yuan Zhou , Ehrlich Samuel M. , Li Kaitao , Zheng Corey , Son Jeonghwan , Silva Trenkle Aaron D. , Kwong Gabriel A. , Zhu Cheng , Dahlman James E. , Jia Shu 
Published: March 2024

AbstractImaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
Mating harassment may boost the effectiveness of the sterile insect technique for Aedes mosquitoes
Authors: Zhang Dongjing , Maiga Hamidou , Li Yongjun , Bakhoum Mame Thierno , Wang Gang , Sun Yan , Damiens David , Mamai Wadaka , Bimbilé Somda Nanwintoum Séverin , Wallner Thomas , Bueno-Masso Odet , Martina Claudia , Kotla Simran Singh , Yamada Hanano , Lu Deng , Tan Cheong Huat , Guo Jiatian , Feng Qingdeng , Zhang Junyan , Zhao Xufei , Paerhande Dilinuer , Pan Wenjie , Wu Yu , Zheng Xiaoying , Wu Zhongdao , Xi Zhiyong , Vreysen Marc J. B. , Bouyer Jérémy 
Published: March 2024

AbstractThe sterile insect technique is based on the overflooding of a target population with released sterile males inducing sterility in the wild female population. It has proven to be effective against several insect pest species of agricultural and veterinary importance and is under development forAedesmosquitoes. Here, we show that the release of sterile males at high sterile male to wild female ratios may also impact the target female population through mating harassment. Under laboratory conditions, male to female ratios above 50 to 1 reduce the longevity of femaleAedesmosquitoes by reducing their feeding success. Under controlled conditions, blood uptake of females from an artificial host or from a mouse and biting rates on humans are also reduced. Finally, in a field trial conducted in a 1.17 ha area in China, the female biting rate is reduced by 80%, concurrent to a reduction of female mosquito density of 40% due to the swarming of males around humans attempting to mate with the female mosquitoes. This suggests that the sterile insect technique does not only suppress mosquito vector populations through the induction of sterility, but may also reduce disease transmission due to increased female mortality and lower host contact.
Vegetation enhances curvature-driven dynamics in meandering rivers
Authors: Finotello Alvise , Ielpi Alessandro , Lapôtre Mathieu G. A. , Lazarus Eli D. , Ghinassi Massimiliano , Carniello Luca , Favaro Serena , Tognin Davide , D’Alpaos Andrea 
Published: March 2024

AbstractStabilization of riverbanks by vegetation has long been considered necessary to sustain single-thread meandering rivers. However, observation of active meandering in modern barren landscapes challenges this assumption. Here, we investigate a globally distributed set of modern meandering rivers with varying riparian vegetation densities, using satellite imagery and statistical analyses of meander-form descriptors and migration rates. We show that vegetation enhances the coefficient of proportionality between channel curvature and migration rates at low curvatures, and that this effect wanes in curvier channels irrespective of vegetation density. By stabilizing low-curvature reaches and allowing meanders to gain sinuosity as channels migrate laterally, vegetation quantifiably affects river morphodynamics. Any causality between denser vegetation and higher meander sinuosity, however, cannot be inferred owing to more frequent avulsions in modern non-vegetated environments. By illustrating how vegetation affects channel mobility and floodplain reworking, our findings have implications for assessing carbon stocks and fluxes in river floodplains.
Color construction of multi-colored carbon fibers using glucose
Authors: Zhou Sijie , Zhang Chunhua , Fu Zhuan , Zhu Qimeng , Zhou Zhaozixuan , Gong Junyao , Zhu Na , Wang Xiaofeng , Wei Xinjie , Xia Liangjun , Xu Weilin 
Published: March 2024

AbstractCarbon fibers (CFs) have attracted attention in the automotive, aviation, and aerospace industries. However, the coloration of CFs is challenging due to their brittleness, inertness, complexity, and time/energy-intensive processes. Herein, inspired by the naturally grown protrusive nanostructures on the green central surface of peacock back feathers, we report an in-situ self-growing strategy for developing carbon spheres (CSs) on the CFs surface to achieve color tuning. This is achieved via the dynamic growth of CSs using glucose as the feeding material. Combined with the coloration process, the interaction between CSs and CFs promotes stable interfacial forces in integrated molding. This strategy allows the coloring system to continuously vary its color in a designated manner, thereby, endowing it with satisfactory mechanical robustness, acid durability, and light fastness. We anticipate this developed approach can be potentially competitive in the color construction of CFs with multi-colors due to its low-cost manufacturing.
Incorporating long-range electrostatics in neural network potentials via variational charge equilibration from shortsighted ingredients
Authors: Shaidu Yusuf , Pellegrini Franco , Küçükbenli Emine , Lot Ruggero , de Gironcoli Stefano 
Published: March 2024

AbstractWe present a new approach to construct machine-learned interatomic potentials including long-range electrostatic interactions based on a charge equilibration scheme. This new approach can accurately describe the potential energy surface of systems with ionic and covalent interactions as well as systems with multiple charge states. Moreover, it can either be regressed against known atomic charge decompositions or trained without charge targets, without compromising the accuracy of energy and forces. We benchmark our approach against other state-of-the-art models and prove it to have equivalent performances on a set of simple reference systems while being less computationally expensive. Finally, we demonstrate the accuracy of our approach on complex systems: solid and liquid state sodium chloride. We attain accuracy in energy and forces better than the model based on local descriptors and show that our electrostatic approach can capture the density functional theory tail of the potential energy surface of the isolated Na-Cl dimer, which the local descriptor-based model fails to describe.
Relation of life sciences students’ metacognitive monitoring to neural activity during biology error detection
Authors: Behrendt Mei Grace , Clark Carrie , Elliott McKenna , Dauer Joseph 
Published: March 2024

AbstractMetacognitive calibration—the capacity to accurately self-assess one’s performance—forms the basis for error detection and self-monitoring and is a potential catalyst for conceptual change. Limited brain imaging research on authentic learning tasks implicates the lateral prefrontal and anterior cingulate brain regions in expert scientific reasoning. This study aimed to determine how variation in undergraduate life sciences students’ metacognitive calibration relates to their brain activity when evaluating the accuracy of biological models. Fifty undergraduate students enrolled in an introductory life sciences course completed a biology model error detection task during fMRI. Students with higher metacognitive calibration recruited lateral prefrontal regions linked in prior research to expert STEM reasoning to a greater extent than those with lower metacognitive calibration. Findings suggest that metacognition relates to important individual differences in undergraduate students’ use of neural resources during an authentic educational task and underscore the importance of fostering metacognitive calibration in the classroom.
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression
Authors: Claes Katrien , Van Herpe Dries , Vanluchene Robin , Roels Charlotte , Van Moer Berre , Wyseure Elise , Vandewalle Kristof , Eeckhaut Hannah , Yilmaz Semiramis , Vanmarcke Sandrine , Çıtak Erhan , Fijalkowska Daria , Grootaert Hendrik , Lonigro Chiara , Meuris Leander , Michielsen Gitte , Naessens Justine , van Schie Loes , De Rycke Riet , De Bruyne Michiel , Borghgraef Peter , Callewaert Nico 
Published: March 2024

AbstractThe industrial yeast Komagataella phaffii (formerly named Pichia pastoris) is commonly used to synthesize recombinant proteins, many of which are used as human therapeutics or in food. However, the basic strain, named NRRL Y-11430, from which all commercial hosts are derived, is not available without restrictions on its use. Comparative genome sequencing leaves little doubt that NRRL Y-11430 is derived from a K. phaffii type strain deposited in the UC Davis Phaff Yeast Strain Collection in 1954. We analysed four equivalent type strains in several culture collections and identified the NCYC 2543 strain, from which we started to develop an open-access Pichia chassis strain that anyone can use to produce recombinant proteins to industry standards. NRRL Y-11430 is readily transformable, which we found to be due to a HOC1 open-reading-frame truncation that alters cell-wall mannan. We introduced the HOC1 open-reading-frame truncation into NCYC 2543, which increased the transformability and improved secretion of some but not all of our tested proteins. We provide our genome-sequenced type strain, the hoc1tr derivative that we named OPENPichia as well as a synthetic, modular expression vector toolkit under liberal end-user distribution licences as an unencumbered OPENPichia resource for the microbial biotechnology community.