bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level
Authors: John Lukas , Poos Alexandra M. , Brobeil Alexander , Schinke Carolina , Huhn Stefanie , Prokoph Nina , Lutz Raphael , Wagner Barbara , Zangari Maurizio , Tirier Stephan M. , Mallm Jan-Philipp , Schumacher Sabrina , Vonficht Dominik , Solé-Boldo Llorenç , Quick Sabine , Steiger Simon , Przybilla Moritz J. , Bauer Katharina , Baumann Anja , Hemmer Stefan , Rehnitz Christoph , Lückerath Christian , Sachpekidis Christos , Mechtersheimer Gunhild , Haberkorn Uwe , Dimitrakopoulou-Strauss Antonia , Reichert Philipp , Barlogie Bart , Müller-Tidow Carsten , Goldschmidt Hartmut , Hillengass Jens , Rasche Leo , Haas Simon F. , van Rhee Frits , Rippe Karsten , Raab Marc S. , Sauer Sandra , Weinhold Niels 
Published: August 2023

AbstractIn multiple myeloma spatial differences in the subclonal architecture, molecular signatures and composition of the microenvironment remain poorly characterized. To address this shortcoming, we perform multi-region sequencing on paired random bone marrow and focal lesion samples from 17 newly diagnosed patients. Using single-cell RNA- and ATAC-seq we find a median of 6 tumor subclones per patient and unique subclones in focal lesions. Genetically identical subclones display different levels of spatial transcriptional plasticity, including nearly identical profiles and pronounced heterogeneity at different sites, which can include differential expression of immunotherapy targets, such as CD20 and CD38. Macrophages are significantly depleted in the microenvironment of focal lesions. We observe proportional changes in the T-cell repertoire but no site-specific expansion of T-cell clones in intramedullary lesions. In conclusion, our results demonstrate the relevance of considering spatial heterogeneity in multiple myeloma with potential implications for models of cell-cell interactions and disease progression.
RORγt-Raftlin1 complex regulates the pathogenicity of Th17 cells and colonic inflammation
Authors: Singh Amir Kumar , Kumar Ritesh , Yin Jianyi , Brooks II John F. , Kathania Mahesh , Mukherjee Sandip , Kumar Jitendra , Conlon Kevin P. , Basrur Venkatesha , Chen Zhe , Han Xianlin , Hooper Lora V. , Burstein Ezra , Venuprasad K. 
Published: August 2023

AbstractTh17 cells that produce Interleukin IL-17 are pathogenic in many human diseases, including inflammatory bowel disease, but are, paradoxically, essential for maintaining the integrity of the intestinal barrier in a non-inflammatory state. However, the intracellular mechanisms that regulate distinct transcriptional profiles and functional diversity of Th17 cells remain unclear. Here we show Raftlin1, a lipid raft protein, specifically upregulates and forms a complex with RORγt in pathogenic Th17 cells. Disruption of the RORγt-Raftlin1 complex results in the reduction of pathogenic Th17 cells in response to Citrobacter rodentium; however, there is no effect on nonpathogenic Th17 cells in response to commensal segmented filamentous bacteria. Mechanistically, we show that Raftlin1 recruits distinct phospholipids to RORγt and promotes the pathogenicity of Th17 cells. Thus, we have identified a mechanism that drives the pathogenic function of Th17 cells, which could provide a platform for advanced therapeutic strategies to dampen Th17-mediated inflammatory diseases.
The RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors
Authors: Kanarek Katarzyna , Fridman Chaya Mushka , Bosis Eran , Salomon Dor 
Published: August 2023

AbstractBacteria use the type VI secretion system (T6SS) to deliver toxic effectors into bacterial or eukaryotic cells during interbacterial competition, host colonization, or when resisting predation. Identifying effectors is a challenging task, as they lack canonical secretion signals or universally conserved domains. Here, we identify a protein domain, RIX, that defines a class of polymorphic T6SS cargo effectors. RIX is widespread in the Vibrionaceae family and is located at N-termini of proteins containing diverse antibacterial and anti-eukaryotic toxic domains. We demonstrate that RIX-containing proteins are delivered via T6SS into neighboring cells and that RIX is necessary and sufficient for T6SS-mediated secretion. In addition, RIX-containing proteins can enable the T6SS-mediated delivery of other cargo effectors by a previously undescribed mechanism. The identification of RIX-containing proteins significantly enlarges the repertoire of known T6SS effectors, especially those with anti-eukaryotic activities. Furthermore, our findings also suggest that T6SSs may play an underappreciated role in the interactions between vibrios and eukaryotes.
Charge-state lifetimes of single molecules on few monolayers of NaCl
Authors: Kaiser Katharina , Lieske Leonard-Alexander , Repp Jascha , Gross Leo 
Published: August 2023

AbstractIn molecular tunnel junctions, where the molecule is decoupled from the electrodes by few-monolayers-thin insulating layers, resonant charge transport takes place by sequential charge transfer to and from the molecule which implies transient charging of the molecule. The corresponding charge state transitions, which involve tunneling through the insulating decoupling layers, are crucial for understanding electrically driven processes such as electroluminescence or photocurrent generation in such a geometry. Here, we use scanning tunneling microscopy to investigate the decharging of single ZnPc and H2Pc molecules through NaCl films of 3 to 5 monolayers thickness on Cu(111) and Au(111). To this end, we approach the tip to the molecule at resonant tunnel conditions up to a regime where charge transport is limited by tunneling through the NaCl film. The resulting saturation of the tunnel current is a direct measure of the lifetimes of the anionic and cationic states, i.e., the molecule’s charge-state lifetime, and thus provides a means to study charge dynamics and, thereby, exciton dynamics. Comparison of anion and cation lifetimes on different substrates reveals the critical role of the level alignment with the insulator’s conduction and valence band, and the metal-insulator interface state.
Sustainable production of dopamine hydrochloride from softwood lignin
Authors: Dong Lin , Wang Yanqin , Dong Yuguo , Zhang Yin , Pan Mingzhu , Liu Xiaohui , Gu Xiaoli , Antonietti Markus , Chen Zupeng 
Published: August 2023

AbstractDopamine is not only a widely used commodity pharmaceutical for treating neurological diseases but also a highly attractive base for advanced carbon materials. Lignin, the waste from the lignocellulosic biomass industry, is the richest source of renewable aromatics on earth. Efficient production of dopamine direct from lignin is a highly desirable target but extremely challenging. Here, we report an innovative strategy for the sustainable production of dopamine hydrochloride from softwood lignin with a mass yield of 6.4 wt.%. Significantly, the solid dopamine hydrochloride is obtained by a simple filtration process in purity of 98.0%, which avoids the tedious separation and purification steps. The approach begins with the acid-catalyzed depolymerization, followed by deprotection, hydrogen-borrowing amination, and hydrolysis of methoxy group, transforming lignin into dopamine hydrochloride. The technical economic analysis predicts that this process is an economically competitive production process. This study fulfills the unexplored potential of dopamine hydrochloride synthesis from lignin.
Multiple antiferromagnetic phases and magnetic anisotropy in exfoliated CrBr3 multilayers
Authors: Yao Fengrui , Multian Volodymyr , Wang Zhe , Ubrig Nicolas , Teyssier Jérémie , Wu Fan , Giannini Enrico , Gibertini Marco , Gutiérrez-Lezama Ignacio , Morpurgo Alberto F. 
Published: August 2023

AbstractIn twisted two-dimensional (2D) magnets, the stacking dependence of the magnetic exchange interaction can lead to regions of ferromagnetic and antiferromagnetic interlayer order, separated by non-collinear, skyrmion-like spin textures. Recent experimental searches for these textures have focused on CrI3, known to exhibit either ferromagnetic or antiferromagnetic interlayer order, depending on layer stacking. However, the very strong uniaxial anisotropy of CrI3 disfavors smooth non-collinear phases in twisted bilayers. Here, we report the experimental observation of three distinct magnetic phases—one ferromagnetic and two antiferromagnetic—in exfoliated CrBr3 multilayers, and reveal that the uniaxial anisotropy is significantly smaller than in CrI3. These results are obtained by magnetoconductance measurements on CrBr3 tunnel barriers and Raman spectroscopy, in conjunction with density functional theory calculations, which enable us to identify the stackings responsible for the different interlayer magnetic couplings. The detection of all locally stable magnetic states predicted to exist in CrBr3 and the excellent agreement found between theory and experiments, provide complete information on the stacking-dependent interlayer exchange energy and establish twisted bilayer CrBr3 as an ideal system to deterministically create non-collinear magnetic phases.
Genome mining shows that retroviruses are pervasively invading vertebrate genomes
Authors: Wang Jianhua , Han Guan-Zhu 
Published: August 2023

AbstractEndogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
LINE-1 regulates cortical development by acting as long non-coding RNAs
Authors: Mangoni Damiano , Simi Alessandro , Lau Pierre , Armaos Alexandros , Ansaloni Federico , Codino Azzurra , Damiani Devid , Floreani Lavinia , Di Carlo Valerio , Vozzi Diego , Persichetti Francesca , Santoro Claudio , Pandolfini Luca , Tartaglia Gian Gaetano , Sanges Remo , Gustincich Stefano 
Published: August 2023

AbstractLong Interspersed Nuclear Elements-1s (L1s) are transposable elements that constitute most of the genome’s transcriptional output yet have still largely unknown functions. Here we show that L1s are required for proper mouse brain corticogenesis operating as regulatory long non-coding RNAs. They contribute to the regulation of the balance between neuronal progenitors and differentiation, the migration of post-mitotic neurons and the proportions of different cell types. In cortical cultured neurons, L1 RNAs are mainly associated to chromatin and interact with the Polycomb Repressive Complex 2 (PRC2) protein subunits enhancer of Zeste homolog 2 (Ezh2) and suppressor of zeste 12 (Suz12). L1 RNA silencing influences PRC2’s ability to bind a portion of its targets and the deposition of tri-methylated histone H3 (H3K27me3) marks. Our results position L1 RNAs as crucial signalling hubs for genome-wide chromatin remodelling, enabling the fine-tuning of gene expression during brain development and evolution.
Surprising stability of recent global carbon cycling enables improved fossil fuel emission verification
Authors: Birner Benjamin , Rödenbeck Christian , Dohner Julia L. , Schwartzman Armin , Keeling Ralph F. 
Published: August 2023

AbstractThe interannual to decadal variability in natural carbon sinks limits the explanation of recent changes in atmospheric CO2 concentration. Here we account for interannual and decadal variability using a simple quasi-mechanistic model of the net land carbon exchange with terms scaling with atmospheric CO2 and a weighted spatial average of temperature anomalies. This approach reduces the unexplained residual in Earth’s carbon cycle budget from ±0.76 GtC per year obtained using process models to ±0.50 GtC per year, with the largest improvements on decadal timescales despite assuming constant dynamics. Our findings reveal remarkable stability of the carbon cycle and allow verification of reported global emissions to within 4.4% (95% confidence level) over the five-year stocktake cycle of the Paris Agreement—half the uncertainty reported previously.
Developmental changes in exploration resemble stochastic optimization
Authors: Giron Anna P. , Ciranka Simon , Schulz Eric , van den Bos Wouter , Ruggeri Azzurra , Meder Björn , Wu Charley M. 
Published: August 2023

AbstractHuman development is often described as a ‘cooling off’ process, analogous to stochastic optimization algorithms that implement a gradual reduction in randomness over time. Yet there is ambiguity in how to interpret this analogy, due to a lack of concrete empirical comparisons. Using data from n = 281 participants ages 5 to 55, we show that cooling off does not only apply to the single dimension of randomness. Rather, human development resembles an optimization process of multiple learning parameters, for example, reward generalization, uncertainty-directed exploration and random temperature. Rapid changes in parameters occur during childhood, but these changes plateau and converge to efficient values in adulthood. We show that while the developmental trajectory of human parameters is strikingly similar to several stochastic optimization algorithms, there are important differences in convergence. None of the optimization algorithms tested were able to discover reliably better regions of the strategy space than adult participants on this task.
Single-nucleotide variant calling in single-cell sequencing data with Monopogen
Authors: Dou Jinzhuang , Tan Yukun , Kock Kian Hong , Wang Jun , Cheng Xuesen , Tan Le Min , Han Kyung Yeon , Hon Chung-Chau , Park Woong-Yang , Shin Jay W. , Jin Haijing , Wang Yujia , Chen Han , Ding Li , Prabhakar Shyam , Navin Nicholas , Chen Rui , Chen Ken 
Published: August 2023

AbstractSingle-cell omics technologies enable molecular characterization of diverse cell types and states, but how the resulting transcriptional and epigenetic profiles depend on the cell’s genetic background remains understudied. We describe Monopogen, a computational tool to detect single-nucleotide variants (SNVs) from single-cell sequencing data. Monopogen leverages linkage disequilibrium from external reference panels to identify germline SNVs and detects putative somatic SNVs using allele cosegregating patterns at the cell population level. It can identify 100 K to 3 M germline SNVs achieving a genotyping accuracy of 95%, together with hundreds of putative somatic SNVs. Monopogen-derived genotypes enable global and local ancestry inference and identification of admixed samples. It identifies variants associated with cardiomyocyte metabolic levels and epigenomic programs. It also improves putative somatic SNV detection that enables clonal lineage tracing in primary human clonal hematopoiesis. Monopogen brings together population genetics, cell lineage tracing and single-cell omics to uncover genetic determinants of cellular processes.
PCNA recruits cohesin loader Scc2 to ensure sister chromatid cohesion
Authors: Psakhye Ivan , Kawasumi Ryotaro , Abe Takuya , Hirota Kouji , Branzei Dana 
Published: August 2023

AbstractSister chromatid cohesion, established during replication by the ring-shaped multiprotein complex cohesin, is essential for faithful chromosome segregation. Replisome-associated proteins are required to generate cohesion by two independent pathways. One mediates conversion of cohesins bound to unreplicated DNA ahead of replication forks into cohesive entities behind them, while the second promotes cohesin de novo loading onto newly replicated DNA. The latter process depends on the cohesin loader Scc2 (NIPBL in vertebrates) and the alternative PCNA loader CTF18-RFC. However, the mechanism of de novo cohesin loading during replication is unknown. Here we show that PCNA physically recruits the yeast cohesin loader Scc2 via its C-terminal PCNA-interacting protein motif. Binding to PCNA is crucial, as the scc2-pip mutant deficient in Scc2–PCNA interaction is defective in cohesion when combined with replisome mutants of the cohesin conversion pathway. Importantly, the role of NIPBL recruitment to PCNA for cohesion generation is conserved in vertebrate cells.
Towards the automation of NIR spectroscopy to assess vineyard water status spatial–temporal variability from a ground moving vehicle
Authors: Fernández-Novales Juan , Barrio Ignacio , Diago María Paz 
Published: August 2023

AbstractIrrigation has a strong impact in terms of yield regulation and grape and wine quality, so the implementation of precision watering systems would facilitate the decision-making process about the water use efficiency and the irrigation scheduling in viticulture. The objectives of this work were two-fold. On one hand, to compare and assess grapevine water status using two different spectral devices assembled in a mobile platform and to evaluate their capability to map the spatial variability of the plant water status in two commercial vineyards from July to early October in season 2021, and secondly to develop an algorithm capable of automate the spectral acquisition process using one of the two spectral sensors previously tested. Contemporarily to the spectral measurements collected from the ground vehicle at solar noon, stem water potential (Ψs) was used as the reference method to evaluate the grapevine water status. Calibration and prediction models for grapevine water status assessment were performed using the Partial least squares (PLS) regression and the Variable Importance in the Projection (VIP) method. The best regression models returned a determination coefficient for cross validation (R2cv) and external validation (R2p) of 0.70 and 0.75 respectively, and the standard error of cross validation (RMSECV) values were lower than 0.105 MPa and 0.128 MPa for Tempranillo and Graciano varieties using a more expensive and heavier near-infrared (NIR) spectrometer (spectral range 1200–2100 nm). Remarkable models were also built with the miniaturized, low-cost spectral sensor (operating between 900–1860 nm) ranging from 0.69 to 0.71 for R2cv, around 0.74 in both varieties for R2pand the RMSECV values were below 0.157 MPa, while the RMSEP values did not exceed 0.151 MPa in both commercial vineyards. This work also includes the development of a software which automates data acquisition and allows faster (up to 40% of time saving in the field) and more efficient deployment of the developed algorithm. The encouraging results presented in this work demonstrate the great potential of this methodology to assess the water status of the vineyard and estimate its spatial variability in different commercial vineyards, providing useful information for better irrigation scheduling.
Environmental factors induced crop raiding by wild Asian elephant (Elephas maximus) in the Eastern Economic Corridor, Thailand
Authors: Wettasin Maneepailin , Chaiyarat Rattanawat , Youngpoy Namphung , Jieychien Nawee , Sukmasuang Ronglarp , Tanhan Phanwimol 
Published: August 2023

AbstractCrop raiding are an increasing concern in wildlife conservation. This study identified the environmental factors that cause wild Asian elephants (Elephas maximus) to enter sub-urban and rural areas and share resources with humans in the Eastern Economic Corridor (EEC) in the eastern part of Thailand. The snowball method was used to interview villagers that had crop raiding experienced in seven provinces of the EEC and adjacent provinces in the eastern part of Thailand in 2020, and data from 183 households indicated that crop raiding had increased continuously from 2000 to 2020, especially in Chonburi, Chachoengsao, and Prachinburi provinces, which have seen increases in damaged agricultural areas. MaxEnt analysis showed an increase in incidents of crop raiding, while the elephants distribution area decreased from 9534 km2 in 2000 to 5199 km2 in 2010 and 4850 km2 in 2020. The study area has had land use changes in the low elevations from croplands of cassava and sugar cane to eucalyptus, para rubber, and fruits. These mixed crop plantations provide a pseudo-habitat for wild Asian elephants. The results from this study provide evidence that changes in land use and reduction of suitable habitat are factors that influenced the movement of wild Asian elephants to the rural agricultural areas and increased the incidents of crop raiding.
Quantitative analysis of defect states in InGaZnO within 2 eV below the conduction band via photo-induced current transient spectroscopy
Authors: Hong Hyunmin , Kim Min Jung , Yi Dong-Joon , Moon Yeon-Keon , Son Kyoung-Seok , Lim Jun Hyung , Jeong KwangSik , Chung Kwun-Bum 
Published: August 2023

AbstractThis work investigates the function of the oxygen partial pressure in photo-induced current measurement of extended defect properties related to the distribution and quantity of defect states in electronic structures. The Fermi level was adjusted by applying a negative gate bias in the TFT structure, and the measurable range of activation energy was extended to < 2.0 eV. Calculations based on density functional theory are used to investigate the changes in defect characteristics and the role of defects at shallow and deep levels as a function of oxygen partial pressure. Device characteristics, such as mobility and threshold voltage shift under a negative gate bias, showed a linear correlation with the ratio of shallow level to deep level defect density. Shallow level and deep level defects are organically related, and both defects must be considered when understanding device characteristics.