bluuebunny/crossref_metadata_2025_split huggingface dataset:
Late Miocene C4 Grassland Fire Feedbacks on the Indian Subcontinent
Authors: Karp Allison T. , Uno Kevin T. , Polissar Pratigya J. , Freeman Katherine H. 
Published: March 2021

AbstractFire dynamics potentially account for the asynchronous timing of the expansion of C4 grasslands throughout the Mio‐Pliocene world. Yet how fire, climate, and ecosystems interacted in different settings remain poorly constrained because it is difficult to quantify fires and fuel source over these timescales. Here, we apply molecular proxies for fire occurrence alongside records of vegetation change and paleohydrology in Bengal Fan sediments (ODP Leg 116) to examine fire feedbacks on the south Asian continent. We employ abundances of polycyclic aromatic hydrocarbons (PAHs) to reconstruct fire occurrence and δ13C measurements of pyrogenic PAHs to constrain fuel source and grassland burning. This combination allowed us to test whether: (1) a fire‐seasonality forcing facilitated the expansion of grassland ecosystems and (2) a fire‐C4 grass burning feedback maintained these systems. PAHs can be sourced from weathered fossil carbon (i.e., a petrogenic source) and from burned terrestrial biomass (i.e., a pyrogenic source). Alkylated and non‐alkylated structure abundance data distinguished pyrogenic from petrogenic sourced samples. A sharp increase in pyrogenic PAHs along with increases in δ2H and δ13C values of plant waxes at 7.4 Ma indicates increased fire coincided with the onset of C4 expansion and hydrologic change in South Asia. The correlated 13C enrichment in PAHs, 13C enrichment in plant waxes, and increased abundances of PAHs suggest burning of C4 grasslands likely maintained open ecosystems. Our results link fire to the initial opening of grassland ecosystems on a subcontinental‐scale and support disturbance as a critical mechanism of terrestrial biome transition.
Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia
Authors: Lundgren Sofie , Keränen Mikko A. I. , Kankainen Matti , Huuhtanen Jani , Walldin Gunilla , Kerr Cassandra M. , Clemente Michael , Ebeling Freja , Rajala Hanna , Brück Oscar , Lähdesmäki Harri , Hannula Sari , Hannunen Tiina , Ellonen Pekka , Young Neal S. , Ogawa Seishi , Maciejewski Jaroslaw P. , Hellström-Lindberg Eva , Mustjoki Satu 
Published: March 2021

AbstractThe prevalence and functional impact of somatic mutations in nonleukemic T cells is not well characterized, although clonal T-cell expansions are common. In immune-mediated aplastic anemia (AA), cytotoxic T-cell expansions are shown to participate in disease pathogenesis. We investigated the mutation profiles of T cells in AA by a custom panel of 2533 genes. We sequenced CD4+ and CD8+ T cells of 24 AA patients and compared the results to 20 healthy controls and whole-exome sequencing of 37 patients with AA. Somatic variants were common both in patients and healthy controls but enriched to AA patients’ CD8+ T cells, which accumulated most mutations on JAK-STAT and MAPK pathways. Mutation burden was associated with CD8+ T-cell clonality, assessed by T-cell receptor beta sequencing. To understand the effect of mutations, we performed single-cell sequencing of AA patients carrying STAT3 or other mutations in CD8+ T cells. STAT3 mutated clone was cytotoxic, clearly distinguishable from other CD8+ T cells, and attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells are common, associate with clonality, and can alter T-cell phenotype, warranting further investigation of their role in the pathogenesis of AA.
Adaptive immunity at the crossroads of autophagy and metabolism
Authors: Metur Shree Padma , Klionsky Daniel J. 
Published: March 2021

AbstractThe function of lymphocytes is dependent on their plasticity, particularly their adaptation to energy availability and environmental stress, and their protein synthesis machinery. Lymphocytes are constantly under metabolic stress, and macroautophagy/autophagy is the primary metabolic pathway that helps cells overcome stressors. The intrinsic role of autophagy in regulating the metabolism of adaptive immune cells has recently gained increasing attention. In this review, we summarize and discuss the versatile roles of autophagy in regulating cellular metabolism and the implications of autophagy for immune cell function and fate, especially for T and B lymphocytes.
Universal resilience patterns in labor markets
Authors: Moro Esteban , Frank Morgan R. , Pentland Alex , Rutherford Alex , Cebrian Manuel , Rahwan Iyad 
Published: March 2021

AbstractCities are the innovation centers of the US economy, but technological disruptions can exclude workers and inhibit a middle class. Therefore, urban policy must promote the jobs and skills that increase worker pay, create employment, and foster economic resilience. In this paper, we model labor market resilience with an ecologically-inspired job network constructed from the similarity of occupations’ skill requirements. This framework reveals that the economic resilience of cities is universally and uniquely determined by the connectivity within a city’s job network. US cities with greater job connectivity experienced lower unemployment during the Great Recession. Further, cities that increase their job connectivity see increasing wage bills, and workers of embedded occupations enjoy higher wages than their peers elsewhere. Finally, we show how job connectivity may clarify the augmenting and deleterious impact of automation in US cities. Policies that promote labor connectivity may grow labor markets and promote economic resilience.
Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer
Authors: Baca Sylvan C. , Takeda David Y. , Seo Ji-Heui , Hwang Justin , Ku Sheng Yu , Arafeh Rand , Arnoff Taylor , Agarwal Supreet , Bell Connor , O’Connor Edward , Qiu Xintao , Alaiwi Sarah Abou , Corona Rosario I. , Fonseca Marcos A. S. , Giambartolomei Claudia , Cejas Paloma , Lim Klothilda , He Monica , Sheahan Anjali , Nassar Amin , Berchuck Jacob E. , Brown Lisha , Nguyen Holly M. , Coleman Ilsa M. , Kaipainen Arja , De Sarkar Navonil , Nelson Peter S. , Morrissey Colm , Korthauer Keegan , Pomerantz Mark M. , Ellis Leigh , Pasaniuc Bogdan , Lawrenson Kate , Kelly Kathleen , Zoubeidi Amina , Hahn William C. , Beltran Himisha , Long Henry W. , Brown Myles , Corey Eva , Freedman Matthew L. 
Published: March 2021

AbstractLineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. Here, we investigate the epigenomic basis of this resistance mechanism by profiling histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identify a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying cancer dependencies through epigenomic profiling.
Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales
Authors: Messelink Joris J. B. , van Teeseling Muriel C. F. , Janssen Jacqueline , Thanbichler Martin , Broedersz Chase P. 
Published: March 2021

AbstractThe order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi–C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.
Nanostructure of nickel-promoted indium oxide catalysts drives selectivity in CO2 hydrogenation
Authors: Frei Matthias S. , Mondelli Cecilia , García-Muelas Rodrigo , Morales-Vidal Jordi , Philipp Michelle , Safonova Olga V. , López Núria , Stewart Joseph A. , Ferré Daniel Curulla , Pérez-Ramírez Javier 
Published: March 2021

AbstractMetal promotion in heterogeneous catalysis requires nanoscale-precision architectures to attain maximized and durable benefits. Herein, we unravel the complex interplay between nanostructure and product selectivity of nickel-promoted In2O3in CO2hydrogenation to methanol through in-depth characterization, theoretical simulations, and kinetic analyses. Up to 10 wt.% nickel, InNi3patches are formed on the oxide surface, which cannot activate CO2but boost methanol production supplying neutral hydrogen species. Since protons and hydrides generated on In2O3drive methanol synthesis rather than the reverse water-gas shift but radicals foster both reactions, nickel-lean catalysts featuring nanometric alloy layers provide a favorable balance between charged and neutral hydrogen species. For nickel contents >10 wt.%, extended InNi3structures favor CO production and metallic nickel additionally present produces some methane. This study marks a step ahead towards green methanol synthesis and uncovers chemistry aspects of nickel that shall spark inspiration for other catalytic applications.
Fault zone heterogeneities explain depth-dependent pattern and evolution of slow earthquakes in Cascadia
Authors: Luo Yingdi , Liu Zhen 
Published: March 2021

AbstractSlow earthquakes including tremor and slow-slip events are recent additions to the conventional earthquake family and have a close link to megathrust earthquakes. Slow earthquakes along the Cascadia subduction zone display a diverse behavior at different spatiotemporal scales and an intriguing increase of events frequency with depth. However, what causes such variability, especially the depth-dependent behavior is not well understood. Here we build on a heterogeneous asperities-in-matrix fault model that incorporates differential pore pressure in a rate-and-state friction framework to investigate the underlying processes of the observed episodic tremor and slow-slip (ETS) variability. We find that the variations of effective normal stress (pore pressure) is one important factor in controlling ETS behavior. Our model reproduces the full complexity of ETS patterns and the depth-frequency scaling that agree quantitatively well with observations, suggesting that fault zone heterogeneities can be one viable mechanism to explain a broad spectrum of transient fault behaviors.
1/f-noise-free optical sensing with an integrated heterodyne interferometer
Authors: Jin Ming , Tang Shui-Jing , Chen Jin-Hui , Yu Xiao-Chong , Shu Haowen , Tao Yuansheng , Chen Antony K. , Gong Qihuang , Wang Xingjun , Xiao Yun-Feng 
Published: March 2021

AbstractOptical evanescent sensors can non-invasively detect unlabeled nanoscale objects in real time with unprecedented sensitivity, enabling a variety of advances in fundamental physics and biological applications. However, the intrinsic low-frequency noise therein with an approximately 1/f-shaped spectral density imposes an ultimate detection limit for monitoring many paramount processes, such as antigen-antibody reactions, cell motions and DNA hybridizations. Here, we propose and demonstrate a 1/f-noise-free optical sensor through an up-converted detection system. Experimentally, in a CMOS-compatible heterodyne interferometer, the sampling noise amplitude is suppressed by two orders of magnitude. It pushes the label-free single-nanoparticle detection limit down to the attogram level without exploiting cavity resonances, plasmonic effects, or surface charges on the analytes. Single polystyrene nanobeads and HIV-1 virus-like particles are detected as a proof-of-concept demonstration for airborne biosensing. Based on integrated waveguide arrays, our devices hold great potentials for multiplexed and rapid sensing of diverse viruses or molecules.
Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications
Authors: Chen Feng , Bai Min , Cao Xiaowen , Xue Jing , Zhao Yue , Wu Na , Wang Lei , Zhang Dexin , Zhao Yongxi 
Published: March 2021

AbstractExploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3’-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.
Small extracellular vesicles derived from interferon-γ pre-conditioned mesenchymal stromal cells effectively treat liver fibrosis
Authors: Takeuchi Suguru , Tsuchiya Atsunori , Iwasawa Takahiro , Nojiri Shunsuke , Watanabe Takayuki , Ogawa Masahiro , Yoshida Tomoaki , Fujiki Katsunori , Koui Yuta , Kido Taketomo , Yoshioka Yusuke , Fujita Mayu , Kikuta Junichi , Itoh Tohru , Takamura Masaaki , Shirahige Katsuhiko , Ishii Masaru , Ochiya Takahiro , Miyajima Atsushi , Terai Shuji 
Published: March 2021

AbstractMesenchymal stromal cells (MSCs) are used for ameliorating liver fibrosis and aiding liver regeneration after cirrhosis; Here, we analyzed the therapeutic potential of small extracellular vesicles (sEVs) derived from interferon-γ (IFN-γ) pre-conditioned MSCs (γ-sEVs). γ-sEVs effectively induced anti-inflammatory macrophages with high motility and phagocytic abilities in vitro, while not preventing hepatic stellate cell (HSC; the major source of collagen fiber) activation in vitro. The proteome analysis of MSC-derived sEVs revealed anti-inflammatory macrophage inducible proteins (e.g., annexin-A1, lactotransferrin, and aminopeptidase N) upon IFN-γ stimulation. Furthermore, by enabling CX3CR1+ macrophage accumulation in the damaged area, γ-sEVs ameliorated inflammation and fibrosis in the cirrhosis mouse model more effectively than sEVs. Single cell RNA-Seq analysis revealed diverse effects, such as induction of anti-inflammatory macrophages and regulatory T cells, in the cirrhotic liver after γ-sEV administration. Overall, IFN-γ pre-conditioning altered sEVs resulted in efficient tissue repair indicating a new therapeutic strategy.
Micro-RNA miR-542-3p suppresses decidualization by targeting ILK pathways in human endometrial stromal cells
Authors: Qu Xinlan , Fang Yuan , Zhuang Siying , Zhang Yuanzhen 
Published: March 2021

AbstractDecidualization of human endometrial stromal cells (HESCs) is a vital step for successful pregnancy. However, the process by which micro-RNAs (miRNAs) regulate decidualization remains elusive. Our current study was designed to identify the mechanism of miRNA miR-542-3p and its potential targets in regulating decidualization. The results showed that miR-542-3p was down-regulated in HESCs. Luciferase assay confirmed that integrin-linked kinase (ILK) is a direct target of miR-542-3p. Overexpression of miR-542-3p resulted in decreased ILK and downstream transforming growth factor β1 (TGF-β1) and SMAD family member 2 (SMAD2) expression. Additional expression of ILK attenuates the miR542-3p-induced down-regulation of TGF-β1 and SMAD2, changes properties such as suppression of proliferation and invasion, and induction of apoptosis, thereby affecting the differentiation of HESCs. Moreover, miR-542-3p overexpression caused down-regulation of the angiogenic factors vascular endothelial growth factor (VEGF), cyclooxygenase-2 (COX-2) and matrix metalloproteinase-9 (MMP-9), and the supernatant of HESCs overexpressing miR-542-3p inhibited the formation of tubular structures in human umbilical vein endothelial cells (HUVECs), suggesting that miR-542-3p inhibits angiogenesis of HUVECs. Furthermore, in our mouse model, following injection of miR-542-3p mimic into the endometrium of mice at pregnancy day 8 (D8), we found decreased miR-542-3p expression and loss of embryo implantation sites. In conclusion, miR-542-3p can affect the process of endometrial decidualization by down-regulating ILK. The present study adds further understanding of the process and regulation of decidualization.
Core–shell hydrogel microcapsules enable formation of human pluripotent stem cell spheroids and their cultivation in a stirred bioreactor
Authors: Fattahi Pouria , Rahimian Ali , Slama Michael Q. , Gwon Kihak , Gonzalez-Suarez Alan M. , Wolf Jadon , Baskaran Harihara , Duffy Caden D. , Stybayeva Gulnaz , Peterson Quinn P. , Revzin Alexander 
Published: March 2021

AbstractCellular therapies based on human pluripotent stem cells (hPSCs) offer considerable promise for treating numerous diseases including diabetes and end stage liver failure. Stem cell spheroids may be cultured in stirred bioreactors to scale up cell production to cell numbers relevant for use in humans. Despite significant progress in bioreactor culture of stem cells, areas for improvement remain. In this study, we demonstrate that microfluidic encapsulation of hPSCs and formation of spheroids. A co-axial droplet microfluidic device was used to fabricate 400 μm diameter capsules with a poly(ethylene glycol) hydrogel shell and an aqueous core. Spheroid formation was demonstrated for three hPSC lines to highlight broad utility of this encapsulation technology. In-capsule differentiation of stem cell spheroids into pancreatic β-cells in suspension culture was also demonstrated.
Global phylogeography of a pantropical mangrove genus Rhizophora
Authors: Takayama Koji , Tateishi Yoichi , Kajita Tadashi 
Published: March 2021

AbstractRhizophorais a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario ofRhizophorathat achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except forR. samoensisandR. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution ofRhizophorais updated.
Geographical distribution of the dispersal ability of alien plant species in China and its socio-climatic control factors
Authors: Zhou Quanlai , Wu Jing , Cui Xue , Li Xuehua , Liu Zhimin , Musa Ala , Ma Qun , Yu Haibin , Liang Wei , Jiang Shaoyan , Wang Yongcui 
Published: March 2021

AbstractDispersal ability is important for the introduction, establishment, and spread of alien plant species. Therefore, determination of the geographical distribution of the dispersal ability of such species, and the relationship between dispersal ability and socio-climatic factors are essential to elucidate the invasion strategies of the alien plant species. Analytic hierarchy process and inventory, risk rank, and dispersal mode data available on Chinese alien plant species were used to determine their dispersal ability, the geographical distribution thereof, and the relationship between socio-climatic factors and dispersal ability. High-risk alien plant species had a higher natural dispersal ability (or several natural dispersal modes) but a lower anthropogenic dispersal ability (or few anthropogenic dispersal modes) than low-risk alien plant species. The geographical distribution of the dispersal ability of the alien plant species showed an inverse relationship with species density. Alien plant species with low dispersal ability (i.e., with fewer dispersal modes and distribution in the southeast) showed a tendency to adapt to environments with mild climates, while those with high dispersal ability (i.e., with more disposal nodes and distribution in the northwest) showed a tendency to adapt to harsh environments. It is essential for land managers and policy makers to understand the geographical distribution of the dispersal ability of alien plant species and their socio-climatic control factors to formulate strategies to control the natural and anthropogenic dispersal of such plants.