bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate Drives Modeled Forest Carbon Cycling Resistance and Resilience in the Upper Great Lakes Region, USA
Authors: Dorheim Kalyn , Gough Christopher M. , Haber Lisa T. , Mathes Kayla C. , Shiklomanov Alexey N. , Bond‐Lamberty Ben 
Published: December 2021

AbstractForests dominate the global terrestrial carbon budget, but their ability to continue doing so in the face of a changing climate is uncertain. A key uncertainty is how forests will respond to (resistance) and recover from (resilience) rising levels of disturbance of varying intensities. This knowledge gap can optimally be addressed by integrating manipulative field experiments with ecophysiological modeling. We used the Ecosystem Demography‐2.2 (ED‐2.2) model to project carbon fluxes for a northern temperate deciduous forest subjected to a real‐world disturbance severity manipulation experiment. ED‐2.2 was run for 150 years, starting from near bare ground in 1900 (approximating the clear‐cut conditions at the time), and subjected to three disturbance treatments under an ensemble of climate conditions. Both disturbance severity and climate strongly affected carbon fluxes such as gross primary production (GPP), and interacted with one another. We then calculated resistance and resilience, two dimensions of ecosystem stability. Modeled GPP exhibited a two‐fold decrease in mean resistance across disturbance severities of 45%, 65%, and 85% mortality; conversely, resilience increased by a factor of two with increasing disturbance severity. This pattern held for net primary production and net ecosystem production, indicating a trade‐off in which greater initial declines were followed by faster recovery. Notably, however, heterotrophic respiration responded more slowly to disturbance, and it's highly variable response was affected by different drivers. This work provides insight into how future conditions might affect the functional stability of mature forests in this region under ongoing climate change and changing disturbance regimes.
High‐Resolution 3‐D Imaging of Daytime Sporadic‐E Over Japan by Using GNSS TEC and Ionosondes
Authors: Fu Weizheng , Ssessanga Nicholas , Yokoyama Tatsuhiro , Yamamoto Mamoru 
Published: December 2021

AbstractA novel two‐step three‐dimensional (3‐D) computerized ionospheric tomography (CIT) technique has been developed to image the structure of daytime midlatitude sporadic‐E (Es). The CIT relies on total electron content (TEC) from a dense ground‐based Global Navigation Satellite System (GNSS) receiver network over the Japan area. First, on a coarse grid, the TEC data and a multiplicative algebraic reconstruction technique (MART) are used to reconstruct the F region from a smooth background. Then, on a fine grid and using singular value decomposition (SVD), the residues after deducting the F region contribution to TEC are utilized in reconstructing the E region, extending 80–180 km in altitude. To vertically constrain the E region solution, we introduced a family of subsets of time‐dependent empirical orthogonal functions (EOFs) from a Chapman model function tuned to manually scaled ionosonde observations. We analyzed three event days to validate the results. East‐West (E‐W) aligned frontal structures, spanning several hundred kilometers, migrating northward in the morning and southward in the afternoon, were observed. The new technique effectively tracks the Es‐height variation over time, which had proved difficult to reproduce in earlier tempts at 3‐D Es reconstructions.
Negative Pore Water Pressure in Aquitard Enhances Land Subsidence: Field, Laboratory, and Numerical Evidence
Authors: Liu Chun , Shi Bin , Gu Kai , Zhang Tiansheng , Tang Chaosheng , Wang Yue , Liu Suping 
Published: December 2021

AbstractLand subsidence in the south Yangtze River delta area did not cease when the ground water table has risen during the last 20 years. This issue was generally interpreted as a result of the slow release of excess pore water pressure in the aquitards and the creep of soil. Recent distributed strain monitoring data in boreholes shows a great compressive strain in the aquitard above the main exploited aquifer. In laboratory tests, such great compressive strain also is observed in the clay layer during the draining of the underlying sand layer. Furthermore, a negative pore water pressure is observed in the clay layer, which significantly correlates with the change of the compressive strain. An improved discrete element model was used to simulate the deformation of soil layers under the effect of the negative pressure. The simulation results coincide with the tests, and the negative pressure enhances the compression of aquitard. Due to the effect of the negative pore water pressure, aquitards may be compressed during the draining and recharging cycles in the south Yangtze River delta area.
Sediment Reworking in Streambeds With Fine Sediment Deposits and Its Influence on Hyporheic Flow Regime
Authors: Shrivastava S. , Stewardson M. J. , Arora M. 
Published: December 2021

AbstractThe mobilization and mixing of sediments by the activities of in‐stream fauna, referred to as sediment reworking, constantly modifies the hydro‐physical properties of streambeds. This sediment‐organism interaction has been increasingly recognized to influence the hyporheic exchange flows in stream ecosystems, particularly in low flow environments (e.g., during base flow). In this work, we advance the knowledge of sediment reworking process by studying its impact on hyporheic exchange flows in streambeds with fine sediment deposits. Laboratory experiments are conducted in re‐circulating flumes following a control (only fine sediments) and treatment‐ (fine sediments + organisms) based design. The experiments involve studying the interaction of model organisms (Lumbriculus variegatus) with fine sediment (clay) deposits, and its subsequent influence on hyporheic flow regime in homogenous streambeds with fine sand, coarse sand, and gravel as substrate sediments. We observe that model organisms burrowed extensively into the fine sediment layer, mixed the clay particles with underlying grains, and eventually exposed the substrate sediments in the treatment flumes. Consequently, the treatment flumes exhibited greater solute penetration depth, shorter residence times, and higher hyporheic exchange flux compared to their respective control flumes. The results also suggest that the modification of hyporheic exchange flows depends on the overall reworking of the beds that is, the interaction of organisms with both substrate material and deposited fine sediments. It is critical to comprehend the influence of streambed inhabitants on mass and energy exchange across the sediment‐water interface as it has implications on the overall quality of both stream and groundwater.
Estimating Spatially Explicit Irrigation Water Use Based on Remotely Sensed Evapotranspiration and Modeled Root Zone Soil Moisture
Authors: Zhang Caijin , Long Di 
Published: December 2021

AbstractEstimation of irrigation water use (IWU) is critical to assessing water use efficiency and optimizing water resource allocation. However, diversity in irrigation scheduling, irrigation system, and crop type has imposed restrictions on deriving the accurate spatial distribution of IWU. Existing approaches of deriving IWU may have large uncertainty, due mostly to methodological limitations, inadequate inputs, and the mismatch in spatiotemporal scale between IWU estimates and in situ counterparts. Remote sensing has the potential to provide valuable information on moisture transport, which could unravel water consumption by crops. First, we developed a robust relationship between root zone soil moisture (RZSM) and the ratio of actual evapotranspiration (ETa) to reference ET from the land components of European ReAnalysis‐5 (ERA5L) without an irrigation module across the Contiguous United States (CONUS). Second, RZSM under irrigation was derived from the developed relationship and remotely sensed ETa from the operational Simplified Surface Energy Balance (SSEBop) model during 2000–2020. Third, IWU over the two decades was derived based on increases in RZSM and ETa due to irrigation using remotely sensed and model‐based variables, along with our derived formulas considering groundwater recharge originating from irrigation. The IWU estimates were fairly reliable compared with reported IWU from the Farm and Ranch Irrigation Survey at the state‐level in four years, with the coefficient of determination ranging from 0.74 to 0.84, root mean square error ranging from 1.90 to 2.33 km3/yr, and bias ranging from −0.11 to 0.15 km3/yr. Integration of remotely sensed ETa with ERA5L output resulted in IWU estimates of much higher accuracy than published studies. The IWU estimates across the CONUS reflected an increasing trend (∼2.71 km3/yr2) during 2000–2007 but a decreasing trend (∼0.90 km3/yr2) during 2008–2020, due to efficient irrigation practices and increased precipitation.
Comprehensive transcriptomic characterization reveals core genes and module associated with immunological changes via 1619 samples of brain glioma
Authors: Zhang Ying , Ma Wenping , Fan Wenhua , Ren Changyuan , Xu Jianbao , Zeng Fan , Bao Zhaoshi , Jiang Tao , Zhao Zheng 
Published: December 2021

AbstractGlioma is the most common primary malignant brain tumor with limited treatment options and poor prognosis. To investigate the potential relationships between transcriptional characteristics and clinical phenotypes, we applied weighted gene co-expression network analysis (WGCNA) to construct a free-scale gene co-expression network yielding four modules in gliomas. Turquoise and yellow modules were positively correlated with the most malignant glioma subtype (IDH-wildtype glioblastomas). Of them, genes in turquoise module were mainly involved in immune-related terms and were regulated by NFKB1, RELA, SP1, STAT1 and STAT3. Meanwhile, genes in yellow module mainly participated in cell-cycle and division processes and were regulated by E2F1, TP53, E2F4, YBX1 and E2F3. Furthermore, 14 genes in turquoise module were screened as hub genes. Among them, five prognostic hub genes (TNFRSF1B, LAIR1, TYROBP, VAMP8, and FCGR2A) were selected to construct a prognostic risk score model via LASSO method. The risk score of this immune-related gene signature is associated with clinical features, malignant phenotype, and somatic alterations. Moreover, this signature showed an accurate prediction of prognosis across different clinical and pathological subgroups in three independent datasets including 1619 samples. Our results showed that the high-risk group was characterized by active immune-related activities while the low-risk group enriched in neurophysiological-related pathway. Importantly, the high-risk score of our immune signature predicts an enrichment of glioma-associated microglia/macrophages and less response to immune checkpoint blockade (ICB) therapy in gliomas. This study not only provides new insights into the molecular pathogenesis of glioma, but may also help optimize the immunotherapies for glioma patients.
Rab35 and glucocorticoids regulate APP and BACE1 trafficking to modulate Aβ production
Authors: Zhuravleva Viktoriya , Vaz-Silva João , Zhu Mei , Gomes Patricia , Silva Joana M. , Sousa Nuno , Sotiropoulos Ioannis , Waites Clarissa L. 
Published: December 2021

AbstractChronic stress and elevated glucocorticoids (GCs), the major stress hormones, are risk factors for Alzheimer’s disease (AD) and promote AD pathomechanisms, including overproduction of toxic amyloid-β (Aβ) peptides and intraneuronal accumulation of hyperphosphorylated Tau protein. The latter is linked to downregulation of the small GTPase Rab35, which mediates Tau degradation via the endolysosomal pathway. Whether Rab35 is also involved in Aβ overproduction remains an open question. Here, we find that hippocampal Rab35 levels are decreased not only by stress/GC but also by aging, another AD risk factor. Moreover, we show that Rab35 negatively regulates Aβ production by sorting amyloid precursor protein (APP) and β-secretase (BACE1) out of the endosomal network, where they interact to produce Aβ. Interestingly, Rab35 coordinates distinct intracellular trafficking steps for BACE1 and APP, mediated by its effectors OCRL and ACAP2, respectively. Finally, we demonstrate that Rab35 overexpression prevents the amyloidogenic trafficking of APP and BACE1 induced by high GC levels. These studies identify Rab35 as a key regulator of APP processing and suggest that its downregulation may contribute to stress-related and AD-related amyloidogenesis.
Proactive and reactive accumulation-to-bound processes compete during perceptual decisions
Authors: Hernández-Navarro Lluís , Hermoso-Mendizabal Ainhoa , Duque Daniel , de la Rocha Jaime , Hyafil Alexandre 
Published: December 2021

AbstractStandard models of perceptual decision-making postulate that a response is triggered in reaction to stimulus presentation when the accumulated stimulus evidence reaches a decision threshold. This framework excludes however the possibility that informed responses are generated proactively at a time independent of stimulus. Here, we find that, in a free reaction time auditory task in rats, reactive and proactive responses coexist, suggesting that choice selection and motor initiation, commonly viewed as serial processes, are decoupled in general. We capture this behavior by a novel model in which proactive and reactive responses are triggered whenever either of two competing processes, respectively Action Initiation or Evidence Accumulation, reaches a bound. In both types of response, the choice is ultimately informed by the Evidence Accumulation process. The Action Initiation process readily explains premature responses, contributes to urgency effects at long reaction times and mediates the slowing of the responses as animals get satiated and tired during sessions. Moreover, it successfully predicts reaction time distributions when the stimulus was either delayed, advanced or omitted. Overall, these results fundamentally extend standard models of evidence accumulation in decision making by showing that proactive and reactive processes compete for the generation of responses.
Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling
Authors: Coyote-Maestas Willow , Nedrud David , Suma Antonio , He Yungui , Matreyek Kenneth A. , Fowler Douglas M. , Carnevale Vincenzo , Myers Chad L. , Schmidt Daniel 
Published: December 2021

AbstractProtein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about biophysical mechanisms that determine whether protein domains can be combined into viable protein folds. Here, we use massively parallel insertional mutagenesis to determine compatibility of over 300,000 domain recombination variants of the Inward Rectifier K+ channel Kir2.1 with channel surface expression. Our data suggest that genomic and biophysical mechanisms acted in concert to favor gain of large, structured domain at protein termini during ion channel evolution. We use machine learning to build a quantitative biophysical model of domain compatibility in Kir2.1 that allows us to derive rudimentary rules for designing domain insertion variants that fold and traffic to the cell surface. Positional Kir2.1 responses to motif insertion clusters into distinct groups that correspond to contiguous structural regions of the channel with distinct biophysical properties tuned towards providing either folding stability or gating transitions. This suggests that insertional profiling is a high-throughput method to annotate function of ion channel structural regions.
Single-cell analysis identifies a key role for Hhip in murine coronal suture development
Authors: Holmes Greg , Gonzalez-Reiche Ana S. , Saturne Madrikha , Motch Perrine Susan M. , Zhou Xianxiao , Borges Ana C. , Shewale Bhavana , Richtsmeier Joan T. , Zhang Bin , van Bakel Harm , Jabs Ethylin Wang 
Published: December 2021

AbstractCraniofacial development depends on formation and maintenance of sutures between bones of the skull. In sutures, growth occurs at osteogenic fronts along the edge of each bone, and suture mesenchyme separates adjacent bones. Here, we perform single-cell RNA-seq analysis of the embryonic, wild type murine coronal suture to define its population structure. Seven populations at E16.5 and nine at E18.5 comprise the suture mesenchyme, osteogenic cells, and associated populations. Expression ofHhip, an inhibitor of hedgehog signaling, marks a mesenchymal population distinct from those of other neurocranial sutures. Tracing of the neonatalHhip-expressing population shows that descendant cells persist in the coronal suture and contribute to calvarial bone growth. InHhip−/−coronal sutures at E18.5, the osteogenic fronts are closely apposed and the suture mesenchyme is depleted with increased hedgehog signaling compared to those of the wild type. Collectively, these data demonstrate thatHhipis required for normal coronal suture development.
Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – targeting P-pocket by fragment screening
Authors: Singh Abhimanyu K. , Martinez Sergio E. , Gu Weijie , Nguyen Hoai , Schols Dominique , Herdewijn Piet , De Jonghe Steven , Das Kalyan 
Published: December 2021

AbstractHIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3’-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography that identifies two leads that bind the P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized, two of which show noticeable RT inhibition. An engineered RT/DNA aptamer complex could trap the transient P-pocket in solution, and structures of the RT/DNA complex were determined in the presence of an inhibitory fragment. A synthesized analog bound at P-pocket is further analyzed by single-particle cryo-EM. Identification of the P-pocket within HIV RT and the developed structure-based platform provide an opportunity for the design new types of polymerase inhibitors.
GPR180 is a component of TGFβ signalling that promotes thermogenic adipocyte function and mediates the metabolic effects of the adipocyte-secreted factor CTHRC1
Authors: Balazova Lucia , Balaz Miroslav , Horvath Carla , Horváth Áron , Moser Caroline , Kovanicova Zuzana , Ghosh Adhideb , Ghoshdastider Umesh , Efthymiou Vissarion , Kiehlmann Elke , Sun Wenfei , Dong Hua , Ding Lianggong , Amri Ez-Zoubir , Nuutila Pirjo , Virtanen Kirsi A. , Niemi Tarja , Ukropcova Barbara , Ukropec Jozef , Pelczar Pawel , Lamla Thorsten , Hamilton Bradford , Neubauer Heike , Wolfrum Christian 
Published: December 2021

AbstractActivation of thermogenic brown and beige adipocytes is considered as a strategy to improve metabolic control. Here, we identify GPR180 as a receptor regulating brown and beige adipocyte function and whole-body glucose homeostasis, whose expression in humans is associated with improved metabolic control. We demonstrate that GPR180 is not a GPCR but a component of the TGFβ signalling pathway and regulates the activity of the TGFβ receptor complex through SMAD3 phosphorylation. In addition, using genetic and pharmacological tools, we provide evidence that GPR180 is required to manifest Collagen triple helix repeat containing 1 (CTHRC1) action to regulate brown and beige adipocyte activity and glucose homeostasis. In this work, we show that CTHRC1/GPR180 signalling integrates into the TGFβ signalling as an alternative axis to fine-tune and achieve low-grade activation of the pathway to prevent pathophysiological response while contributing to control of glucose and energy metabolism.
Changing impacts of Alaska-Aleutian subduction zone tsunamis in California under future sea-level rise
Authors: Dura Tina , Garner Andra J. , Weiss Robert , Kopp Robert E. , Engelhart Simon E. , Witter Robert C. , Briggs Richard W. , Mueller Charles S. , Nelson Alan R. , Horton Benjamin P. 
Published: December 2021

AbstractThe amplification of coastal hazards such as distant-source tsunamis under future relative sea-level rise (RSLR) is poorly constrained. In southern California, the Alaska-Aleutian subduction zone has been identified as an earthquake source region of particular concern for a worst-case scenario distant-source tsunami. Here, we explore how RSLR over the next century will influence future maximum nearshore tsunami heights (MNTH) at the Ports of Los Angeles and Long Beach. Earthquake and tsunami modeling combined with local probabilistic RSLR projections show the increased potential for more frequent, relatively low magnitude earthquakes to produce distant-source tsunamis that exceed historically observed MNTH. By 2100, under RSLR projections for a high-emissions representative concentration pathway (RCP8.5), the earthquake magnitude required to produce >1 m MNTH falls from ~Mw9.1 (required today) to Mw8.0, a magnitude that is ~6.7 times more frequent along the Alaska-Aleutian subduction zone.
Optogenetic relaxation of actomyosin contractility uncovers mechanistic roles of cortical tension during cytokinesis
Authors: Yamamoto Kei , Miura Haruko , Ishida Motohiko , Mii Yusuke , Kinoshita Noriyuki , Takada Shinji , Ueno Naoto , Sawai Satoshi , Kondo Yohei , Aoki Kazuhiro 
Published: December 2021

AbstractActomyosin contractility generated cooperatively by nonmuscle myosin II and actin filaments plays essential roles in a wide range of biological processes, such as cell motility, cytokinesis, and tissue morphogenesis. However, subcellular dynamics of actomyosin contractility underlying such processes remains elusive. Here, we demonstrate an optogenetic method to induce relaxation of actomyosin contractility at the subcellular level. The system, named OptoMYPT, combines a protein phosphatase 1c (PP1c)-binding domain of MYPT1 with an optogenetic dimerizer, so that it allows light-dependent recruitment of endogenous PP1c to the plasma membrane. Blue-light illumination is sufficient to induce dephosphorylation of myosin regulatory light chains and a decrease in actomyosin contractile force in mammalian cells and Xenopus embryos. The OptoMYPT system is further employed to understand the mechanics of actomyosin-based cortical tension and contractile ring tension during cytokinesis. We find that the relaxation of cortical tension at both poles by OptoMYPT accelerated the furrow ingression rate, revealing that the cortical tension substantially antagonizes constriction of the cleavage furrow. Based on these results, the OptoMYPT system provides opportunities to understand cellular and tissue mechanics.
Quantifying uncertainty in aggregated climate change risk assessments
Authors: Harrington Luke J. , Schleussner Carl-Friedrich , Otto Friederike E. L. 
Published: December 2021

AbstractHigh-level assessments of climate change impacts aggregate multiple perils into a common framework. This requires incorporating multiple dimensions of uncertainty. Here we propose a methodology to transparently assess these uncertainties within the ‘Reasons for Concern’ framework, using extreme heat as a case study. We quantitatively discriminate multiple dimensions of uncertainty, including future vulnerability and exposure to changing climate hazards. High risks from extreme heat materialise after 1.5–2 °C and very high risks between 2–3.5 °C of warming. Risks emerge earlier if global assessments were based on national risk thresholds, underscoring the need for stringent mitigation to limit future extreme heat risks.