bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parameterizing Vegetation Traits With a Process‐Based Ecohydrological Model and Xylem Water Isotopic Observations
Authors: Li K. , Kuppel S. , Knighton J. 
Published: December 2022

AbstractKnowledge of plant hydraulic traits is critical for simulating terrestrial water storage, ecosystem water use, and tree responses to drought. The isotopic composition of tree xylem water (δXYLEM) has proven to be useful for understanding rooting strategies and for tracing terrestrial water flowpaths. Despite the broad collection of δXYLEM observations, few studies have estimated other plant traits from these data. We demonstrate the sensitivity of process‐based isotope‐enabled ecohydrological model (EcH2O‐iso) simulations of rooting depth distributions (KROOT), maximum stomatal conductance (gsMAX), optimal growth temperatures (TOPT), canopy light interception (KBEERS), stomatal sensitivity to vapor pressure deficits (gs‐VPD), and tree water storage capacity (TreeV) to δXYLEM observations. We sampled the δXYLEM of 30 Eastern hemlock (Tsuga canadensis) trees across 7 months, spanning a range of topographic positions and diameters. We calibrated the model 30 times with δXYLEM from each sampled tree. Calibrated values for gsMAX, KBEERS, and KROOT were validated with independent datasets of latent heat flux, canopy light interception, and xylem observations from independent hemlock stands. The calibrated values of several vegetation traits were significantly correlated with the diameters and topographic positions of the trees sampled in the field. These results indicate that δXYLEM reflects the characteristics and locations of the individual trees that are sampled, and therefore care must be taken in upscaling calibrated or measured plant traits for individual trees to larger horizontal scales. This research demonstrates that isotope‐enabled hydrological‐, land surface‐, and Earth systems‐models can leverage widely available water isotopic data to accurately estimate plant hydraulic traits.
Hydrodynamics of Non‐Equilibrium Soil Water Retention
Authors: Einav Itai , Liu Mario 
Published: December 2022

AbstractWater retention in soil exhibits diverse phenomena, including suction‐saturation hysteresis, non‐unique air entrapment at zero suction and negative suction under partial saturations. The constancy of suction after a long rest can be broken by relatively minor mechanical or hydraulic agitations such as low‐amplitude wetting cycles—this fact is here being related to metastable states that differ from the true equilibrium. The complete suction‐saturation relationships are thus being recovered using non‐equilibrium Landau's hydrodynamic theory and Onsager's reciprocity principles. Equilibrium suction does not pertain to hysteresis, yet can be approached through small amplitude agitations over long duration. Conditions for rate independence are being described, while rate‐dependency are also accommodated and illustrated. Finally, it is shown that the new non‐equilibrium theory retains the rigorously derived equilibrium result of the effective stress of partially saturated soils.
Tripterin liposome relieves severe acute respiratory syndrome as a potent COVID-19 treatment
Authors: Que Haiying , Hong Weiqi , Lan Tianxia , Zeng Hao , Chen Li , Wan Dandan , Bi Zhenfei , Ren Wenyan , Luo Min , Yang Jingyun , He Cai , Zhong Ailing , Wei Xiawei 
Published: December 2022

AbstractFor coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 15–30% of patients are likely to develop COVID-19-related acute respiratory distress syndrome (ARDS). There are still few effective and well-understood therapies available. Novel variants and short-lasting immunity are posing challenges to vaccine efficacy, so finding antiviral and antiinflammatory treatments remains crucial. Here, tripterin (TP), a traditional Chinese medicine, was encapsulated into liposome (TP lipo) to investigate its antiviral and antiinflammatory effects in severe COVID-19. By using two severe COVID-19 models in human ACE2-transgenic (hACE2) mice, an analysis of TP lipo’s effects on pulmonary immune responses was conducted. Pulmonary pathological alterations and viral burden were reduced by TP lipo treatment. TP lipo inhibits SARS-CoV-2 replication and hyperinflammation in infected cells and mice, two crucial events in severe COVID-19 pathophysiology, it is a promising drug candidate to treat SARS-CoV-2-induced ARDS.
Impact of direct physical association and motility on fitness of a synthetic interkingdom microbial community
Authors: Scarinci Giovanni , Sourjik Victor 
Published: December 2022

Abstract
Mutualistic exchange of metabolites can play an important role in microbial communities. Under natural environmental conditions, such exchange may be compromised by the dispersal of metabolites and by the presence of non-cooperating microorganisms. Spatial proximity between members during sessile growth on solid surfaces has been shown to promote stabilization of cross-feeding communities against these challenges. Nonetheless, many natural cross-feeding communities are not sessile but rather pelagic and exist in turbulent aquatic environments, where partner proximity is often achieved via direct cell-cell adhesion, and cooperation occurs between physically associated cells. Partner association in aquatic environments could be further enhanced by motility of individual planktonic microorganisms. In this work, we establish a model bipartite cross-feeding community between bacteria and yeast auxotrophs to investigate the impact of direct adhesion between prokaryotic and eukaryotic partners and of bacterial motility in a stirred mutualistic co-culture. We demonstrate that adhesion can provide fitness benefit to the bacterial partner, likely by enabling local metabolite exchange within co-aggregates, and that it counteracts invasion of the community by a non-cooperating cheater strain. In a turbulent environment and at low cell densities, fitness of the bacterial partner and its competitiveness against a non-cooperating strain are further increased by motility that likely facilitates partner encounters and adhesion. These results suggest that, despite their potential fitness costs, direct adhesion between partners and its enhancement by motility may play key roles as stabilization factors for metabolic communities in turbulent aquatic environments.
Dissecting the fate of Foxl2-expressing cells in fetal ovary using lineage tracing and single-cell transcriptomics
Authors: Zhou Jingjing , Jiang Xiangxiang , Wu Haowei , Zhang Lianjun , Chen Min , Chen Min , Shen Zhiming , Guo Xudong , Wang Hongmei , Gao Fei 
Published: December 2022

AbstractGonad somatic cells acquire sex-specific fates during sex determination. In XX gonad, a subset of somatic cells expresses Foxl2 after sex determination which is considered the progenitor of granulosa cells. However, whether these cells also contribute to other cell types at later developmental stages is unknown. In the present study, the cell fate of Foxl2-expressing cells in fetal ovaries was analyzed by lineage tracing and single-cell transcriptomics. We found that Foxl2-expressing cells gave rise to three cell types at later developmental stages, including granulosa cells, theca-interstitial cells, and stromal cells. Series single-cell RNA sequencing revealed FOXL2-positive cells were divided into two clusters at P0. One group further differentiated into granulosa cells and Theca-G (Theca-interstitial cells derived from granulosa) at P14. Another group was classified as stromal cell lineage, then a small portion of them further differentiated into 3β-HSD-positive Theca-S (Theca-interstitial cells derived from stroma). Cyp17a1 was expressed in Theca-S, but not in Theca-G. This study demonstrated that Folx2-expressing cells in XX gonad after sex determination are multipotent and theca-interstitial cells are derived from different progenitors. Our data provided an important resource, at single-cell resolution, for a better understanding of somatic cell differentiation in ovary development.
Topographic organization of eye-position dependent gain fields in human visual cortex
Authors: Fabius Jasper H. , Moravkova Katarina , Fracasso Alessio 
Published: December 2022

AbstractThe ability to move has introduced animals with the problem of sensory ambiguity: the position of an external stimulus could change over time because the stimulus moved, or because the animal moved its receptors. This ambiguity can be resolved with a change in neural response gain as a function of receptor orientation. Here, we developed an encoding model to capture gain modulation of visual responses in high field (7 T) fMRI data. We characterized population eye-position dependent gain fields (pEGF). The information contained in the pEGFs allowed us to reconstruct eye positions over time across the visual hierarchy. We discovered a systematic distribution of pEGF centers: pEGF centers shift from contra- to ipsilateral following pRF eccentricity. Such a topographical organization suggests that signals beyond pure retinotopy are accessible early in the visual hierarchy, providing the potential to solve sensory ambiguity and optimize sensory processing information for functionally relevant behavior.
Genome-wide identification of genes required for alternative peptidoglycan cross-linking in Escherichia coli revealed unexpected impacts of β-lactams
Authors: Voedts Henri , Kennedy Sean P. , Sezonov Guennadi , Arthur Michel , Hugonnet Jean-Emmanuel 
Published: December 2022

AbstractThe d,d-transpeptidase activity of penicillin-binding proteins (PBPs) is the well-known primary target of β-lactam antibiotics that block peptidoglycan polymerization. β-lactam-induced bacterial killing involves complex downstream responses whose causes and consequences are difficult to resolve. Here, we use the functional replacement of PBPs by a β-lactam-insensitive l,d-transpeptidase to identify genes essential to mitigate the effects of PBP inactivation by β-lactams in actively dividing bacteria. The functions of the 179 conditionally essential genes identified by this approach extend far beyond l,d-transpeptidase partners for peptidoglycan polymerization to include proteins involved in stress response and in the assembly of outer membrane polymers. The unsuspected effects of β-lactams include loss of the lipoprotein-mediated covalent bond that links the outer membrane to the peptidoglycan, destabilization of the cell envelope in spite of effective peptidoglycan cross-linking, and increased permeability of the outer membrane. The latter effect indicates that the mode of action of β-lactams involves self-promoted penetration through the outer membrane.
Importance of interface open circuit potential on aqueous hydrogenolytic reduction of benzyl alcohol over Pd/C
Authors: Cheng Guanhua , Zhang Wei , Jentys Andreas , Ember Erika E. , Gutiérrez Oliver Y. , Liu Yue , Lercher Johannes A. 
Published: December 2022

AbstractThe open circuit potential (OCP) established by the quasi-equilibrated electrode reaction of H2 and H3O+(hydr.), complicates catalytic reactions significantly. The hydrogenolysis rate of benzylic alcohol on Pd/C increases 2-3 orders of magnitude with the pH decreasing from 7 to 0.6. The reaction follows a pathway of protonated benzyl alcohol dehydration to a benzylic carbenium ion, followed by a hydride addition to form toluene. The dehydration of protonated benzyl alcohol is kinetic relevent, thus, being enhanced at lower pH. The OCP stabilizes all cationic species in the elementary steps. Particularly, the initial state (benzyl alcohol oxonium ion) is less stabilized than the dehydration transition state and the product (benzylic carbenium), thus, lowering the free energy barrier of the rate-determining step. In accordance, the rate increased with increasingly negative OCP. Beside OCP, an external negative electric potential in an electrocatlaytic system was also demonstrated to enhance the rate in the same way.
Quantifying the role of variability in future intensification of heat extremes
Authors: Simolo Claudia , Corti Susanna 
Published: December 2022

AbstractHeat extremes have grown disproportionately since the advent of industrialization and are expected to intensify further under unabated greenhouse warming, spreading unevenly across the globe. However, amplification mechanisms are highly uncertain because of the complex interplay between regional physical responses to human forcing and the statistical properties of atmospheric temperatures. Here, focusing on the latter, we explain how and to what extent the leading moments of thermal distributions sway the future trajectories of heat extremes. Crucially, we show that daily temperature variability is the key to understanding global patterns of change in the frequency and severity of the extremes and their exacerbation in many places. Variability accounts for at least half of the highly differential regional sensitivities and may well outweigh the background warming. These findings provide fundamental insights for assessing the reliability of climate models and improving their future projections.
Continuous cholinergic-dopaminergic updating in the nucleus accumbens underlies approaches to reward-predicting cues
Authors: Skirzewski Miguel , Princz-Lebel Oren , German-Castelan Liliana , Crooks Alycia M. , Kim Gerard Kyungwook , Tarnow Sophie Henke , Reichelt Amy , Memar Sara , Palmer Daniel , Li Yulong , Jane Rylett R. , Saksida Lisa M. , Prado Vania F. , Prado Marco A. M. , Bussey Timothy J. 
Published: December 2022

AbstractThe ability to learn Pavlovian associations from environmental cues predicting positive outcomes is critical for survival, motivating adaptive behaviours. This cued-motivated behaviour depends on the nucleus accumbens (NAc). NAc output activity mediated by spiny projecting neurons (SPNs) is regulated by dopamine, but also by cholinergic interneurons (CINs), which can release acetylcholine and glutamate via the activity of the vesicular acetylcholine transporter (VAChT) or the vesicular glutamate transporter (VGLUT3), respectively. Here we investigated behavioural and neurochemical changes in mice performing a touchscreen Pavlovian approach task by recording dopamine, acetylcholine, and calcium dynamics from D1- and D2-SPNs using fibre photometry in control, VAChT or VGLUT3 mutant mice to understand how these signals cooperate in the service of approach behaviours toward reward-predicting cues. We reveal that NAc acetylcholine-dopaminergic signalling is continuously updated to regulate striatal output underlying the acquisition of Pavlovian approach learning toward reward-predicting cues.
An astrocytic signaling loop for frequency-dependent control of dendritic integration and spatial learning
Authors: Bohmbach Kirsten , Masala Nicola , Schönhense Eva M. , Hill Katharina , Haubrich André N. , Zimmer Andreas , Opitz Thoralf , Beck Heinz , Henneberger Christian 
Published: December 2022

AbstractDendrites of hippocampal CA1 pyramidal cells amplify clustered glutamatergic input by activation of voltage-gated sodium channels and N-methyl-D-aspartate receptors (NMDARs). NMDAR activity depends on the presence of NMDAR co-agonists such as D-serine, but how co-agonists influence dendritic integration is not well understood. Using combinations of whole-cell patch clamp, iontophoretic glutamate application, two-photon excitation fluorescence microscopy and glutamate uncaging in acute rat and mouse brain slices we found that exogenous D-serine reduced the threshold of dendritic spikes and increased their amplitude. Triggering an astrocytic mechanism controlling endogenous D-serine supply via endocannabinoid receptors (CBRs) also increased dendritic spiking. Unexpectedly, this pathway was activated by pyramidal cell activity primarily in the theta range, which required HCN channels and astrocytic CB1Rs. Therefore, astrocytes close a positive and frequency-dependent feedback loop between pyramidal cell activity and their integration of dendritic input. Its disruption in mice led to an impairment of spatial memory, which demonstrated its behavioral relevance.
Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level
Authors: Zhu Rong , Canena Daniel , Sikora Mateusz , Klausberger Miriam , Seferovic Hannah , Mehdipour Ahmad Reza , Hain Lisa , Laurent Elisabeth , Monteil Vanessa , Wirnsberger Gerald , Wieneke Ralph , Tampé Robert , Kienzl Nikolaus F. , Mach Lukas , Mirazimi Ali , Oh Yoo Jin , Penninger Josef M. , Hummer Gerhard , Hinterdorfer Peter 
Published: December 2022

AbstractRecent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.
Phase I study of LZM005 in patients with HER2-positive metastatic breast cancer
Authors: Xue Cong , Li Haifeng , Yao Herui , Lin Ying , An Xin , Chen Meiting , Huang Riqing , Li Lu , Hu Anqi , Ni Mengqian , Zhang Lulu , Yang Wei , Xu Zhonghui , Li Su , Shi Yanxia 
Published: December 2022

AbstractThe prognosis of human epidermal growth factor receptor 2 (HER2) positive metastatic breast cancer (MBC) remained unsatisfactory currently, more anti-HER2 agents are needed. Here we report a phase I study that evaluated the safety, activity, and biomarkers of LZM005, a HER2 antibody, used as a monotherapy or in combination with trastuzumab plus docetaxel in patients with HER2-positive MBC. From October 2017 to December 2019, 34 patients received LZM005 (14 monotherapy, 20 combination therapy). No DLT was observed. The common adverse events (AEs) in phase Ia included diarrhea (21.4%), infusion reaction (21.4%), and hypertriglyceridemia (21.4%), while those in phase Ib were leukopenia (85.0%), neutropenia (75.0%), anemia (60.0%), diarrhea (60.0%), and rash/pruritus (50.0%). All AEs were manageable. In phase Ia, partial response (PR) was achieved in one case (1/14, overall response rate [ORR]: 7.1%); the disease control rate was 42.90% (6/14). In phase Ib, 11 patients (55.0%) achieved PR, and eight (40.0%) had stable disease. The ORR was 100% (6/6) in trastuzumab-naive and 35.7% (5/14) in trastuzumab-pretreated patients. Biomarker analysis showed that chromatin remodeling genesKMT2BandBRWD1were associated with better progression-free survival. LZM005 is well tolerated and shows potent activity in patients with HER2-positive MBC.
Machine learning guided discovery of ternary compounds involving La and immiscible Co and Pb elements
Authors: Wang Renhai , Xia Weiyi , Slade Tyler J. , Fan Xinyu , Dong Huafeng , Ho Kai-Ming , Canfield Paul C. , Wang Cai-Zhuang 
Published: December 2022

AbstractTernary compounds with an immiscible pair of elements are relatively unexplored but promising for novel quantum materials discovery. Exploring what third element and its ratio that can be added to make stable ternary compounds out of an immiscible pair of elements remains a great challenge. In this work, we combine a machine learning (ML) method with ab initio calculations to efficiently search for the energetically favorable ternary La-Co-Pb compounds containing immiscible elements Co and Pb. Three previously reported structures are correctly captured by our approach. Moreover, we predict a ground state La3CoPb compound and 57 low-energy La-Co-Pb ternary compounds. Attempts to synthesize La3CoPb via multiple techniques produce mixed or multi-phases samples with, at best, ambiguous signals of the predicted lowest-energy La3CoPb and the second lowest-energy La18Co28Pb3 phases. The calculated results of Gibbs free energy are consistent with experiments, and will provide very useful guidance for further experimental synthesis.
Graph neural network modeling of grain-scale anisotropic elastic behavior using simulated and measured microscale data
Authors: Pagan Darren C. , Pash Calvin R. , Benson Austin R. , Kasemer Matthew P. 
Published: December 2022

AbstractHere we assess the applicability of graph neural networks (GNNs) for predicting the grain-scale elastic response of polycrystalline metallic alloys. Using GNN surrogate models, grain-averaged stresses during uniaxial elastic tension in low solvus high-refractory (LSHR) Ni Superalloy and Ti 7 wt%Al (Ti-7Al) are predicted as example face-centered cubic and hexagonal closed packed alloys, respectively. A transfer learning approach is taken in which GNN surrogate models are trained using crystal elasticity finite element method (CEFEM) simulations and then the trained surrogate models are used to predict the mechanical response of microstructures measured using high-energy X-ray diffraction microscopy (HEDM). The performance of using various microstructural and micromechanical descriptors for input nodal features to the GNNs is explored through comparisons to traditional mean-field theory predictions, reserved full-field CEFEM data, and measured far-field HEDM data. The effects of elastic anisotropy on GNN model performance and outlooks for the extension of the framework are discussed.