bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of Spontaneous Waterfall Development on Bedrock River Longitudinal Profile Morphology
Authors: Rothman Sophie D. , Scheingross Joel S. , McCoy Scott W. , Dow Helen W. 
Published: July 2023

AbstractRiver profiles are shaped by climatic and tectonic history, lithology, and internal feedbacks between flow hydraulics, sediment transport and erosion. In steep channels, waterfalls may self‐form without changes in external forcing (i.e., autogenic formation) and erode at rates faster or slower than an equivalent channel without waterfalls. We use a 1‐D numerical model to investigate how self‐formed waterfalls alter the morphology of bedrock river longitudinal profiles. We modify the standard stream power model to include a slope threshold above which waterfalls spontaneously form and a rate constant allowing waterfalls to erode faster or slower than other fluvial processes. Using this model, we explore how waterfall formation alters both steady state and transient longitudinal profile forms. Our model predicts that fast waterfalls create km‐scale reaches in a dynamic equilibrium with channel slope held approximately constant at the threshold slope for waterfall formation, while slow waterfalls can create local channel slope maxima at the location of slow waterfall development. Furthermore, slow waterfall profiles integrate past base level histories, leading to multiple possible profile forms, even at steady‐state. Consistency between our model predictions and field observations of waterfall‐rich rivers in the Kings and Kaweah drainages in the southern Sierra Nevada, California, supports the hypothesis that waterfall formation can modulate river profiles in nature. Our findings may help identify how bedrock channels are influenced by waterfall erosion and aid in distinguishing between signatures of external and internal perturbations, thereby strengthening our ability to interpret past climate and tectonic changes from river longitudinal profiles.
Microphysical Modeling of Fault Slip and Stability Transition in Hydrothermal Conditions
Authors: Mei Cheng , Rudnicki John W. 
Published: July 2023

AbstractField and laboratory observations indicate that the frictional behaviors of faults depend on hydrothermal conditions. We extend the microphysical Chen‐Niemeijer‐Spiers (CNS) model to hydrothermal conditions by using the observed temperature variation of indentation hardness to infer the temperature dependence of a microphysical parameter . This parameter is assumed constant in previous versions of the CNS model. A simple spring‐slider system is used to simulate the fault system and investigate the steady‐state frictional behaviors of wet granite gouges. Our numerical results quantitatively reproduce experimental data showing the frictional‐plastic transition. The results also describe the transition from velocity‐strengthening at low temperatures (<160°C), to velocity‐weakening at intermediate temperatures (160°C–370°C), then back to velocity‐strengthening at high temperatures (>370°C). In our extended CNS model, these results suggest that the dominant shear deformation mechanism does transition from frictional granular flow to fully plastic creep with increasing temperature.
The Role of Storm‐Driven Seaward Sediment Flux in Coastal Barrier Dynamics Is an Enduring Puzzle
Authors: Lazarus Eli D. 
Published: July 2023

AbstractCoastal barrier systems are low‐lying environments that bear the brunt of storm impacts, with cumulative and complex consequences for barrier evolution. Most studies of barrier responses to storms examine what happens when water and sediment get driven landward across a barrier from its ocean side. Sherwood et al. (2023, https://doi.org/10.1029/2022jf006934) investigate the effects of overland flow and sediment transport forced across a barrier in the opposite direction—from its sheltered side, seaward. Using high‐resolution imagery of a barrier island observed before and after a hurricane, Sherwood et al. (2023, https://doi.org/10.1029/2022jf006934) show that “outwash” flow across the barrier shifted several times more sediment by volume than is typically reported for beach and dune erosion from onshore forcing. Their findings are remarkable because they are not exceptional: a related survey of barriers along the Atlantic and Gulf Coasts of the USA observed patterns of outwash morphology essentially everywhere. Insights into outwash morphology open exciting questions regarding the overlooked role of storm‐driven seaward sediment transport in barrier dynamics, with important implications for post‐storm barrier recovery and barrier evolution over decades to centuries.
Methane Emissions From Land and Aquatic Ecosystems in Western Siberia: An Analysis With Methane Biogeochemistry Models
Authors: Xi Xuan , Zhuang Qianlai , Kim Seungbum , Zhang Zhen 
Published: July 2023

AbstractWestern Siberia contains extensive wetlands and aquatic ecosystems, contributing a significant amount of methane (CH4) emissions to the atmosphere. However, estimates of CH4 fluxes over the region are poorly constrained partly due to the uncertainties from the inundated area data. This study applied two process‐based biogeochemistry models to quantify the emissions from land and aquatic ecosystems over the region within the period 2000–2021 using different inundation datasets. To drive land methane modeling, we use one static wetland map and one dynamic wetland area data set called Wetland Area and Dynamics for Methane Modeling (WAD2M) (2000–2020). To drive lake methane modeling, we use the surface area of aquatic ecosystems from three datasets: (a) HydroLAKES; (b) Global Surface Water (GSW); and (c) surface water inundation from Soil Moisture Active Passive (SMAP) (2016–2021). Using these datasets, we conduct four simulations to compare emissions over the region. We find that the net methane emissions from land using the static wetland map are larger than those using WAD2M. SMAP and GSW estimate larger emissions than HydroLAKES does from aquatic ecosystems. Total emissions over the region range from 4.80 ± 0.43 to 8.29 ± 0.81 Tg CH4/year from 2016 to 2020, which is the intersection period of four simulations. This study is among the first to investigate methane emissions from the whole landscape in the region. Our study highlights the importance of dynamic wetland and aquatic area data in quantifying regional methane emissions.
Differential contribution of nitrifying prokaryotes to groundwater nitrification
Authors: Krüger Markus , Chaudhari Narendrakumar , Thamdrup Bo , Overholt Will A , Bristow Laura A , Taubert Martin , Küsel Kirsten , Jehmlich Nico , von Bergen Martin , Herrmann Martina 
Published: July 2023

Abstract
The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.
Voice acoustics allow classifying autism spectrum disorder with high accuracy
Authors: Briend Frédéric , David Céline , Silleresi Silvia , Malvy Joëlle , Ferré Sandrine , Latinus Marianne 
Published: July 2023

AbstractEarly identification of children on the autism spectrum is crucial for early intervention with long-term positive effects on symptoms and skills. The need for improved objective autism detection tools is emphasized by the poor diagnostic power in current tools. Here, we aim to evaluate the classification performance of acoustic features of the voice in children with autism spectrum disorder (ASD) with respect to a heterogeneous control group (composed of neurotypical children, children with Developmental Language Disorder [DLD] and children with sensorineural hearing loss with Cochlear Implant [CI]). This retrospective diagnostic study was conducted at the Child Psychiatry Unit of Tours University Hospital (France). A total of 108 children, including 38 diagnosed with ASD (8.5 ± 0.25 years), 24 typically developing (TD; 8.2 ± 0.32 years) and 46 children with atypical development (DLD and CI; 7.9 ± 0.36 years) were enrolled in our studies. The acoustic properties of speech samples produced by children in the context of a nonword repetition task were measured. We used a Monte Carlo cross-validation with an ROC (Receiving Operator Characteristic) supervised k-Means clustering algorithm to develop a classification model that can differentially classify a child with an unknown disorder. We showed that voice acoustics classified autism diagnosis with an overall accuracy of 91% [CI95%, 90.40%-91.65%] against TD children, and of 85% [CI95%, 84.5%–86.6%] against an heterogenous group of non-autistic children. Accuracy reported here with multivariate analysis combined with Monte Carlo cross-validation is higher than in previous studies. Our findings demonstrate that easy-to-measure voice acoustic parameters could be used as a diagnostic aid tool, specific to ASD.
Genomic and evolutionary characteristics of metastatic gastric cancer by routes
Authors: Lee Jae Eun , Kim Ki Tae , Shin Su-Jin , Cheong Jae-Ho , Choi Yoon Young 
Published: July 2023

Abstract
Background
In gastric cancer (GC) patients, metastatic progression through the lymphatic, hematogenous, peritoneal, and ovarian routes, is the ultimate cause of death. However, the genomic and evolutionary characteristics of metastatic GC have not been widely evaluated.

Methods
Whole-exome sequencing data were analyzed for 99 primary and paired metastatic gastric cancers from 15 patients who underwent gastrectomy and metastasectomy.

Results
Hematogenous metastatic tumors were associated with increased chromosomal instability and de novo gain/amplification in cancer driver genes, whereas peritoneal/ovarian metastasis was linked to sustained chromosomal stability and de novo somatic mutations in driver genes. The genomic distance of the hematogenous and peritoneal metastatic tumors was found to be closer to the primary tumors than lymph node (LN) metastasis, while ovarian metastasis was closer to LN and peritoneal metastasis than the primary tumor. Two migration patterns for metastatic GCs were identified; branched and diaspora. Both molecular subtypes of the metastatic tumors, rather than the primary tumor, and their migration patterns were related to patient survival.

Conclusions
Genomic characteristics of metastatic gastric cancer is distinctive by routes and associated with patients’ prognosis along with genomic evolution pattenrs, indicating that both primary and metastatic gastric cancers require genomic evaluation.
Effects of altered glycolysis levels on CD8+ T cell activation and function
Authors: Cao Jiaying , Liao Shan , Zeng Feng , Liao Qianjin , Luo Gengqiu , Zhou Yanhong 
Published: July 2023

AbstractCD8+ T cells are an important component of the body’s adaptive immune response. During viral or intracellular bacterial infections, CD8+ T cells are rapidly activated and differentiated to exert their immune function by producing cytokines. Alterations in the glycolysis of CD8+ T cells have an important effect on their activation and function, while glycolysis is important for CD8+ T cell functional failure and recovery. This paper summarizes the importance of CD8+ T cell glycolysis in the immune system. We discuss the link between glycolysis and CD8+ T cell activation, differentiation, and proliferation, and the effect of altered glycolysis on CD8+ T cell function. In addition, potential molecular targets to enhance and restore the immune function of CD8+ T cells by affecting glycolysis and the link between glycolysis and CD8+ T cell senescence are summarized. This review provides new insights into the relationship between glycolysis and CD8+ T cell function, and proposes novel strategies for immunotherapy by targeting glycolysis.
Impact of cell cycle on repair of ruptured nuclear envelope and sensitivity to nuclear envelope stress in glioblastoma
Authors: Kamikawa Yasunao , Wu Zuqian , Nakazawa Nayuta , Ito Taichi , Saito Atsushi , Imaizumi Kazunori 
Published: July 2023

AbstractThe nuclear envelope (NE) is often challenged by various stresses (known as “NE stress”), leading to its dysfunction. Accumulating evidence has proven the pathological relevance of NE stress in numerous diseases ranging from cancer to neurodegenerative diseases. Although several proteins involved in the reassembly of the NE after mitosis have been identified as the NE repair factors, the regulatory mechanisms modulating the efficiency of NE repair remain unclear. Here, we showed that response to NE stress varied among different types of cancer cell lines. U251MG derived from glioblastoma exhibited severe nuclear deformation and massive DNA damage at the deformed nuclear region upon mechanical NE stress. In contrast, another cell line derived from glioblastoma, U87MG, only presented mild nuclear deformation without DNA damage. Time-lapse imaging demonstrated that repairing of ruptured NE often failed in U251MG, but not in U87MG. These differences were unlikely to have been due to weakened NE in U251MG because the expression levels of lamin A/C, determinants of the physical property of the NE, were comparable and loss of compartmentalization across the NE was observed just after laser ablation of the NE in both cell lines. U251MG proliferated more rapidly than U87MG concomitant with reduced expression of p21, a major inhibitor of cyclin-dependent kinases, suggesting a correlation between NE stress response and cell cycle progression. Indeed, visualization of cell cycle stages using fluorescent ubiquitination-based cell cycle indicator reporters revealed greater resistance of U251MG to NE stress at G1 phase than at S and G2 phases. Furthermore, attenuation of cell cycle progression by inducing p21 in U251MG counteracted the nuclear deformation and DNA damage upon NE stress. These findings imply that dysregulation of cell cycle progression in cancer cells causes loss of the NE integrity and its consequences such as DNA damage and cell death upon mechanical NE stress.
The ELK3-DRP1 axis determines the chemosensitivity of triple-negative breast cancer cells to CDDP by regulating mitochondrial dynamics
Authors: Park Joo Dong , Jang Hye Jung , Choi Seung Hee , Jo Gae Hoon , Choi Jin-Ho , Hwang Sohyun , Park Wooram , Park Kyung-Soon 
Published: July 2023

AbstractTriple-negative breast cancer (TNBC) is the most lethal form of breast cancer. TNBC patients have higher rates of metastasis and restricted therapy options. Although chemotherapy is the conventional treatment for TNBC, the frequent occurrence of chemoresistance significantly lowers the efficacy of treatment. Here, we demonstrated that ELK3, an oncogenic transcriptional repressor that is highly expressed in TNBC, determined the chemosensitivity of two representative TNBC cell lines (MDA-MB231 and Hs578T) to cisplatin (CDDP) by regulating mitochondrial dynamics. We observed that the knockdown of ELK3 in MDA-MB231 and Hs578T rendered these cell lines more susceptible to the effects of CDDP. We further demonstrated that the chemosensitivity of TNBC cells was caused by the CDDP-mediated acceleration of mitochondrial fission, excessive mitochondrial reactive oxygen species production, and subsequent DNA damage. In addition, we identified DNM1L, a gene encoding the dynamin-related protein 1 (a major regulator of mitochondrial fission), as a direct downstream target of ELK3. Based on these results, we propose that the suppression of ELK3 expression could be used as a potential therapeutic strategy for overcoming the chemoresistance or inducing the chemosensitivity of TNBC.
Reinforcement learning establishes a minimal metacognitive process to monitor and control motor learning performance
Authors: Sugiyama Taisei , Schweighofer Nicolas , Izawa Jun 
Published: July 2023

AbstractHumans and animals develop learning-to-learn strategies throughout their lives to accelerate learning. One theory suggests that this is achieved by a metacognitive process of controlling and monitoring learning. Although such learning-to-learn is also observed in motor learning, the metacognitive aspect of learning regulation has not been considered in classical theories of motor learning. Here, we formulated a minimal mechanism of this process as reinforcement learning of motor learning properties, which regulates a policy for memory update in response to sensory prediction error while monitoring its performance. This theory was confirmed in human motor learning experiments, in which the subjective sense of learning-outcome association determined the direction of up- and down-regulation of both learning speed and memory retention. Thus, it provides a simple, unifying account for variations in learning speeds, where the reinforcement learning mechanism monitors and controls the motor learning process.
High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217
Authors: Li Fenglin , Hou Chun-Feng David , Lokareddy Ravi K. , Yang Ruoyu , Forti Francesca , Briani Federica , Cingolani Gino 
Published: July 2023

AbstractE217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4.
DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing
Authors: Ni Peng , Nie Fan , Zhong Zeyu , Xu Jinrui , Huang Neng , Zhang Jun , Zhao Haochen , Zou You , Huang Yuanfeng , Li Jinchen , Xiao Chuan-Le , Luo Feng , Wang Jianxin 
Published: July 2023

AbstractLong single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.
Global environmental implications of atmospheric methane removal through chlorine-mediated chemistry-climate interactions
Authors: Li Qinyi , Meidan Daphne , Hess Peter , Añel Juan A. , Cuevas Carlos A. , Doney Scott , Fernandez Rafael P. , van Herpen Maarten , Höglund-Isaksson Lena , Johnson Matthew S. , Kinnison Douglas E. , Lamarque Jean-François , Röckmann Thomas , Mahowald Natalie M. , Saiz-Lopez Alfonso 
Published: July 2023

AbstractAtmospheric methane is both a potent greenhouse gas and photochemically active, with approximately equal anthropogenic and natural sources. The addition of chlorine to the atmosphere has been proposed to mitigate global warming through methane reduction by increasing its chemical loss. However, the potential environmental impacts of such climate mitigation remain unexplored. Here, sensitivity studies are conducted to evaluate the possible effects of increasing reactive chlorine emissions on the methane budget, atmospheric composition and radiative forcing. Because of non-linear chemistry, in order to achieve a reduction in methane burden (instead of an increase), the chlorine atom burden needs to be a minimum of three times the estimated present-day burden. If the methane removal target is set to 20%, 45%, or 70% less global methane by 2050 compared to the levels in the Representative Concentration Pathway 8.5 scenario (RCP8.5), our modeling results suggest that additional chlorine fluxes of 630, 1250, and 1880 Tg Cl/year, respectively, are needed. The results show that increasing chlorine emissions also induces significant changes in other important climate forcers. Remarkably, the tropospheric ozone decrease is large enough that the magnitude of radiative forcing decrease is similar to that of methane. Adding 630, 1250, and 1880 Tg Cl/year to the RCP8.5 scenario, chosen to have the most consistent current-day trends of methane, will decrease the surface temperature by 0.2, 0.4, and 0.6 °C by 2050, respectively. The quantity and method in which the chlorine is added, its interactions with climate pathways, and the potential environmental impacts on air quality and ocean acidity, must be carefully considered before any action is taken.
Spin-orbit coupling-enhanced valley ordering of malleable bands in twisted bilayer graphene on WSe2
Authors: Bhowmik Saisab , Ghawri Bhaskar , Park Youngju , Lee Dongkyu , Datta Suvronil , Soni Radhika , Watanabe K. , Taniguchi T. , Ghosh Arindam , Jung Jeil , Chandni U. 
Published: July 2023

AbstractRecent experiments in magic-angle twisted bilayer graphene have revealed a wealth of novel electronic phases as a result of interaction-driven spin-valley flavour polarisation. In this work, we investigate correlated phases due to the combined effect of spin-orbit coupling-enhanced valley polarisation and the large density of states below half filling of the moiré band in twisted bilayer graphene coupled to tungsten diselenide. We observe an anomalous Hall effect, accompanied by a series of Lifshitz transitions that are highly tunable with carrier density and magnetic field. The magnetisation shows an abrupt change of sign near half-filling, confirming its orbital nature. While the Hall resistance is not quantised at zero magnetic fields—indicating a ground state with partial valley polarisation—perfect quantisation and complete valley polarisation are observed at finite fields. Our results illustrate that singularities in the flat bands in the presence of spin-orbit coupling can stabilise ordered phases even at non-integer moiré band fillings.