bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of 3‐D Curved Fracture Swarms in Shale Rock Driven by Rapid Fluid Pressure Buildup: Insights From Numerical Modeling
Authors: Li Sanbai , Zhang Dongxiao 
Published: April 2021

AbstractDespite the variety of studies that have investigated the development of fracture networks during kerogen maturation in organic‐rich shale, the fracture interaction modes and generation mechanisms in three‐dimensions are not yet fully understood. In this study, we introduce a novel numerical approach to model the evolution of fracture swarms with three‐dimensional nonplanar geometries. This model enables precise simulation of the propagation, interplay, and coalescence of the fracture swarms with variable apertures and geometries via solving fluid flow, fracture growth, and stress interference. Our results suggest five basic fracture interaction modes between neighboring fractures. The evolving fracture swarms exhibit simultaneous, alternant, and differential growth characteristics at different development phases. We also elucidate the mechanical mechanisms that determine the evolution of three‐dimensional curved fracture swarms. This work yields an improved understanding of fluid‐driven fracture swarms' development in organic‐rich shale due to rapid fluid generation.
PRDM4 inhibits cell proliferation and tumorigenesis by inactivating the PI3K/AKT signaling pathway through targeting of PTEN in cervical carcinoma
Authors: Yang Wen-Ting , Chen Mei , Xu Rui , Zheng Peng-Sheng 
Published: April 2021

AbstractPR domain zinc finger protein 4 (PRDM4) is a transcription factor that plays key roles in stem cell self-renewal and tumorigenesis. However, its biological role and exact mechanism in cervical cancer remain unknown. Here, both immunohistochemistry (IHC) and Western blot assays demonstrated that the expression of PRDM4 in cervical cancer tissues was much lower than that in the normal cervix. A xenograft assay showed that PRDM4 overexpression in the cervical cancer cell lines SiHa and HeLa dramatically inhibited cell proliferation and tumorigenic potential in vivo. Conversely, the silencing of PRDM4 promoted cervical cancer cell proliferation and tumorigenic potential. Mechanistically, PRDM4 induced cell cycle arrest at the transition from G0/G1 phase to S phase by upregulating p27 and p21 expression and downregulating Cyclin D1 and CDK4 expression. Furthermore, the PI3K/AKT signaling pathway was inactivated in PRDM4-overexpressing cells, which decreased the levels of p-AKT and upregulated the expression of PTEN, an inhibitor of the PI3K/AKT signaling pathway, at both the transcriptional and translational levels. Dual-luciferase reporter assays and qChIP assays confirmed that PRDM4 transactivated the expression of PTEN by binding to two specific regions in thePTENpromoter. Furthermore, PTEN silencing or a PTEN inhibitor rescued the cell defects induced by PRDM4 overexpression. Therefore, our data suggest that PRDM4 inhibits cell proliferation and tumorigenesis by downregulating the activity of the PI3K/AKT signaling pathway by directly transactivating PTEN expression in cervical cancer.
Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures
Authors: Numis Adam L. , da Gente Gilberto , Sherr Elliott H. , Glass Hannah C. 
Published: April 2021

Abstract
Background
The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known.

Methods
Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches.

Results
Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy.

Conclusions
In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy.

Impact

We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures.

Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy.

Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.
The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution
Authors: Garcia Amanda K , Cavanaugh Colleen M , Kacar Betul 
Published: April 2021

Abstract
The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic 13C/12C values has remained remarkably unchanged over &gt;3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO2 fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth’s atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO2-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.
Attractor cortical neurodynamics, schizophrenia, and depression
Authors: Rolls Edmund T. 
Published: April 2021

AbstractThe local recurrent collateral connections between cortical neurons provide a basis for attractor neural networks for memory, attention, decision-making, and thereby for many aspects of human behavior. In schizophrenia, a reduction of the firing rates of cortical neurons, caused for example by reduced NMDA receptor function or reduced spines on neurons, can lead to instability of the high firing rate attractor states that normally implement short-term memory and attention in the prefrontal cortex, contributing to the cognitive symptoms. Reduced NMDA receptor function in the orbitofrontal cortex by reducing firing rates may produce negative symptoms, by reducing reward, motivation, and emotion. Reduced functional connectivity between some brain regions increases the temporal variability of the functional connectivity, contributing to the reduced stability and more loosely associative thoughts. Further, the forward projections have decreased functional connectivity relative to the back projections in schizophrenia, and this may reduce the effects of external bottom-up inputs from the world relative to internal top-down thought processes. Reduced cortical inhibition, caused by a reduction of GABA neurotransmission, can lead to instability of the spontaneous firing states of cortical networks, leading to a noise-induced jump to a high firing rate attractor state even in the absence of external inputs, contributing to the positive symptoms of schizophrenia. In depression, the lateral orbitofrontal cortex non-reward attractor network system is over-connected and has increased sensitivity to non-reward, providing a new approach to understanding depression. This is complemented by under-sensitivity and under-connectedness of the medial orbitofrontal cortex reward system in depression.
Impaired AGO2/miR-185-3p/NRP1 axis promotes colorectal cancer metastasis
Authors: Liu Xisheng , Meng Xiaole , Peng Xiao , Yao Qianlan , Zhu Fangming , Ding Zhongyi , Sun Hongze , Liu Xueni , Li Dan , Lu Ying , Tang Huamei , Li Bin , Peng Zhihai 
Published: April 2021

AbstractIncreasing evidence suggests that global downregulation of miRNA expression is a hallmark of human cancer, potentially due to defects in the miRNA processing machinery. In this study, we found that the protein expression of Argonaute 2 (AGO2), a key regulator of miRNA processing, was downregulated in colorectal cancer (CRC) tissues, which was also consistent with the findings of the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Furthermore, the correlation between the levels of AGO2 and epithelial-mesenchymal transition (EMT) markers (E-cadherin and vimentin) indicated that reduced levels of AGO2 promoted EMT in CRC. Low expression of AGO2 was an indicator of a poor prognosis among CRC patients. Knockdown of AGO2 in CRC cells promoted migration, invasion and metastasis formation in vitro and in vivo but had no influence on proliferation. To provide detailed insight into the regulatory roles of AGO2, we performed integrated transcriptomic, quantitative proteomic and microRNA sequencing (miRNA-seq) analyses of AGO2 knockdown cells and the corresponding wild-type cells and identified neuropilin 1 (NRP1) as a new substrate of AGO2 via miR-185-3p. Our data provided evidence that knockdown of AGO2 resulted in a reduction of miR-185-3p expression, leading to the upregulation of the expression of NRP1, which is a direct target of miR-185-3p, and elevated CRC cell metastatic capacity. Inhibition of NRP1 or treatment with a miR-185-3p mimic successfully rescued the phenotypes of impaired AGO2, which suggested that therapeutically targeting the AGO2/miR-185-3p/NRP1 axis may be a potential treatment approach for CRC.
Cellular fate of intersex differentiation
Authors: Wang Xin , Lai Fengling , Shang Dantong , Cheng Yibin , Lan Tian , Cheng Hanhua , Zhou Rongjia 
Published: April 2021

AbstractInfertile ovotestis (mixture of ovary and testis) often occurs in intersex individuals under certain pathological and physiological conditions. However, how ovotestis is formed remains largely unknown. Here, we report the first comprehensive single-cell developmental atlas of the model ovotestis. We provide an overview of cell identities and a roadmap of germline, niche, and stem cell development in ovotestis by cell lineage reconstruction and a uniform manifold approximation and projection. We identify common progenitors of germline stem cells with two states, which reveal their bipotential nature to differentiate into both spermatogonial stem cells and female germline stem cells. Moreover, we found that ovotestis infertility was caused by degradation of female germline cells via liquid–liquid phase separation of the proteasomes in the nucleus, and impaired histone-to-protamine replacement in spermatid differentiation. Notably, signaling pathways in gonadal niche cells and their interaction with germlines synergistically determined distinct cell fate of both male and female germlines. Overall, we reveal a cellular fate map of germline and niche cell development that shapes cell differentiation direction of ovotestis, and provide novel insights into ovotestis development.
Inositol treatment inhibits medulloblastoma through suppression of epigenetic-driven metabolic adaptation
Authors: Badodi Sara , Pomella Nicola , Zhang Xinyu , Rosser Gabriel , Whittingham John , Niklison-Chirou Maria Victoria , Lim Yau Mun , Brandner Sebastian , Morrison Gillian , Pollard Steven M. , Bennett Christopher D. , Clifford Steven C. , Peet Andrew , Basson M. Albert , Marino Silvia 
Published: April 2021

AbstractDeregulation of chromatin modifiers plays an essential role in the pathogenesis of medulloblastoma, the most common paediatric malignant brain tumour. Here, we identify a BMI1-dependent sensitivity to deregulation of inositol metabolism in a proportion of medulloblastoma. We demonstrate mTOR pathway activation and metabolic adaptation specifically in medulloblastoma of the molecular subgroup G4 characterised by a BMI1High;CHD7Low signature and show this can be counteracted by IP6 treatment. Finally, we demonstrate that IP6 synergises with cisplatin to enhance its cytotoxicity in vitro and extends survival in a pre-clinical BMI1High;CHD7Low xenograft model.
Role of Hakai in m6A modification pathway in Drosophila
Authors: Wang Yanhua , Zhang Lifeng , Ren Hang , Ma Lijuan , Guo Jian , Mao Decai , Lu Zhongwen , Lu Lijun , Yan Dong 
Published: April 2021

AbstractN6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNA, is installed by a multi-component writer complex; however, the exact roles of each component remain poorly understood. Here we show that a potential E3 ubiquitin ligase Hakai colocalizes and interacts with other m6A writer components, and Hakai mutants exhibit typical m6A pathway defects in Drosophila, such as lowered m6A levels in mRNA, aberrant Sxl alternative splicing, wing and behavior defects. Hakai, Vir, Fl(2)d and Flacc form a stable complex, and disruption of either Hakai, Vir or Fl(2)d led to the degradation of the other three components. Furthermore, MeRIP-seq indicates that the effective m6A modification is mostly distributed in 5’ UTRs in Drosophila, in contrast to the mammalian system. Interestingly, we demonstrate that m6A modification is deposited onto the Sxl mRNA in a sex-specific fashion, which depends on the m6A writer. Together, our work not only advances the understanding of mechanism and regulation of the m6A writer complex, but also provides insights into how Sxl cooperate with the m6A pathway to control its own splicing.
Poaceae-specific cell wall-derived oligosaccharides activate plant immunity via OsCERK1 during Magnaporthe oryzae infection in rice
Authors: Yang Chao , Liu Rui , Pang Jinhuan , Ren Bin , Zhou Huanbin , Wang Gang , Wang Ertao , Liu Jun 
Published: April 2021

AbstractMany phytopathogens secrete cell wall degradation enzymes (CWDEs) to damage host cells and facilitate colonization. As the major components of the plant cell wall, cellulose and hemicellulose are the targets of CWDEs. Damaged plant cells often release damage-associated molecular patterns (DAMPs) to trigger plant immune responses. Here, we establish that the fungal pathogenMagnaporthe oryzaesecretes the endoglucanases MoCel12A and MoCel12B during infection of rice (Oryza sativa). These endoglucanases target hemicellulose of the rice cell wall and release two specific oligosaccharides, namely the trisaccharide 31-β-D-Cellobiosyl-glucose and the tetrasaccharide 31-β-D-Cellotriosyl-glucose. 31-β-D-Cellobiosyl-glucose and 31-β-D-Cellotriosyl-glucose bind the immune receptor OsCERK1 but not the chitin binding protein OsCEBiP. However, they induce the dimerization of OsCERK1 and OsCEBiP. In addition, these Poaceae cell wall-specific oligosaccharides trigger a burst of reactive oxygen species (ROS) that is largely compromised inoscerk1andoscebipmutants. We conclude that 31-β-D-Cellobiosyl-glucose and 31-β-D-Cellotriosyl-glucose are specific DAMPs released from the hemicellulose of rice cell wall, which are perceived by an OsCERK1 and OsCEBiP immune complex duringM. oryzaeinfection in rice.
Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase
Authors: Teixeira Raphael D. , Holzschuh Fabian , Schirmer Tilman 
Published: April 2021

AbstractDiguanylate cyclases synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain, but how activation proceeds mechanistically is, apart from a few examples, still largely unknown. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR from Leptospira biflexa is a constitutively dimeric prototype of this class of diguanylate cyclases. Full-length crystal structures reveal that BeF3- pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coil via a localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many diguanylate cyclases with N-terminal coiled-coil linkers.
RA3 is a reference-guided approach for epigenetic characterization of single cells
Authors: Chen Shengquan , Yan Guanao , Zhang Wenyu , Li Jinzhao , Jiang Rui , Lin Zhixiang 
Published: April 2021

AbstractThe recent advancements in single-cell technologies, including single-cell chromatin accessibility sequencing (scCAS), have enabled profiling the epigenetic landscapes for thousands of individual cells. However, the characteristics of scCAS data, including high dimensionality, high degree of sparsity and high technical variation, make the computational analysis challenging. Reference-guided approaches, which utilize the information in existing datasets, may facilitate the analysis of scCAS data. Here, we present RA3 (Reference-guided Approach for the Analysis of single-cell chromatin Accessibility data), which utilizes the information in massive existing bulk chromatin accessibility and annotated scCAS data. RA3 simultaneously models (1) the shared biological variation among scCAS data and the reference data, and (2) the unique biological variation in scCAS data that identifies distinct subpopulations. We show that RA3 achieves superior performance when used on several scCAS datasets, and on references constructed using various approaches. Altogether, these analyses demonstrate the wide applicability of RA3 in analyzing scCAS data.
Substitutional adsorptions of chloride at grain boundary sites on hydroxylated alumina surfaces initialize localized corrosion
Authors: Sundar Aditya , Chen Ganlin , Qi Liang 
Published: April 2021

AbstractTo understand the chloride (Cl)-induced initiation mechanism of localized corrosion of Aluminum (Al) alloys, we apply density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations to investigate the interactions between Cl and hydroxylated α–Al2O3 surfaces, mainly (0001) orientation, under aqueous electrochemical conditions. Hydroxylated alumina surfaces thermodynamically stable in aqueous environments are constructed based on DFT calculations for both the single-crystal and bicrystal configurations. AIMD simulations suggest a Cl anion can only be stabilized on these surfaces by substituting a surface hydroxyl (OH) group. This substitution is thermodynamically favorable at sites on surface terminations of grain boundaries (GBs) in bicrystal configurations but not favorable at sites on single-crystal surfaces. Electronic structure analyses show that the different adsorption behaviors originate from the higher sensitivity of the Al–OH bond strength to the local coordination than its counterpart of the Al–Cl bond. The adsorbed Cl significantly increases the thermodynamic driving force for Al cation dissolution from alumina surfaces into the aqueous electrolyte, which can initiate localized corrosion.
Regenerative medicine meets mathematical modelling: developing symbiotic relationships
Authors: Waters S. L. , Schumacher L. J. , El Haj A. J. 
Published: April 2021

AbstractSuccessful progression from bench to bedside for regenerative medicine products is challenging and requires a multidisciplinary approach. What has not yet been fully recognised is the potential for quantitative data analysis and mathematical modelling approaches to support this process. In this review, we highlight the wealth of opportunities for embedding mathematical and computational approaches within all stages of the regenerative medicine pipeline. We explore how exploiting quantitative mathematical and computational approaches, alongside state-of-the-art regenerative medicine research, can lead to therapies that potentially can be more rapidly translated into the clinic.
Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
Authors: Yoshitake Kazutoshi , Fujiwara Atushi , Matsuura Aiko , Sekino Masashi , Yasuike Motoshige , Nakamura Yoji , Nakamichi Reiichiro , Kodama Masaaki , Takahama Yumiko , Takasuka Akinori , Asakawa Shuichi , Nishikiori Kazuomi , Kobayashi Takanori , Watabe Shugo 
Published: April 2021

AbstractMany studies have investigated the ability to identify species from environmental DNA (eDNA). However, even when individual species are identified, the accurate estimation of their abundances by traditional eDNA analyses has been still difficult. We previously developed a novel analytical method called HaCeD-Seq (Haplotype Count from eDNA), which focuses on the mitochondrial D-loop sequence. The D-loop is a rapidly evolving sequence and has been used to estimate the abundance of eel species in breeding water. In the current study, we have further improved this method by applying unique molecular identifier (UMI) tags, which eliminate the PCR and sequencing errors and extend the detection range by an order of magnitude. Based on this improved HaCeD-Seq pipeline, we computed the abundance of Pacific bluefin tuna (Thunnus orientalis) in aquarium tanks at the Tokyo Sea Life Park (Kasai, Tokyo, Japan). This tuna species is commercially important but is at high risk of resource depletion. With the developed UMI tag method, 90 out of 96 haplotypes (94%) were successfully detected from Pacific bluefin tuna eDNA. By contrast, only 29 out of 96 haplotypes (30%) were detected when UMI tags were not used. Our findings indicate the potential for conducting non-invasive fish stock surveys by sampling eDNA.