bluuebunny/crossref_metadata_2025 huggingface dataset:
Coupled Climate Models Systematically Underestimate Radiation Response to Surface Warming
Authors: Olonscheck Dirk , Rugenstein Maria
Published: March 2024

A realistic representation of top‐of‐the‐atmosphere (TOA) radiation response to surface warming is key for trusting climate model projections. We show that coupled models with freely evolving ocean‐atmosphere interactions systematically underestimate the observed global TOA radiation trend during 2001–2022 in 552 simulations. Locally, even if a simulation spontaneously reproduces observed surface temperature trends, TOA radiation trends are more likely under‐ than overestimated. This response bias stems from the models' inability to reproduce the observed large‐scale surface warming pattern and from errors in the atmospheric physics affecting short‐ and longwave radiation. Models with a better representation of the TOA radiation response to local surface warming have a relatively low equilibrium climate sensitivity. Our bias metric is a novel process‐based approach which links a model's current response to climate change to its behavior in the future.
Albedo‐Induced Global Warming Potential Following Disturbances in Global Temperate and Boreal Forests
Authors: Zhu Qingsong , Chen Jiquan , Charles P.‐A. Bourque , Sonnentag Oliver , Montagnani Leonardo , O’Halloran Thomas L. , Scott Russell L. , Forsythe Jeremy , Song Bo , Zou Huimin , Duan Meihui , Li Xianglan
Published: March 2024

Forest disturbances can result in very different canopies that carry elevated albedo, thus causing substantial cooling effects on the climate. Unfortunately, the resulting dynamic global warming potential from altered albedo (GWPΔα) is poorly understood. We examined and modeled the changes in albedo over time after disturbances (i.e., forest age) by forest type, disturbance type and geographic location using direct measurements from 107 sites in temperate and boreal regions. Albedo in undisturbed forests was used as the reference to calculate albedo changes (Δα) and GWPΔα after a disturbance. We found that age is a significant factor for predicting albedo amid the obvious regulations from forest type and geographic locations. We found the strongest cooling GWPΔα in the first 10 years after a disturbance, but it decreased rapidly with time. The changes in GWPΔα were very different from the chronosequence of net ecosystem production (NEP). In the first decade after disturbances, GWPΔα was negative (i.e., cooling) and surprisingly larger in magnitude, with an average of −0.609 kg CO2 m−2 yr−1, compared to NEP of −0.166 kg CO2 m−2 yr−1. Albedo continued to decrease and approached pre‐disturbance levels until around 50 years, resulting in a nearly zero GWPΔα. This research illustrates that many forests in temperate and boreal regions can be considered significant cooling agents by taking into account the high albedo of young forests following disturbances.
p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs
Authors: Grit Jamie L. , McGee Lauren E. , Tovar Elizabeth A. , Essenburg Curt J. , Wolfrum Emily , Beddows Ian , Williams Kaitlin , Sheridan Rachael T. C. , Schipper Joshua L. , Adams Marie , Arumugam Menusha , Vander Woude Thomas , Gurunathan Sharavana , Field Jeffrey M. , Wulfkuhle Julia , Petricoin Emanuel F. , Graveel Carrie R. , Steensma Matthew R.
Published: March 2024

Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity. TP53 mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlying TP53-mediated therapy responses are unclear in the context of NF1-deficiency. We evaluated the role of two commonly altered genes, MET and TP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed that MET amplification occurs early in human MPNST progression and that Trp53 loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity. Trp53 loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes in Trp53-deficient lines suggesting Trp53 loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility.
Combination of stem cell-derived secretome from human exfoliated deciduous teeth with Yemeni Sidr honey on cell viability and migration: an in vitro study
Authors: Al-Hadi Mona Abdulrahman Abdullah
Published: March 2024

Introduction

Bone diseases have a profound global impact, especially when the body’s innate regenerative capacity falls short in the face of extensive damage. Stem cells from human exfoliated deciduous teeth (SHEDs), discovered in 2003, offer a promising solution for tissue repair, as they self-renew naturally and are easily obtainable. Mesenchymal stem cells (MSCs), including SHEDs, are believed to promote tissue regeneration by releasing growth factors, collectively known as the secretome.

Aims

This study explored the potential of combining SHED-derived secretome with Yemeni Sidr honey to improve osteoblast and fibroblast cell viability and migration.

Materials and methods

The experiment involved treating cell cultures of two types of rat cell lines - 7F2 osteoblast and BHK-21 fibroblast immortalized cells - with SHED-derived secretome and Yemeni Sidr honey. After the treatment, cell viability was measured using the MTT assay, which calculates OD at 590 nm. Additionally, the scratch assay was conducted to evaluate cell migration, and ImageJ software was used for data processing.

Results

The findings indicated that combining SHED-derived secretome and Yemeni Sidr honey enhanced osteoblast and fibroblast cell viability and migration. Furthermore, the study highlighted the difference in the stimulative potential of SHED-derived secretome, Yemeni Sidr honey, and their combination, on the viability and migration of the cultured cells.

Conclusion

The research concludes that combining SHED-derived secretome with Yemeni Sidr honey has the potential to promote cell viability and migration in in-vitro settings. The synergistic application of these substances has been found to be more effective -when combined in a dose-dependent manner- than their counterparts. Overall, the current study serves as a foundation for further investigations to establish if the explored substance has any useful clinical applications.
Single-cell RNA sequencing analysis of vestibular schwannoma reveals functionally distinct macrophage subsets
Authors: Baruah Paramita , Mahony Christopher , Marshall Jennifer L. , Smith Charlotte G. , Monksfield Peter , Irving Richard I. , Dumitriu Ingrid E. , Buckley Christopher D. , Croft Adam P.
Published: March 2024

Background

Vestibular schwannomas (VSs) remain a challenge due to their anatomical location and propensity to growth. Macrophages are present in VS but their roles in VS pathogenesis remains unknown.

Objectives

The objective was to assess phenotypic and functional profile of macrophages in VS with single-cell RNA sequencing (scRNAseq).

Methods

scRNAseq was carried out in three VS samples to examine characteristics of macrophages in the tumour. RT-qPCR was carried out on 10 VS samples for CD14, CD68 and CD163 and a panel of macrophage-associated molecules.

Results

scRNAseq revealed macrophages to be a major constituent of VS microenvironment with three distinct subclusters based on gene expression. The subclusters were also defined by expression of CD163, CD68 and IL-1β. AREG and PLAUR were expressed in the CD68+CD163+IL-1β+ subcluster, PLCG2 and NCKAP5 were expressed in CD68+CD163+IL-1β− subcluster and AUTS2 and SPP1 were expressed in the CD68+CD163−IL-1β+ subcluster. RT-qPCR showed expression of several macrophage markers in VS of which CD14, ALOX15, Interleukin-1β, INHBA and Colony Stimulating Factor-1R were found to have a high correlation with tumour volume.

Conclusions

Macrophages form an important component of VS stroma. scRNAseq reveals three distinct subsets of macrophages in the VS tissue which may have differing roles in the pathogenesis of VS.
Ferroptosis: a new hunter of hepatocellular carcinoma
Authors: Jiang Yulang , Yu Yongxin , Pan Ziyang , Glandorff Christian , Sun Mingyu
Published: March 2024

Ferroptosis is an iron ion-dependent, regulatory cell death modality driven by intracellular lipid peroxidation that plays a key role in the development of HCC. Studies have shown that various clinical agents (e.g., sorafenib) have ferroptosis inducer-like effects and can exert therapeutic effects by modulating different key factors in the ferroptosis pathway. This implies that targeting tumor cell ferroptosis may be a very promising strategy for tumor therapy. In this paper, we summarize the prerequisites and defense systems for the occurrence of ferroptosis and the regulatory targets of drug-mediated ferroptosis action in HCC, the differences and connections between ferroptosis and other programmed cell deaths. We aim to summarize the theoretical basis, classical inducers of ferroptosis and research progress of ferroptosis in HCC cells, clued to the treatment of HCC by regulating ferroptosis network. Further investigation of the specific mechanisms of ferroptosis and the development of hepatocellular carcinoma and interventions at different stages of hepatocellular carcinoma will help us to deepen our understanding of hepatocellular carcinoma, with a view to providing new and more precise preventive as well as therapeutic measures for patients.
Hypoxia and low-glucose environments co-induced HGDILnc1 promote glycolysis and angiogenesis
Authors: Zhang Qing-Wei , Lin Xiao-Lu , Dai Zi-Hao , Zhao Ran , Hou Yi-Chao , Liang Qian , Zhang Yan , Ge Zhi-Zheng
Published: March 2024

Small bowel vascular malformation disease (SBVM) commonly causes obscure gastrointestinal bleeding (OGIB). However, the pathogenetic mechanism and the role of lncRNAs in SBVM remain largely unknown. Here, we found that hypoxia and low-glucose environments co-augment angiogenesis and existed in SBVM. Mechanistically, hypoxia and low-glucose environments supported angiogenesis via activation of hypoxia and glucose deprivation-induced lncRNA (HGDILnc1) transcription by increasing binding of the NeuroD1 transcription factor to the HGDILnc1 promoter. Raised HGDILnc1 acted as a suppressor of α-Enolase 1 (ENO1) small ubiquitin-like modifier modification (SUMOylation)-triggered ubiquitination, and an activator of transcription of Aldolase C (ALDOC) via upregulation of Histone H2B lysine 16 acetylation (H2BK16ac) level in the promoter of ALDOC, and consequently promoting glycolysis and angiogenesis. Moreover, HGDILnc1 was clinically positively correlated with Neurogenic differentiation 1 (NeuroD1), ENO1, and ALDOC in SBVM tissues, and could function as a biomarker for SBVM diagnosis and therapy. These findings suggest that hypoxia and low-glucose environments were present in SBVM tissues, and co-augmented angiogenesis. Hypoxia and low-glucose environments co-induced HGDILnc1, which is higher expressed in SBVM tissue compared with normal tissue, could promoted glycolysis and angiogenesis.
Pivotal role of BCL11B in the immune, hematopoietic and nervous systems: a review of the BCL11B-associated phenotypes from the genetic perspective
Authors: García-Aznar José María , Alonso Alvarez Sara , Bernal del Castillo Teresa
Published: March 2024

The transcription factor BCL11B plays an essential role in the development of central nervous system and T cell differentiation by regulating the expression of numerous genes involved in several pathways. Monoallelic defects in the BCL11B gene leading to loss-of-function are associated with a wide spectrum of phenotypes, including neurological disorders with or without immunological features and susceptibility to hematological malignancies. From the genetic point of view, the landscape of BCL11B mutations reported so far does not fully explain the genotype-phenotype correlation. In this review, we sought to compile the phenotypic and genotypic variables associated with previously reported mutations in this gene in order to provide a better understanding of the consequences of deleterious variants. We also highlight the importance of a careful evaluation of the mutation type, its location and the pattern of inheritance of the variants in order to assign the most accurate pathogenicity and actionability of the genetic findings.
Intestinal dual-specificity phosphatase 6 regulates the cold-induced gut microbiota remodeling to promote white adipose browning
Authors: Chen Pei-Chen , Tsai Tzu-Pei , Liao Yi-Chu , Liao Yu-Chieh , Cheng Hung-Wei , Weng Yi-Hsiu , Lin Chiao-Mei , Kao Cheng-Yuan , Tai Chih-Cheng , Ruan Jhen-Wei
Published: March 2024

Gut microbiota rearrangement induced by cold temperature is crucial for browning in murine white adipose tissue. This study provides evidence that DUSP6, a host factor, plays a critical role in regulating cold-induced gut microbiota rearrangement. When exposed to cold, the downregulation of intestinal DUSP6 increased the capacity of gut microbiota to produce ursodeoxycholic acid (UDCA). The DUSP6-UDCA axis is essential for driving Lachnospiraceae expansion in the cold microbiota. In mice experiencing cold-room temperature (CR) transitions, prolonged DUSP6 inhibition via the DUSP6 inhibitor (E/Z)-BCI maintained increased cecal UDCA levels and cold-like microbiota networks. By analyzing DUSP6-regulated microbiota dynamics in cold-exposed mice, we identified Marvinbryantia as a genus whose abundance increased in response to cold exposure. When inoculated with human-origin Marvinbryantia formatexigens, germ-free recipient mice exhibited significantly enhanced browning phenotypes in white adipose tissue. Moreover, M. formatexigens secreted the methylated amino acid Nε-methyl-L-lysine, an enriched cecal metabolite in Dusp6 knockout mice that reduces adiposity and ameliorates nonalcoholic steatohepatitis in mice. Our work revealed that host-microbiota coadaptation to cold environments is essential for regulating the browning-promoting gut microbiome.
Deep learning radiomics based prediction of axillary lymph node metastasis in breast cancer
Authors: Liu Han , Zou Liwen , Xu Nan , Shen Haiyun , Zhang Yu , Wan Peng , Wen Baojie , Zhang Xiaojing , He Yuhong , Gui Luying , Kong Wentao
Published: March 2024

This study aimed to develop and validate a deep learning radiomics nomogram (DLRN) for the preoperative evaluation of axillary lymph node (ALN) metastasis status in patients with a newly diagnosed unifocal breast cancer. A total of 883 eligible patients with breast cancer who underwent preoperative breast and axillary ultrasound were retrospectively enrolled between April 1, 2016, and June 30, 2022. The training cohort comprised 621 patients from Hospital I; the external validation cohorts comprised 112, 87, and 63 patients from Hospitals II, III, and IV, respectively. A DLR signature was created based on the deep learning and handcrafted features, and the DLRN was then developed based on the signature and four independent clinical parameters. The DLRN exhibited good performance, yielding areas under the receiver operating characteristic curve (AUC) of 0.914, 0.929, and 0.952 in the three external validation cohorts, respectively. Decision curve and calibration curve analyses demonstrated the favorable clinical value and calibration of the nomogram. In addition, the DLRN outperformed five experienced radiologists in all cohorts. This has the potential to guide appropriate management of the axilla in patients with breast cancer, including avoiding overtreatment.
Stoner instability-mediated large magnetoelectric effects in 2D stacking electrides
Authors: Gui Zhigang , Zhu Haiyan , Wang Zhe , Farooq M. Umar , Bellaiche Laurent , Huang Li
Published: March 2024

Strong magnetoelectric effects in single-phase two-dimensional (2D) materials are extremely rare in nature. Here by first-principles calculations, we find a strong magnetoelectric coupling in polar stacking bilayer Hf2S that allows the reversal of net magnetic moments with the reversal of electric dipoles. Further analysis shows that such strong magnetoelectric effects benefit from the Stoner instability of surface Hf atoms triggered by polar stacking. Moreover, an unexpectedly large out-of-plane electric polarization (which is at least two times larger than that of bilayer BN) survives in the material, despite its metallicity. The large electric polarization is ascribed to the delocalized interlayer electrons which generally present in layered electride materials. It is quite interesting that large electric polarization, metallicity and magnetism coexist in one single-phase material. Our findings reveal rich physical phenomena to be explored in 2D stacking multiferroics and suggest an alternative way of searching for strong magnetoelectric materials with ultrathin thickness.
Pipeline quantum processor architecture for silicon spin qubits
Authors: Patomäki S. M. , Gonzalez-Zalba M. F. , Fogarty M. A. , Cai Z. , Benjamin S. C. , Morton J. J. L.
Published: March 2024

We propose a quantum processor architecture, the qubit ‘pipeline’, in which run-time scales additively as functions of circuit depth and run repetitions. Run-time control is applied globally, reducing the complexity of control and interconnect resources. This simplification is achieved by shuttling N-qubit states through a large layered physical array of structures which realise quantum logic gates in stages. Thus, the circuit depth corresponds to the number of layers of structures. Subsequent N-qubit states are ‘pipelined’ densely through the structures to efficiently wield the physical resources for repeated runs. Pipelining thus lends itself to noisy intermediate-scale quantum (NISQ) applications, such as variational quantum eigensolvers, which require numerous repetitions of the same or similar calculations. We illustrate the architecture by describing a realisation in the naturally high-density and scalable silicon spin qubit platform, which includes a universal gate set of sufficient fidelity under realistic assumptions of qubit variability.
Observational reinforcement learning in children and young adults
Authors: Rodriguez Buritica Julia M. , Eppinger Ben , Heekeren Hauke R. , Crone Eveline A. , van Duijvenvoorde Anna C. K.
Published: March 2024

Observational learning is essential for the acquisition of new behavior in educational practices and daily life and serves as an important mechanism for human cognitive and social-emotional development. However, we know little about its underlying neurocomputational mechanisms from a developmental perspective. In this study we used model-based fMRI to investigate differences in observational learning and individual learning between children and younger adults. Prediction errors (PE), the difference between experienced and predicted outcomes, related positively to striatal and ventral medial prefrontal cortex activation during individual learning and showed no age-related differences. PE-related activation during observational learning was more pronounced when outcomes were worse than predicted. Particularly, negative PE-coding in the dorsal medial prefrontal cortex was stronger in adults compared to children and was associated with improved observational learning in children and adults. The current findings pave the way to better understand observational learning challenges across development and educational settings.
Recent progress on gene-deleted live-attenuated African swine fever virus vaccines
Authors: Vu Hiep L. X. , McVey D. Scott
Published: March 2024

African Swine Fever (ASF) is a highly lethal viral disease in swine, with mortality rates approaching 100%. The disease has spread to many swine-producing countries, leading to significant economic losses and adversely impacting global food security. Extensive efforts have been directed toward developing effective ASF vaccines. Among the vaccinology approaches tested to date, live-attenuated virus (LAV) vaccines produced by rational deleting virulence genes from virulent African Swine Fever Virus (ASFV) strains have demonstrated promising safety and efficacy in experimental and field conditions. Many gene-deleted LAV vaccine candidates have been generated in recent years. The virulence genes targeted for deletion from the genome of virulent ASFV strains can be categorized into four groups: Genes implicated in viral genome replication and transcription, genes from the multigene family located at both 5′ and 3′ termini, genes participating in mediating hemadsorption and putative cellular attachment factors, and novel genes with no known functions. Some promising LAV vaccine candidates are generated by deleting a single viral virulence gene, whereas others are generated by simultaneously deleting multiple genes. This article summarizes the recent progress in developing and characterizing gene-deleted LAV vaccine candidates.
Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus
Authors: Schäper Simon , Brito António D. , Saraiva Bruno M. , Squyres Georgia R. , Holmes Matthew J. , Garner Ethan C. , Hensel Zach , Henriques Ricardo , Pinho Mariana G.
Published: March 2024

Bacterial cell division requires recruitment of peptidoglycan (PG) synthases to the division site by the tubulin homologue, FtsZ. Septal PG synthases promote septum growth. FtsZ treadmilling is proposed to drive the processive movement of septal PG synthases and septal constriction in some bacteria; however, the precise mechanisms spatio-temporally regulating PG synthase movement and activity and FtsZ treadmilling are poorly understood. Here using single-molecule imaging of division proteins in the Gram-positive pathogen Staphylococcus aureus, we showed that the septal PG synthase complex FtsW/PBP1 and its putative activator protein, DivIB, move with similar velocity around the division site. Impairing FtsZ treadmilling did not affect FtsW or DivIB velocities or septum constriction rates. Contrarily, PG synthesis inhibition decelerated or stopped directional movement of FtsW and DivIB, and septum constriction. Our findings suggest that a single population of processively moving FtsW/PBP1 associated with DivIB drives cell constriction independently of FtsZ treadmilling in S. aureus.
Spatially organized cellular communities form the developing human heart
Authors: Farah Elie N. , Hu Robert K. , Kern Colin , Zhang Qingquan , Lu Ting-Yu , Ma Qixuan , Tran Shaina , Zhang Bo , Carlin Daniel , Monell Alexander , Blair Andrew P. , Wang Zilu , Eschbach Jacqueline , Li Bin , Destici Eugin , Ren Bing , Evans Sylvia M. , Chen Shaochen , Zhu Quan , Chi Neil C.
Published: March 2024

The heart, which is the first organ to develop, is highly dependent on its form to function1,2. However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart function remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization to resolve the identity of the cardiac cell types that develop the human heart. This approach also provided a spatial mapping of individual cells that enables illumination of their organization into cellular communities that form distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, which support their specialization according to the cellular ecosystem and anatomical region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell–cell interactions within these communities using in vivo conditional genetic mouse models and in vitro human pluripotent stem cell systems revealed multicellular signalling pathways that orchestrate the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. These detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodelling the human heart offer new insights into structural heart diseases and the engineering of complex multicellular tissues for human heart repair.
APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia
Authors: Haney Michael S. , Pálovics Róbert , Munson Christy Nicole , Long Chris , Johansson Patrik K. , Yip Oscar , Dong Wentao , Rawat Eshaan , West Elizabeth , Schlachetzki Johannes C. M. , Tsai Andy , Guldner Ian Hunter , Lamichhane Bhawika S. , Smith Amanda , Schaum Nicholas , Calcuttawala Kruti , Shin Andrew , Wang Yung-Hua , Wang Chengzhong , Koutsodendris Nicole , Serrano Geidy E. , Beach Thomas G. , Reiman Eric M. , Glass Christopher K. , Abu-Remaileh Monther , Enejder Annika , Huang Yadong , Wyss-Coray Tony
Published: March 2024

Several genetic risk factors for Alzheimer’s disease implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells1. However, the relationship between lipid metabolism in glia and Alzheimer’s disease pathology remains poorly understood. Through single-nucleus RNA sequencing of brain tissue in Alzheimer’s disease, we have identified a microglial state defined by the expression of the lipid droplet-associated enzyme ACSL1 with ACSL1-positive microglia being most abundant in patients with Alzheimer’s disease having theAPOE4/4genotype. In human induced pluripotent stem cell-derived microglia, fibrillar Aβ inducesACSL1expression, triglyceride synthesis and lipid droplet accumulation in an APOE-dependent manner. Additionally, conditioned media from lipid droplet-containing microglia lead to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for Alzheimer’s disease with microglial lipid droplet accumulation and neurotoxic microglia-derived factors, potentially providing therapeutic strategies for Alzheimer’s disease.
Blueprinting extendable nanomaterials with standardized protein blocks
Authors: Huddy Timothy F. , Hsia Yang , Kibler Ryan D. , Xu Jinwei , Bethel Neville , Nagarajan Deepesh , Redler Rachel , Leung Philip J. Y. , Weidle Connor , Courbet Alexis , Yang Erin C. , Bera Asim K. , Coudray Nicolas , Calise S. John , Davila-Hernandez Fatima A. , Han Hannah L. , Carr Kenneth D. , Li Zhe , McHugh Ryan , Reggiano Gabriella , Kang Alex , Sankaran Banumathi , Dickinson Miles S. , Coventry Brian , Brunette T. J. , Liu Yulai , Dauparas Justas , Borst Andrew J. , Ekiert Damian , Kollman Justin M. , Bhabha Gira , Baker David
Published: March 2024

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight ‘train track’ assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence–structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints.
Neural and behavioural state switching during hippocampal dentate spikes
Authors: Farrell Jordan S. , Hwaun Ernie , Dudok Barna , Soltesz Ivan
Published: March 2024

Distinct brain and behavioural states are associated with organized neural population dynamics that are thought to serve specific cognitive functions1–3. Memory replay events, for example, occur during synchronous population events called sharp-wave ripples in the hippocampus while mice are in an ‘offline’ behavioural state, enabling cognitive mechanisms such as memory consolidation and planning4–11. But how does the brain re-engage with the external world during this behavioural state and permit access to current sensory information or promote new memory formation? Here we found that the hippocampal dentate spike, an understudied population event that frequently occurs between sharp-wave ripples12, may underlie such a mechanism. We show that dentate spikes are associated with distinctly elevated brain-wide firing rates, primarily observed in higher order networks, and couple to brief periods of arousal. Hippocampal place coding during dentate spikes aligns to the mouse’s current spatial location, unlike the memory replay accompanying sharp-wave ripples. Furthermore, inhibiting neural activity during dentate spikes disrupts associative memory formation. Thus, dentate spikes represent a distinct brain state and support memory during non-locomotor behaviour, extending the repertoire of cognitive processes beyond the classical offline functions.
Numerical analyses for three-dimensional face stability of circular tunnels in purely cohesive soils with linearly increasing strength
Authors: Huang Bing , Yu Daidai , Zhao Yinting , Zhu Junfeng
Published: March 2024

The tunnel face stability in purely cohesive soils with linearly increasing strength was investigated using three-dimensional finite element limit analysis (FELA). Both the collapse (active failure) and blow-out (passive failure) of the tunnel face were considered in the analysis. The rigorous upper bound (UB) and lower bound (LB) solutions of the load factor were calculated with a wide range of ground conditions to cover a broad scope of practical application. The results showed that the whole surface of the face is at failure in the collapse case; while in the blow-out case, there exists a gradual evolution process from partial failure to global failure within the tunnel face with increasing buried depth. Later, based on 960 finite element limit analysis results, a series of practical equations were proposed for tunnel face stability analysis in purely cohesive soils. These equations can be employed to quickly calculate the UB and LB solutions of the limit support pressure and the stability number of a tunnel face in both the collapse and blow-out cases. Finally, the calculation results from these equations were compared with those from previous studies in detail. The comparisons showed that the proposed equations make an improvement over existing methods and can be used as an efficient tool in practical engineering.
Geohazard assessment of Mexico City’s Metro system derived from SAR interferometry observations
Authors: Solano-Rojas Darío , Wdowinski Shimon , Cabral-Cano Enrique , Osmanoğlu Batuhan
Published: March 2024

Land subsidence rates in Mexico City reach 500 mm/year, causing progressive damage to the city’s core infrastructure, including the Metro system. A deadly overpass collapse in 2021, along a Metro line that had operated for less than 10 years, brought subsidence-related structural damage to the attention of the system’s authorities and led to major repairs to two of the twelve Metro lines. Still, the need for quantifying the magnitude and extent of subsidence affecting the Metro system’s widespread infrastructure prevails. Using a wealth of satellite radar interferometry observations, levelling surveys, subsurface profiles, linear gradient and differential displacement analyses, and structural-engineering parameters, we assess the vulnerability of the Metro system’s street-level and elevated segments to land subsidence. Our results reveal that high subsidence velocity gradients occur over sharp transitional zones between stable and fast-subsiding areas, reaching values of 1 $$\times \,10 ^{-3}$$

×

10

-
3

year$$^{-1}$$

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1

, resulting in slope changes up to 3.5% over a 20-year period and differential displacements between columns. Our findings suggest locations where the consequences of subsidence have compromised the train’s braking safety design, increased railway flooding hazard, produced railway bending, and reduced the conceived 50-year service life of the Metro’s elevated overpasses.
Optimization of Chinese land spatial pattern in the transformation process of resource-based cities: a case study in Tongling City, China
Authors: Ye Yun , Qin Yan , Yu Ran , Wu Qun
Published: March 2024

Optimizing the spatial layout of the national territory is crucial for realizing the transformation and development of resource-oriented cities in the context of high-quality development in the new period. This paper takes Tongling City as a case study, based on the analysis of the historical development foundation, then uses the SD-FLUS comprehensive model to carry out a systematic analysis of the transformation in five dimensions of economy, society, population, science and technology, resources and environment, and discusses the optimization of spatial pattern under the contextual simulation. The conclusions are as follows: ① The hierarchical framework of “system-indicator-element” is not only internally interconnected, but also inextricably linked with the relationship between the various categories of the land use system. ② Decrease of cropland, forest, water, grassland, and barren decreases from the economic development, social progress, and comprehensive development, and there is a small increase in the area under the scenario of resource and environmental protection, and the direction of the change of the impervious is in the opposite direction. ③ Cultivated land is retained in situ and concentrated to a small extent, forested land is reduced to a small extent while the status quo is maintained, and the Yangtze River water system will be retained and protected to a large extent, but part of the waters of Zongyang County will give way to the expansion of construction land under the development objectives of the new county. Building land will be expanded and extended to the northeast in the original site area, while the southwest corner of the original county center will be expanded to some extent in Zongyang County to promote the county’s economic development.
Isolation and characterization of a newly discovered plant growth-promoting endophytic fungal strain from the genus Talaromyces
Authors: Kharkwal Amit C. , Joshi Hemesh , Shandilya Cheshta , Dabral Surbhi , Kumar Niraj , Varma Ajit
Published: March 2024

In the Kandi zone of Punjab, India, root and rhizospheric soil samples were collected from the local vegetation near the Shivalik mountain foothills. Fifteen fungal colonies exhibiting distinct cultural morphology on Potato Dextrose Agar (PDA) plates were selected for plant–microbe interaction studies. Among these, the isolate HNB9 was identified as a nonpathogenic root colonizer. Morphological and molecular analyses confirmed HNB9 as Talaromyces albobiverticillius, characterized by the secretion of a red pigment as a secondary metabolite. Plants colonized with T. albobiverticillius HNB9 exhibited enhanced growth, manifesting in increased shoot and root length compared to untreated controls. This study unveiled the first evidence that a species from the Talaromyces genus, specifically T. albobiverticillius, possesses dual capabilities of root colonization and plant growth promotion. Moreover, HNB9 demonstrated the production of plant growth-regulating compounds like Indole Acetic Acid (IAA) and proficient solubilization of crucial nutrients (Phosphorous, Zinc, and Silica) through plate culture methods. This finding represents a significant contribution to the understanding of root-colonizing fungi with plant growth-promoting attributes, challenging the existing knowledge gap within the Talaromyces genus.
7 Dimensions of software change patterns
Authors: Janke Mario , Mäder Patrick
Published: March 2024

Evolving software is a highly complex and creative problem in which a number of different strategies are used to solve the tasks at hand. These strategies and reoccurring coding patterns can offer insights into the process. However, they can be highly project or even task-specific. We aim to identify code change patterns in order to draw conclusions about the software development process. For this, we propose a novel way to calculate high-level file overarching diffs, and a novel way to parallelize pattern mining. In a study of 1000 Java projects, we mined and analyzed a total of 45,000 patterns. We present 13 patterns, showing extreme points of the 7 pattern categories we identified. We found that a large number of high-level change patterns exist and occur frequently. The majority of mined patterns were associated with a specific project and contributor, where and by whom it was more likely to be used. While a large number of different code change patterns are used, only a few, mostly unsurprising ones, are common under all circumstances. The majority of code change patterns are highly specific to different context factors that we further explore.
Titanate-based high-entropy perovskite oxides relaxor ferroelectrics
Authors: Bunpang Ketkaeo , Singkammo Suparat , Cann David P. , Raengthon Natthaphon
Published: March 2024

Different combinations of monovalent and trivalent A-cations in high-entropy perovskite oxides (HEPOs) were investigated. The multicomponent (A′0.2A″0.2Ba0.2Sr0.2Ca0.2)TiO3 (A′ = Na+, K+, A″ = Bi3+, La3+) perovskite compounds were successfully synthesized by solid-state reaction method persisting average cubic perovskite phase. The trivalent cation exhibited distinct effects on local structure, dielectric properties and relaxor ferroelectric behavior. Highly dense ceramics (> 95%), high dielectric constant (~ 3000), low dielectric loss (~ 0.1), and relaxor ferroelectric characteristics were obtained in the compound containing Bi3+. The La3+ containing compounds revealed lower dielectric constant, higher dielectric loss and linear dielectric behavior. The effect of monovalent cation on the dielectric properties was minimal. However, it affected relaxor ferroelectric behavior at elevated temperatures and conduction behavior at high temperatures. The (K0.2Bi0.2Ba0.2Sr0.2Ca0.2)TiO3 ceramic maintained the relaxor ferroelectric behavior with low PREM at high temperatures suggesting more stable relaxor ferroelectric characteristics than that of the (Na0.2Bi0.2Ba0.2Sr0.2Ca0.2)TiO3. Moreover, between these two compounds, the homogeneous electrical characteristics could be obtained from the compound consisting of K + and Bi + at A-site. This study suggests that tuning the chemical composition, particularly choosing appropriate combination of mono/trivalent cations in high entropy perovskite oxides, could be the effective approach to develop high-performance relaxor ferroelectrics with the desired properties.
KSRP improves pancreatic beta cell function and survival
Authors: Barssotti Leticia , Soares Gabriela Moreira , Marconato-Júnior Emílio , Lourençoni Alves Bruna , Oliveira Kênia Moreno , Carneiro Everardo Magalhães , Boschero Antonio Carlos , Barbosa Helena Cristina Lima
Published: March 2024

Impaired insulin production and/or secretion by pancreatic beta cells can lead to high blood glucose levels and type 2 diabetes (T2D). Therefore, investigating new proteins involved in beta cell response to stress conditions could be useful in finding new targets for therapeutic approaches. KH-type splicing regulatory protein (KSRP) is a protein usually involved in gene expression due to its role in post-transcriptional regulation. Although there are studies describing the important role of KSRP in tissues closely related to glucose homeostasis, its effect on pancreatic beta cells has not been explored so far. Pancreatic islets from diet-induced obese mice (C57BL/6JUnib) were used to determine KSRP expression and we also performed in vitro experiments exposing INS-1E cells (pancreatic beta cell line) to different stressors (palmitate or cyclopiazonic acid—CPA) to induce cellular dysfunction. Here we show that KSRP expression is reduced in all the beta cell dysfunction models tested. In addition, when manipulated to knock down KSRP, beta cells exhibited increased death and impaired insulin secretion, whereas KSRP overexpression prevented cell death and increased insulin secretion. Taken together, our findings suggest that KSRP could be an important target to protect beta cells from impaired functioning and death.
Maternal attachment security modulates the relationship between vulnerability to anxiety and attentional bias to threat in healthy children
Authors: Raymond Catherine , Cernik Rebecca , Beaudin Myriam , Arcand Maryse , Pichette Florence , Marin Marie-France
Published: March 2024

This study aimed to investigate whether attentional bias to threat, commonly observed in clinically anxious children, also manifests in healthy children, potentially aiding the early detection of at-risk individuals. Additionally, it sought to explore the moderating role of parent–child attachment security on the association between vulnerability factors (anxiety sensitivity, intolerance of uncertainty, perseverative cognitions) as indicators of vulnerability to anxiety, and attentional bias towards threat in healthy children. A total of 95 children aged 8 to 12 years completed the Visual Search Task to assess attentional bias. Vulnerability to anxiety was measured using a composite score derived from the Childhood Anxiety Sensitivity Index, Intolerance of Uncertainty Scale for Children, and Perseverative Thinking Questionnaire. Parent–child attachment security was assessed using the Security Scale-Child Self-Report. Analyses revealed that higher vulnerability to anxiety was associated with faster detection of anger-related stimuli compared to neutral ones, and this association was further influenced by high maternal security. These findings in healthy children suggest an interaction between specific factors related to anxiety vulnerability and the security of the mother–child relationship, leading to cognitive patterns resembling those seen in clinically anxious individuals. These results hold promise for early identification of children at risk of developing anxiety disorders.
Synchronization analyze of k-uniform hyper-networks
Authors: Du Juan , Ma Xiujuan , Ma Fuxiang , Yu Wenqian
Published: March 2024

Hyper-networks tend to perform better in representing multivariate relationships among nodes. Yet, due to the complexity of the hyper-network structure, research in synchronization dynamics is rarely involved. In this paper, a Kuramoto model more suitable for k-uniform hyper-networks is proposed. And the generalized Laplacian matrix expression of the k-uniform hyper-network is present. We use the eigenvalue ratio of the generalized Laplacian matrix to quantify synchronization. And we studied the effects of some important structure parameters on the synchronization of three types of k-uniform hyper-networks. And obtained different relationships between synchronization and these parameters. The results show the synchronization of the k-uniform hyper-networks is related to both structure and parameters. And as the size of the nodes increases, the synchronization ability gradually increases for ER random hyper-network, while that gradually decreases for NW small-world hyper-network and BA scale-free hyper-network. As the uniformity increases, the synchronization ability of all three types of uniform hyper-networks increases. In addition, when the structure and node size are fixed, the synchronization ability increases with the increase of the hyper-clustering coefficient in BA scale-free hyper-network and ER random hyper-network, while it decreases with the increase of the hyper-clustering coefficient in NW small-world hyper-network.
Characterization of yeast mutant strains for starter culture in Arabica coffee fermentation
Authors: Meeampun Yaowapa , Panyachanakul Titiporn , Samosorn Siritron , Dolsophon Kulvadee , Jiamjariyatam Rossaporn , Lorliam Wanlapa , Arnthong Jantima , Suwannarangsee Surisa , Tantayotai Prapakorn , Krajangsang Sukhumaporn
Published: March 2024

Arabica coffee is the most popular and best-selling type of coffee. During coffee fermentation, microorganisms are essential for the production of metabolites and volatile compounds that affect coffee flavor quality. This work aimed to study the mutation, selection, and characterization of the Wickerhamomyces anomalus strain YWP1-3 as a starter culture to enhance the flavor quality of Arabica coffee. The results revealed that six mutants could produce relatively high levels of the pectinase enzyme on pectin agar media and exhibited high activity levels, ranging from 332.35 to 415.88 U/ml in mucilage broth. Strains UV22-2, UV22-3, UV41-1 and UV32-1 displayed higher levels of amylase activity than did the wild type. The UV22-2 and UV22-3 mutants exhibited the highest pectin degradation indices of 49.22% and 45.97%, respectively, and displayed significantly enhanced growth rates in nitrogen yeast base media supplemented with various sugars; thus, these mutants were evaluated for their ability to serve as a starter for fermentation of Arabica coffee. The cupping scores of coffees derived from UV22-2 and UV22-3 were 83.5 ± 1.5 and 82.0 ± 2.14, respectively. The volatile compounds in the roasted coffee fermented by UV22-2 were analyzed by GC‒MS, which revealed higher levels of furfuryl alcohol and furfuryl acetate than did the other samples. These findings suggested that UV22-2 could be an influential starter culture for Arabica coffee fermentation.