bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fracture Permeability Enhancement During Fluid Injection Modulated by Pressurization Rate and Surface Asperities
Authors: Ji Yinlin , Zhang Wei , Hofmann Hannes , Cappa Frédéric , Zhang Supeng 
Published: September 2023

AbstractWe present a series of controlled fluid injection experiments in the laboratory on a pre‐stressed natural rough fracture with a high initial permeability (∼10−13 m2) in granite using different fluid pressurization rates. Our results show that fluid injection on a fracture with a slight velocity‐strengthening frictional behavior exhibits dilatant slow slip in association with a permeability increase up to ∼41 times attained at the maximum slip velocity of 0.085 mm/s for the highest‐rate injection case. Under these conditions, the slip velocity‐dependent change in hydraulic aperture is a dominant process to explain the transient evolution of fracture permeability, which is modulated by fluid pressurization rate and fracture surface asperities. This leads to the conclusion that permeability evolution can be engineered for subsurface geoenergy applications by controlling the fluid pressurization rate on slowly slipping fractures.
The Hydrologic Cycle and Atmospheric Rivers in CESM2 Simulations of the Last Glacial Maximum
Authors: Lora J. M. , Skinner C. B. , Rush W. D. , Baek S. H. 
Published: September 2023

AbstractProxy reconstructions and model simulations of precipitation during Earth's glacial periods suggest that the locations and mechanisms of atmospheric moisture transport have changed considerably during Earth's past. We investigate the hydroclimate of the Last Glacial Maximum (LGM) using simulations with the Community Earth System Model, with a focus on the extratropics and the influence of atmospheric rivers (ARs), a key driver of modern‐day moisture transport globally. Mean and extreme precipitation increase significantly over southwestern Patagonia, Iberia, and southwestern North America—mid‐latitude regions affected by ARs in the modern climate—despite overall decreases elsewhere. In each, the associated moisture transport changes are different, with increased transport and AR activity mainly occurring in the North Atlantic. The overall LGM response is dominated by the response to ice sheets, with other forcings causing additional cooling and drying over the extratropics and a strong decrease of moisture transport over the subpolar North Atlantic.
A copper-iodide cluster microcube-based X-ray scintillator
Authors: Qiu Jian , Liu Xiaogang 
Published: September 2023

AbstractNewly developed copper-iodide cluster microcubes offer a solution to the issues commonly faced by powder scintillation screens. These problems include inadequate scintillation performance and significant light scattering, resulting in poor image quality. With the advent of monodisperse copper-iodide cluster microparticle scintillators, efficient and long-term stable scintillation is achieved, while ensuring biocompatibility. Moreover, they enable high-resolution static and dynamic X-ray imaging, providing high image quality.
Polarization patterns of light enable geolocalization in oceans
Authors: Wang Lihong V. 
Published: September 2023

AbstractThe deep ocean, characterized by its immense depths and absence of global positioning system (GPS) functionality, presents considerable challenges for search and rescue missions. Inspired by the geolocalization capabilities of migratory marine animals, Bai et al. present a novel method for underwater geolocalization using the polarization patterns of light in the underwater environment. Emulating a sextant using these underwater polarization patterns, the study determines geolocation in underwater settings. Despite prior skepticism, even in low-visibility waters, these patterns, learned through a deep neural network, provide geolocation accuracies of 55 km at 8 m and 255 km at 50 m. This pioneering approach offers implications for search and rescue and hints at navigation mechanisms in marine animals.
Long non-coding RNA SNHG8 drives stress granule formation in tauopathies
Authors: Bhagat Reshma , Minaya Miguel A. , Renganathan Arun , Mehra Muneshwar , Marsh Jacob , Martinez Rita , Eteleeb Abdallah M. , Nana Alissa L. , Spina Salvatore , Seeley William W. , Grinberg Lea T. , Karch Celeste M. 
Published: September 2023

AbstractTauopathies are a heterogenous group of neurodegenerative disorders characterized by tau aggregation in the brain. In a subset of tauopathies, rare mutations in the MAPT gene, which encodes the tau protein, are sufficient to cause disease; however, the events downstream of MAPT mutations are poorly understood. Here, we investigate the role of long non-coding RNAs (lncRNAs), transcripts >200 nucleotides with low/no coding potential that regulate transcription and translation, and their role in tauopathy. Using stem cell derived neurons from patients carrying a MAPT p.P301L, IVS10 + 16, or p.R406W mutation and CRISPR-corrected isogenic controls, we identified transcriptomic changes that occur as a function of the MAPT mutant allele. We identified 15 lncRNAs that were commonly differentially expressed across the three MAPT mutations. The commonly differentially expressed lncRNAs interact with RNA-binding proteins that regulate stress granule formation. Among these lncRNAs, SNHG8 was significantly reduced in a mouse model of tauopathy and in FTLD-tau, progressive supranuclear palsy, and Alzheimer’s disease brains. We show that SNHG8 interacts with tau and stress granule-associated RNA-binding protein TIA1. Overexpression of mutant tau in vitro is sufficient to reduce SNHG8 expression and induce stress granule formation. Rescuing SNHG8 expression leads to reduced stress granule formation and reduced TIA1 levels in immortalized cells and in MAPT mutant neurons, suggesting that dysregulation of this non-coding RNA is a causal factor driving stress granule formation via TIA1 in tauopathies.
Amphiregulin normalizes altered circuit connectivity for social dominance of the CRTC3 knockout mouse
Authors: Park Ji-Seon , Heo Hwon , Kim Min-Seok , Lee Seung-Eun , Park Sukyoung , Kim Ki-Hyun , Kang Young-Ho , Kim Je Seong , Sung Young Hoon , Shim Woo Hyun , Kim Dong-Hou , Song Youngsup , Yoon Seung-Yong 
Published: September 2023

AbstractSocial hierarchy has a profound impact on social behavior, reward processing, and mental health. Moreover, lower social rank can lead to chronic stress and often more serious problems such as bullying victims of abuse, suicide, or attack to society. However, its underlying mechanisms, particularly their association with glial factors, are largely unknown. In this study, we report that astrocyte-derived amphiregulin plays a critical role in the determination of hierarchical ranks. We found that astrocytes-secreted amphiregulin is directly regulated by cAMP response element-binding (CREB)-regulated transcription coactivator 3 (CRTC3) and CREB. Mice with systemic and astrocyte-specific CRTC3 deficiency exhibited a lower social rank with reduced functional connectivity between the prefrontal cortex, a major social hierarchy center, and the parietal cortex. However, this effect was reversed by astrocyte-specific induction of amphiregulin expression, and the epidermal growth factor domain was critical for this action of amphiregulin. These results provide evidence of the involvement of novel glial factors in the regulation of social dominance and may shed light on the clinical application of amphiregulin in the treatment of various psychiatric disorders.
Sex- and suicide-specific alterations in the kynurenine pathway in the anterior cingulate cortex in major depression
Authors: Brown Samara J. , Christofides Katerina , Weissleder Christin , Huang Xu-Feng , Shannon Weickert Cynthia , Lim Chai K. , Newell Kelly A. 
Published: September 2023

AbstractMajor depressive disorder (MDD) is a serious psychiatric disorder that in extreme cases can lead to suicide. Evidence suggests that alterations in the kynurenine pathway (KP) contribute to the pathology of MDD. Activation of the KP leads to the formation of neuroactive metabolites, including kynurenic acid (KYNA) and quinolinic acid (QUIN). To test for changes in the KP, postmortem anterior cingulate cortex (ACC) was obtained from the National Institute of Health NeuroBioBank. Gene expression of KP enzymes and relevant neuroinflammatory markers were investigated via RT-qPCR (Fluidigm) and KP metabolites were measured using liquid chromatography-mass spectrometry in tissue from individuals with MDD (n = 44) and matched nonpsychiatric controls (n = 36). We report increased IL6 and IL1B mRNA in MDD. Subgroup analysis found that female MDD subjects had significantly decreased KYNA and a trend decrease in the KYNA/QUIN ratio compared to female controls. In addition, MDD subjects that died by suicide had significantly decreased KYNA in comparison to controls and MDD subjects that did not die by suicide, while subjects that did not die by suicide had increased KYAT2 mRNA, which we hypothesise may protect against a decrease in KYNA. Overall, we found sex- and suicide-specific alterations in the KP in the ACC in MDD. This is the first molecular evidence in the brain of subgroup specific changes in the KP in MDD, which not only suggests that treatments aimed at upregulation of the KYNA arm in the brain may be favourable for female MDD sufferers but also might assist managing suicidal behaviour.
Neoadjuvant botensilimab plus balstilimab response pattern in locally advanced mismatch repair proficient colorectal cancer
Authors: Kasi Pashtoon Murtaza , Hidalgo Manuel , Jafari Mehraneh D. , Yeo Heather , Lowenfeld Lea , Khan Uqba , Nguyen Alana T. H. , Siolas Despina , Swed Brandon , Hyun Jini , Khan Sahrish , Wood Madeleine , Samstein Benjamin , Rocca Juan P. , Ocean Allyson J. , Popa Elizabeta C. , Hunt Daniel H. , Uppal Nikhil P. , Garrett Kelly A. , Pigazzi Alessio , Zhou Xi Kathy , Shah Manish A. , Hissong Erika 
Published: September 2023

AbstractIn patients with locally advanced cancer without distant metastases, the neoadjuvant setting presents a platform to evaluate new drugs. For mismatch repair proficient/microsatellite stable (pMMR/MSS) colon and rectal cancer, immunotherapy has shown limited efficacy. Herein, we report exceptional responses observed with neoadjuvant botensilimab (BOT), an Fc-enhanced next-generation anti–CTLA-4 antibody, alongside balstilimab (BAL; an anti-PD-1 antibody) in two patients with pMMR/MSS colon and rectal cancer. The histological pattern of rapid immune response observed (“inside-out” (serosa-to-mucosa) tumor regression) has not been described previously in this setting. Spatial biology analyses (RareCyte Inc.) reveal mechanisms of actions of BOT, a novel innate-adaptive immune activator. These observations have downstream implications for clinical trial designs using neoadjuvant immunotherapy and potentially sparing patients chemotherapy.
The role of cell death in SARS-CoV-2 infection
Authors: Yuan Cui , Ma Zhenling , Xie Jiufeng , Li Wenqing , Su Lijuan , Zhang Guozhi , Xu Jun , Wu Yaru , Zhang Min , Liu Wei 
Published: September 2023

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), showing high infectiousness, resulted in an ongoing pandemic termed coronavirus disease 2019 (COVID-19). COVID-19 cases often experience acute respiratory distress syndrome, which has caused millions of deaths. Apart from triggering inflammatory and immune responses, many viral infections can cause programmed cell death in infected cells. Cell death mechanisms have a vital role in maintaining a suitable environment to achieve normal cell functionality. Nonetheless, these processes are dysregulated, potentially contributing to disease pathogenesis. Over the past decades, multiple cell death pathways are becoming better understood. Growing evidence suggests that the induction of cell death by the coronavirus may significantly contributes to viral infection and pathogenicity. However, the interaction of SARS-CoV-2 with cell death, together with its associated mechanisms, is yet to be elucidated. In this review, we summarize the existing evidence concerning the molecular modulation of cell death in SARS-CoV-2 infection as well as viral-host interactions, which may shed new light on antiviral therapy against SARS-CoV-2.
Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography
Authors: ter Horst Anneliek M , Fudyma Jane D , Sones Jacqueline L , Emerson Joanne B 
Published: September 2023

Abstract
Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.
Feasibility of mass cytometry proteomic characterisation of circulating tumour cells in head and neck squamous cell carcinoma for deep phenotyping
Authors: Payne Karl , Brooks Jill , Batis Nikolaos , Khan Naeem , El-Asrag Mohammed , Nankivell Paul , Mehanna Hisham , Taylor Graham 
Published: September 2023

Abstract
Background
Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC.

Methods
Parsortix microfluidic-enriched CTCs from 14 treatment-naïve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data.

Results
CTCs were detected in 13/14 patients with CTC counts of 2–24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype.

Discussion
We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.
Sheptide A: an antimalarial cyclic pentapeptide from a fungal strain in the Herpotrichiellaceae
Authors: Shepherd Robert A. , Earp Cody E. , Cank Kristof B. , Raja Huzefa A. , Burdette Joanna , Maher Steven P. , Marin Adriana A. , Ruberto Anthony A. , Mai Sarah Lee , Darveaux Blaise A. , Kyle Dennis E. , Pearce Cedric J. , Oberlies Nicholas H. 
Published: September 2023

AbstractAs part of ongoing efforts to isolate biologically active fungal metabolites, a cyclic pentapeptide, sheptide A (1), was discovered from strain MSX53339 (Herpotrichiellaceae). The structure and sequence of 1 were determined primarily by analysis of 2D NMR and HRMS/MS data, while the absolute configuration was assigned using a modified version of Marfey’s method. In an in vitro assay for antimalarial potency, 1 displayed a pEC50 value of 5.75 ± 0.49 against malaria-causing Plasmodium falciparum. Compound 1 was also tested in a counter screen for general cytotoxicity against human hepatocellular carcinoma (HepG2), yielding a pCC50 value of 5.01 ± 0.45 and indicating a selectivity factor of ~6. This makes 1 the third known cyclic pentapeptide biosynthesized by fungi with antimalarial activity.
Diagnostic accuracy of self-reported age-related macular degeneration in the ASPREE Longitudinal Study of Older Persons
Authors: McGuinness Myra B. , Robman Liubov , Hodgson Lauren A. B. , Tran Cammie , Woods Robyn L. , Owen Alice J. , McNeil John J. , Makeyeva Galina , Abhayaratna Walter P. , Guymer Robyn H. 
Published: September 2023

Abstract
Background
The validity of findings from epidemiological studies using self-report of ophthalmic conditions depends on several factors. We assessed the diagnostic accuracy of self-reported age-related macular degeneration (AMD) among older Australians enroled in a primary prevention clinical trial and compared diagnostic accuracy between demographic subgroups.

Methods
At baseline (2010–2015), Australian sub-study participants of the ASPirin in Reducing Events in the Elderly (ASPREE) trial, underwent bilateral two-field, 45° non-mydriatic colour retinal photography. Beckman classification of any-stage AMD was used as the reference standard diagnosis. Participants were asked whether a doctor had ever diagnosed them with “macular degeneration” (the index test) via a paper-based questionnaire as part of the ASPREE Longitudinal Study of Older Persons (ALSOP) within the first year of enrolment.

Results
In total, 4193 participants were included (aged 70–92 years, 50.8% female). Of those, 262 (6.3%) reported having AMD and 92 (2.2%) were unsure. Retinal grading detected 2592 (61.8%) with no AMD, 867 (20.7%) with early, 686 (16.4%) with intermediate and 48 (1.1%) with late AMD (n = 1601 with any-stage AMD, 38.2%). Self-reported AMD had 11.4% sensitivity (95% CI 9.9–13.1) and 96.9% specificity (95% CI 96.2–97.6) for any-stage AMD, with 69.8% and 63.9% positive and negative predictive values. Sensitivity was higher among participants with late-stage AMD (87.5%), older participants (26.8%), and those with poorer vision (41.0%).

Conclusions
Although most participants with late-stage AMD were aware of having AMD, the majority with early and intermediate AMD were not. Therefore, findings from studies that rely on disease self-report should be interpreted with caution.
A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
Authors: Nicolas Alexa M. , Sieradzki Ella T. , Pett-Ridge Jennifer , Banfield Jillian F. , Taga Michiko E. , Firestone Mary K. , Blazewicz Steven J. 
Published: September 2023

AbstractViruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following “wet-up”, when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils.
epiAneufinder identifies copy number alterations from single-cell ATAC-seq data
Authors: Ramakrishnan Akshaya , Symeonidi Aikaterini , Hanel Patrick , Schmid Katharina T. , Richter Maria L. , Schubert Michael , Colomé-Tatché Maria 
Published: September 2023

AbstractSingle-cell open chromatin profiling via scATAC-seq has become a mainstream measurement of open chromatin in single-cells. Here we present epiAneufinder, an algorithm that exploits the read count information from scATAC-seq data to extract genome-wide copy number alterations (CNAs) for individual cells, allowing the study of CNA heterogeneity present in a sample at the single-cell level. Using different cancer scATAC-seq datasets, we show that epiAneufinder can identify intratumor clonal heterogeneity in populations of single cells based on their CNA profiles. We demonstrate that these profiles are concordant with the ones inferred from single-cell whole genome sequencing data for the same samples. EpiAneufinder allows the inference of single-cell CNA information from scATAC-seq data, without the need of additional experiments, unlocking a layer of genomic variation which is otherwise unexplored.
Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K+ during entry
Authors: Hover Samantha , Charlton Frank W. , Hellert Jan , Swanson Jessica J. , Mankouri Jamel , Barr John N. , Fontana Juan 
Published: September 2023

AbstractFollowing endocytosis, enveloped viruses employ the changing environment of maturing endosomes as cues to promote endosomal escape, a process often mediated by viral glycoproteins. We previously showed that both high [K+] and low pH promote entry of Bunyamwera virus (BUNV), the prototypical bunyavirus. Here, we use sub-tomogram averaging and AlphaFold, to generate a pseudo-atomic model of the whole BUNV glycoprotein envelope. We unambiguously locate the Gc fusion domain and its chaperone Gn within the floor domain of the spike. Furthermore, viral incubation at low pH and high [K+], reminiscent of endocytic conditions, results in a dramatic rearrangement of the BUNV envelope. Structural and biochemical assays indicate that pH 6.3/K+ in the absence of a target membrane elicits a fusion-capable triggered intermediate state of BUNV GPs; but the same conditions induce fusion when target membranes are present. Taken together, we provide mechanistic understanding of the requirements for bunyavirus entry.