bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal and Interannual Variability of the Subtropical South Indian Ocean Sea Surface Salinity Maximum
Authors: Bingham F. M. , Brodnitz S. K. , Gordon A. L. 
Published: February 2023

AbstractThe sea surface salinity (SSS) maximum of the South Indian Ocean (the SISSS‐max) is a high‐salinity feature centered at 30°S, 90°E, near the center of the South Indian subtropical gyre. It is located poleward of a region of strong evaporation and weak precipitation. Using several different satellites and in situ data sets, we track changes in this feature since the early 2000s. The centroid of the SISSS‐max moves seasonally north and south, furthest north in late winter and farthest south in late summer. Interannually, the SISSS‐max has moved on a northeast‐southwest path about 1,500 km in length. The size and maximum SSS of the feature vary in tandem with this motion. It gets larger (smaller) and saltier (fresher) as it moves to the northeast (southwest) closer to (further from) the area of strongest surface freshwater flux. The area of the SISSS‐max almost doubles from its smallest to largest extent. It was maximum in area in 2006, decreased steadily until it reached a minimum in 2013, and then increased again. The seasonal variability of the SISSS‐max is controlled by the changes that occur on its poleward, or southern, side, whereas interannual variability is controlled by changes on its equatorward side. The variations in the SISSS‐max are a complex dance between changes in evaporation, precipitation, wind forcing, gyre‐scale ocean circulation, and downward Ekman pumping. Its motion correlated with SSS changes throughout the South Indian Ocean and may be an indicator of changes in the basin's subtropical circulation.
Causes and Characteristics of Electrical Resistivity Variability in Shallow (<4 m) Soils in Taylor Valley, East Antarctica
Authors: Gutterman W. S. , Doran P. T. , Virginia R. A. , Barrett J. E. , Myers K. F. , Tulaczyk S. M. , Foley N. T. , Mikucki J. A. , Dugan H. A. , Grombacher D. J. , Bording T. S. , Auken E. 
Published: February 2023

AbstractAirborne electromagnetic surveys collected in December 2011 and November 2018 and three soil sampling transects were used to analyze the spatial heterogeneity of shallow (<4 m) soil properties in lower Taylor Valley (TV), East Antarctica. Soil resistivities from 2011 to 2018 ranged from ∼33 Ωm to ∼3,500 Ωm with 200 Ωm assigned as an upper boundary for brine‐saturated sediments. Elevations below ∼50 m above sea level (masl) typically exhibit the lowest resistivities with resistivity increasing at high elevations on steeper slopes. Soil water content was empirically estimated from electrical resistivities using Archie's Law and range from ∼<1% to ∼68% by volume. An increase in silt‐ and clay‐sized particles at low elevations increases soil porosity but decreases hydraulic conductivity, promoting greater residence times of soil water at low elevations near Lake Fryxell. Soil resistivity variability between 2011 and 2018 shows soils at different stages of soil freeze‐thaw cycles, which are caused predominantly by solar warming of soils as opposed to air temperature. This study furthers the understanding of the hydrogeologic structure of the shallow subsurface in TV and identifies locations of soils that are potentially prone to greater rates of thaw and resulting ecosystem homogenization of soil properties from projected increases in hydrological connectivity across the region over the coming decades.
Can Hydrological Models Benefit From Using Global Soil Moisture, Evapotranspiration, and Runoff Products as Calibration Targets?
Authors: Mei Yiwen , Mai Juliane , Do Hong Xuan , Gronewold Andrew , Reeves Howard , Eberts Sandra , Niswonger Richard , Regan R. Steven , Hunt Randall J. 
Published: February 2023

AbstractHydrological models are usually calibrated to in‐situ streamflow observations with reasonably long and uninterrupted records. This is challenging for poorly gage or ungaged basins where such information is not available. Even for gaged basins, the single‐objective calibration to gaged streamflow cannot guarantee reliable forecasts because, as has been documented elsewhere, the inverse problem is mathematically ill‐posed. Therefore, the inclusion of other observations, and the reproduction of other hydrological variables beyond streamflow, become critical components of accurate hydrological forecasting. In this study, six single‐ and multi‐objective model calibration schemes based on different combinations of gaged streamflow, global‐scale gridded soil moisture, actual evapotranspiration (ET), and runoff products are used for the calibration of a process‐based hydrological model for 20 catchments located within the Lake Michigan watershed, of the Laurentian Great Lakes. Results show that the addition of gridded soil moisture to gaged streamflow in model calibration improves the ET simulation performance for most of the catchments, leading to the overall best‐performing models. The monthly streamflow simulation performance for the experiments using gridded runoff products to inform the model is outperformed by those using the gaged streamflow, but the discrepancy is mitigated with increasing catchment scale. A new visualization method that effectively synthesizes model performance for the simulations of streamflow, soil moisture, and ET was also proposed. Based on the method, it is revealed that the streamflow simulation performance is relatively weak for baseflow‐dominated catchments; overall, the 20 catchment models simulate streamflow and ET better than soil moisture.
Targeted dual base editing with Campylobacter jejuni Cas9 by single AAV-mediated delivery
Authors: Kweon Jiyeon , Jang An-Hee , Kwon Eunji , Kim Ungi , Shin Ha Rim , See Jieun , Jang Gayoung , Lee Chaeyeon , Koo Taeyoung , Kim Seokjoong , Kim Yongsub 
Published: February 2023

AbstractVarious CRISPR‒Cas9 orthologs are used in genome engineering. One of the smallest Cas9 orthologs is cjCas9 derived from Campylobacter jejuni, which is a highly specific genome editing tool. Here, we developed cjCas9-based base editors including a cytosine base editor (cjCBEmax) and an adenine base editor (cjABE8e) that can successfully induce endogenous base substitutions by up to 91.2% at the HPD gene in HEK293T cells. Analysis of the base editing efficiency of 13 endogenous target sites showed that the active windows of cjCBEmax and cjABE8e are wider than those of spCas9-based base editors and that their specificities are slightly lower than that of cjCas9. Importantly, engineered cjCas9 and gRNA scaffolds can improve the base editing efficiency of cjABE8e by up to 6.4-fold at the HIF1A gene in HEK293T cells. Due to its small size, cjABE8e can be packaged in a single adeno-associated virus vector with two tandem arrays of gRNAs, and the delivery of the resulting AAV could introduce base substitutions at endogenous ANGPT2 and HPD target sites. Overall, our findings have expanded the potential of the use of base editors for in vivo or ex vivo therapeutic approaches.
Near-zero-dispersion soliton and broadband modulational instability Kerr microcombs in anomalous dispersion
Authors: Xiao Zeyu , Li Tieying , Cai Minglu , Zhang Hongyi , Huang Yi , Li Chao , Yao Baicheng , Wu Kan , Chen Jianping 
Published: February 2023

AbstractThe developing advances of microresonator-based Kerr cavity solitons have enabled versatile applications ranging from communication, signal processing to high-precision measurements. Resonator dispersion is the key factor determining the Kerr comb dynamics. Near the zero group-velocity-dispersion (GVD) regime, low-noise and broadband microcomb sources are achievable, which is crucial to the application of the Kerr soliton. When the GVD is almost vanished, higher-order dispersion can significantly affect the Kerr comb dynamics. Although many studies have investigated the Kerr comb dynamics near the zero-dispersion regime in microresonator or fiber ring system, limited by dispersion profiles and dispersion perturbations, the near-zero-dispersion soliton structure pumped in the anomalous dispersion side is still elusive so far. Here, we theoretically and experimentally investigate the microcomb dynamics in fiber-based Fabry-Perot microresonator with ultra-small anomalous GVD. We obtain 2/3-octave-spaning microcombs with ~10 GHz spacing, >84 THz span, and >8400 comb lines in the modulational instability (MI) state, without any external nonlinear spectral broadening. Such widely-spanned MI combs are also able to enter the soliton state. Moreover, we report the first observation of anomalous-dispersion based near-zero-dispersion solitons, which exhibits a local repetition rate up to 8.6 THz, an individual pulse duration <100 fs, a span >32 THz and >3200 comb lines. These two distinct comb states have their own advantages. The broadband MI combs possess high conversion efficiency and wide existing range, while the near-zero-dispersion soliton exhibits relatively low phase noise and ultra-high local repetition rate. This work complements the dynamics of Kerr cavity soliton near the zero-dispersion regime, and may stimulate cross-disciplinary inspirations ranging from dispersion-controlled microresonators to broadband coherent comb devices.
Proteome analysis of monocytes implicates altered mitochondrial biology in adults reporting adverse childhood experiences
Authors: Zang Johannes C. S. , May Caroline , Hellwig Birte , Moser Dirk , Hengstler Jan G. , Cole Steve , Heinrichs Markus , Rahnenführer Jörg , Marcus Katrin , Kumsta Robert 
Published: February 2023

AbstractThe experience of adversity in childhood has been associated with poor health outcomes in adulthood. In search of the biological mechanisms underlying these effects, research so far focused on alterations of DNA methylation or shifts in transcriptomic profiles. The level of protein, however, has been largely neglected. We utilized mass spectrometry to investigate the proteome of CD14+ monocytes in healthy adults reporting childhood adversity and a control group before and after psychosocial stress exposure. Particular proteins involved in (i) immune processes, such as neutrophil-related proteins, (ii) protein metabolism, or (iii) proteins related to mitochondrial biology, such as those involved in energy production processes, were upregulated in participants reporting exposure to adversity in childhood. This functional triad was further corroborated by protein interaction- and co-expression analyses, was independent of stress exposure, i.e. observed at both pre- and post-stress time points, and became evident especially in females. In line with the mitochondrial allostatic load model, our findings provide evidence for the long-term effects of childhood adversity on mitochondrial biology.
Persistent short nighttime sleep duration is associated with a greater post-COVID risk in fully mRNA-vaccinated individuals
Authors: Xue Pei , Merikanto Ilona , Chung Frances , Morin Charles M. , Espie Colin , Bjorvatn Bjørn , Cedernaes Jonathan , Landtblom Anne-Marie , Penzel Thomas , De Gennaro Luigi , Holzinger Brigitte , Matsui Kentaro , Hrubos-Strøm Harald , Korman Maria , Leger Damien , Mota-Rolim Sérgio , Bolstad Courtney J. , Nadorff Michael , Plazzi Giuseppe , Reis Catia , Chan Rachel Ngan Yin , Wing Yun Kwok , Yordanova Juliana , Bjelajac Adrijana Koscec , Inoue Yuichi , Partinen Markku , Dauvilliers Yves , Benedict Christian 
Published: February 2023

AbstractShort nighttime sleep duration impairs the immune response to virus vaccination, and long nighttime sleep duration is associated with poor health status. Thus, we hypothesized that short (<6 h) and long (>9 h) nighttime sleepers have a higher post-COVID risk than normal nighttime sleepers, despite two doses of mRNA vaccine (which has previously been linked to lower odds of long-lasting COVID-19 symptoms). Post-COVID was defined as experiencing at least one core COVID-19 symptom for at least three months (e.g., shortness of breath). Multivariate logistic regression adjusting for age, sex, BMI, and other factors showed in 9717 respondents (age span 18–99) that two mRNA vaccinations lowered the risk of suffering from post-COVID by about 21% (p < 0.001). When restricting the analysis to double-vaccinated respondents (n = 5918), short and long sleepers exhibited a greater post-COVID risk than normal sleepers (adjusted OR [95%-CI], 1.56 [1.29, 1.88] and 1.87 [1.32, 2.66], respectively). Among respondents with persistent sleep duration patterns during the pandemic compared to before the pandemic, short but not long sleep duration was significantly associated with the post-COVID risk (adjusted OR [95%-CI], 1.59 [1.24, 2.03] and 1.18 [0.70, 1.97], respectively). No significant association between sleep duration and post-COVID symptoms was observed in those reporting positive SARS-CoV-2 test results (n = 538). Our findings suggest that two mRNA vaccinations against SARS-CoV-2 are associated with a lower post-COVID risk. However, this protection may be less pronounced among those sleeping less than 6 h per night. Our findings warrant replication in cohorts with individuals with confirmed SARS-CoV-2 infection.
A split ribozyme that links detection of a native RNA to orthogonal protein outputs
Authors: Gambill Lauren , Staubus August , Mo Kim Wai , Ameruoso Andrea , Chappell James 
Published: February 2023

AbstractIndividual RNA remains a challenging signal to synthetically transduce into different types of cellular information. Here, we describe Ribozyme-ENabled Detection of RNA (RENDR), a plug-and-play strategy that uses cellular transcripts to template the assembly of split ribozymes, triggering splicing reactions that generate orthogonal protein outputs. To identify split ribozymes that require templating for splicing, we use laboratory evolution to evaluate the activities of different split variants of the Tetrahymena thermophila ribozyme. The best design delivers a 93-fold dynamic range of splicing with RENDR controlling fluorescent protein production in response to an RNA input. We further resolve a thermodynamic model to guide RENDR design, show how input signals can be transduced into diverse outputs, demonstrate portability across different bacteria, and use RENDR to detect antibiotic-resistant bacteria. This work shows how transcriptional signals can be monitored in situ and converted into different types of biochemical information using RNA synthetic biology.
Germline T cell receptor exchange results in physiological T cell development and function
Authors: Rollins Meagan R. , Raynor Jackson F. , Miller Ebony A. , Butler Jonah Z. , Spartz Ellen J. , Lahr Walker S. , You Yun , Burrack Adam L. , Moriarity Branden S. , Webber Beau R. , Stromnes Ingunn M. 
Published: February 2023

AbstractT cell receptor (TCR) transgenic mice represent an invaluable tool to study antigen-specific immune responses. In the pre-existing models, a monoclonal TCR is driven by a non-physiologic promoter and randomly integrated into the genome. Here, we create a highly efficient methodology to develop T cell receptor exchange (TRex) mice, in which TCRs, specific to the self/tumor antigen mesothelin (Msln), are integrated into the Trac locus, with concomitant Msln disruption to circumvent T cell tolerance. We show that high affinity TRex thymocytes undergo all sequential stages of maturation, express the exogenous TCR at DN4, require MHC class I for positive selection and undergo negative selection only when both Msln alleles are present. By comparison of TCRs with the same specificity but varying affinity, we show that Trac targeting improves functional sensitivity of a lower affinity TCR and confers resistance to T cell functional loss. By generating P14 TRex mice with the same specificity as the widely used LCMV-P14 TCR transgenic mouse, we demonstrate increased avidity of Trac-targeted TCRs over transgenic TCRs, while preserving physiologic T cell development. Together, our results support that the TRex methodology is an advanced tool to study physiological antigen-specific T cell behavior.
A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea
Authors: Daugeron Marie-Claire , Missoury Sophia , Da Cunha Violette , Lazar Noureddine , Collinet Bruno , van Tilbeurgh Herman , Basta Tamara 
Published: February 2023

AbstractIn Archaea and Eukaryotes, the synthesis of a universal tRNA modification, N6-threonyl-carbamoyl adenosine (t6A), is catalyzed by the KEOPS complex composed of Kae1, Bud32, Cgi121, and Pcc1. A fifth subunit, Gon7, is found only in Fungi and Metazoa. Here, we identify and characterize a fifth KEOPS subunit in Archaea. This protein, dubbed Pcc2, is a paralog of Pcc1 and is widely conserved in Archaea. Pcc1 and Pcc2 form a heterodimer in solution, and show modest sequence conservation but very high structural similarity. The five-subunit archaeal KEOPS does not form dimers but retains robust tRNA binding and t6A synthetic activity. Pcc2 can substitute for Pcc1 but the resulting KEOPS complex is inactive, suggesting a distinct function for the two paralogs. Comparative sequence and structure analyses point to a possible evolutionary link between archaeal Pcc2 and eukaryotic Gon7. Our work indicates that Pcc2 regulates the oligomeric state of the KEOPS complex, a feature that seems to be conserved from Archaea to Eukaryotes.
Phosphorescent extensophores expose elastic nonuniformity in polymer networks
Authors: Zheng Kaikai , Zhang Yifan , Li Bo , Granick Steve 
Published: February 2023

AbstractNetworks and gels are soft elastic solids of tremendous technological importance that consist of cross-linked polymers whose structure and connectivity at the molecular level are fundamentally nonuniform. Pre-failure local mechanical responses are not understood at the level of individual crosslinks, despite the enormous attention given to their macroscopic mechanical responses and to developing optical probes to detect their loci of mechanical failure. Here, introducing the extensophore concept to measure nondestructive forces using an optical probe with continuous force readout proportional to deformation, we show that the crosslinks in an elastic polymer network extend, fluctuate, and deform with a wide range of molecular individuality. Requiring little specialized equipment, this foundational single-molecule phosphorescence approach, applied here to polymer science and engineering, can be useful to a broad science and engineering community.
Distinct relaxation mechanism at room temperature in metallic glass
Authors: Sun Yi-Tao , Zhao Rui , Ding Da-Wei , Liu Yan-Hui , Bai Hai-Yang , Li Mao-Zhi , Wang Wei-Hua 
Published: February 2023

AbstractHow glasses relax at room temperature is still a great challenge for both experimental and simulation studies due to the extremely long relaxation time-scale. Here, by employing a modified molecular dynamics simulation technique, we extend the quantitative measurement of relaxation process of metallic glasses to room temperature. Both energy relaxation and dynamics, at low temperatures, follow a stretched exponential decay with a characteristic stretching exponent β = 3/7, which is distinct from that of supercooled liquid. Such aging dynamics originates from the release of energy, an intrinsic nature of out-of-equilibrium system, and manifests itself as the elimination of defects through localized atomic strains. This finding is also supported by long-time stress-relaxation experiments of various metallic glasses, confirming its validity and universality. Here, we show that the distinct relaxation mechanism can be regarded as a direct indicator of glass transition from a dynamic perspective.
Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis
Authors: Kaltdorf Martin , Breitenbach Tim , Karl Stefan , Fuchs Maximilian , Kessie David Komla , Psota Eric , Prelog Martina , Sarukhanyan Edita , Ebert Regina , Jakob Franz , Dandekar Gudrun , Naseem Muhammad , Liang Chunguang , Dandekar Thomas 
Published: February 2023

AbstractThe signal modelling framework JimenaE simulates dynamically Boolean networks. In contrast to SQUAD, there is systematic and not just heuristic calculation of all system states. These specific features are not present in CellNetAnalyzer and BoolNet. JimenaE is an expert extension of Jimena, with new optimized code, network conversion into different formats, rapid convergence both for system state calculation as well as for all three network centralities. It allows higher accuracy in determining network states and allows to dissect networks and identification of network control type and amount for each protein with high accuracy. Biological examples demonstrate this: (i) High plasticity of mesenchymal stromal cells for differentiation into chondrocytes, osteoblasts and adipocytes and differentiation-specific network control focusses on wnt-, TGF-beta and PPAR-gamma signaling. JimenaE allows to study individual proteins, removal or adding interactions (or autocrine loops) and accurately quantifies effects as well as number of system states. (ii) Dynamical modelling of cell–cell interactions of plant Arapidopsis thaliana against Pseudomonas syringae DC3000: We analyze for the first time the pathogen perspective and its interaction with the host. We next provide a detailed analysis on how plant hormonal regulation stimulates specific proteins and who and which protein has which type and amount of network control including a detailed heatmap of the A.thaliana response distinguishing between two states of the immune response. (iii) In an immune response network of dendritic cells confronted with Aspergillus fumigatus, JimenaE calculates now accurately the specific values for centralities and protein-specific network control including chemokine and pattern recognition receptors.
Poorer sleep impairs brain health at midlife
Authors: Namsrai Tergel , Ambikairajah Ananthan , Cherbuin Nicolas 
Published: February 2023

AbstractSleep is an emerging risk factor for dementia but its association with brain health remains unclear. This study included UK Biobank (n = 29,545; mean age = 54.65) participants at imaging visit with sleep measures and brain scans, and a subset (n = 14,206) with cognitive measures. Multiple linear regression analyses were conducted to study the associations between sleep and brain health. Every additional hour of sleep above 7 h/day was associated with 0.10–0.25% lower brain volumes. In contrast, a negative non-linear association was observed between sleep duration, grey matter, and hippocampal volume. Both longer (> 9 h/day) and shorter sleep (< 6 h/day) durations were associated with lower brain volumes and cognitive measures (memory, reaction time, fluid intelligence). Additionally, daytime dozing was associated with lower brain volumes (grey matter and left hippocampus volume) and lower cognitive measures (reaction time and fluid intelligence). Poor sleep (< 6 h/day, > 9 h/day, daytime dozing) at midlife was associated with lower brain health. Sleep may be an important target to improve brain health into old age and delay the onset of dementia.