bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneous mantle effects on the behaviour of SmKS waves and outermost core imaging
Authors: Frost Daniel A , Garnero Edward J , Creasy Neala , Wolf Jonathan , Bozdağ Ebru , Long Maureen D , Aderoju Adeolu , Vite Reynaldo 
Published: April 2024

SUMMARYSeismic traveltime anomalies of waves that traverse the uppermost 100–200 km of the outer core have been interpreted as evidence of reduced seismic velocities (relative to radial reference models) just below the core–mantle boundary (CMB). These studies typically investigate differential traveltimes of SmKS waves, which propagate as P waves through the shallowest outer core and reflect from the underside of the CMB m times. The use of SmKS and S(m-1)KS differential traveltimes for core imaging are often assumed to suppress contributions from earthquake location errors and unknown and unmodelled seismic velocity heterogeneity in the mantle. The goal of this study is to understand the extent to which differential SmKS traveltimes are, in fact, affected by anomalous mantle structure, potentially including both velocity heterogeneity and anisotropy. Velocity variations affect not only a wave's traveltime, but also the path of a wave, which can be observed in deviations of the wave's incoming direction. Since radial velocity variations in the outer core will only minimally affect the wave path, in contrast to other potential effects, measuring the incoming direction of SmKS waves provides an additional diagnostic as to the origin of traveltime anomalies. Here we use arrays of seismometers to measure traveltime and direction anomalies of SmKS waves that sample the uppermost outer core. We form subarrays of EarthScope's regional Transportable Array stations, thus measuring local variations in traveltime and direction. We observe systematic lateral variations in both traveltime and incoming wave direction, which cannot be explained by changes to the radial seismic velocity profile of the outer core. Moreover, we find a correlation between incoming wave direction and traveltime anomaly, suggesting that observed traveltime anomalies may be caused, at least in part, by changes to the wave path and not solely by perturbations in outer core velocity. Modelling of 1-D ray and 3-D wave propagation in global 3-D tomographic models of mantle velocity anomalies match the trend of the observed traveltime anomalies. Overall, we demonstrate that observed SmKS traveltime anomalies may have a significant contribution from 3-D mantle structure, and not solely from outer core structure.
Underluminous 1991bg-like Type Ia supernovae are standardizable candles
Authors: Graur O 
Published: April 2024

ABSTRACT
It is widely accepted that the width–luminosity relation used to standardize normal Type Ia supernovae (SNe Ia) breaks down in underluminous, 1991bg-like SNe Ia. This breakdown may be due to the choice of parameter used as a stand-in for the width of the SN Ia light curve. Using the colour stretch parameter sBV instead of older parameters resolves this issue. Here, I assemble a sample of 14 nearby 1991bg-like SNe Ia from the literature, all of which have independent host-galaxy distance moduli and little to no reddening. I use Gaussian process regression to fit the light curves of these SNe in U/u, B, V, g, R/r, I/i, and H, and measure their peak absolute magnitudes. I find statistically significant (&gt;5σ confidence level in the optical and &gt;4σ in the near-infrared) correlations between the peak absolute magnitudes of the 1991bg-like SNe Ia and their sBV values in the range 0.2 &lt; sBV &lt; 0.6. These correlations are broadly consistent with fits to sBV &lt; 0.7 SNe Ia with preliminary B- and V-band peak absolute magnitudes from the Carnegie Supernova Project and significantly inconsistent with similar fits to normal and transitional SNe Ia (with 0.7 &lt; sBV &lt; 1.1). The underluminous width–luminosity relation shown here needs to be properly calibrated with a homogeneous sample of 1991bg-like SNe Ia, after which it could be used as a rung on a new cosmological distance ladder. With surface-brightness fluctuations (or another non-Cepheid method) used to calibrate distances to nearby 1991bg-like SNe Ia, such a ladder could produce an independent measurement of the Hubble–Lemaître constant, H0.
A Novel Four‑Gene Biomarker for Tobacco Smoking-Induced Colorectal Cancer Progression
Authors: Jiang Min , Zhang Xinghai , Huang Haoyu , Sun Guixiang , Huang Yefei , Chen Yansu 
Published: April 2024

Abstract

Introduction
Cigarette smoking greatly promotes the progression and poor prognosis of colorectal cancer (CRC) patients, with the molecular mechanism still not fully clear.

Methods
In this study, CRC cells were exposed to tobacco-specific nitrosamine 4‑(methylnitrosamino)‑1‑(3‑pyridyl)-1‑butanone (NNK), and the differentially expressed smoking-related genes were identified based on both NNK-induced CRC cells and a total of 763 CRC tissues from The Cancer Genome Atlas cohort. Cox regression analysis, receiver operating characteristic curve and Kaplan–Meier plot were used to establish the risk score model for CRC prognosis. Moreover, quantitative real-time–PCR, western blotting, colony formation, migration, and invasion assays were performed to verify the core differentially expressed smoking-related gene and its molecular function in NNK-induced CRC progression.

Results
Results indicated NNK significantly enhanced CRC cell proliferation, migration and invasion. Moreover, a four-gene signature containing AKR1B10, CALB2, PLAC1, and GNA15 was established as a CRC prognosis marker. Among these four genes, AKR1B10 was further validated as the core gene, and its expression was significantly inhibited after NNK exposure in CRC cells. Results of gene enrichment analysis and western blotting suggested AKR1B10 might reduce the malignant progression of NNK-induced CRC cells by inhibiting the Wnt signaling pathway by promoting E-Cadherin expression and inhibiting the expression of N-Cadherin, β-Catenin, Vimentin, and Snail.

Conclusions
In conclusion, new four smoking-related genes can be jointly used as prognostic markers for CRC. AKR1B10 served as a tumor suppressor, and can be used as a potential target to inhibit NNK-induced CRC malignant progression by regulating the Wnt signaling pathway.

Implications
This study demonstrates that tobacco-derived NNK dependence would promote the malignant progression of colorectal cancer by regulating the expressions of the AKR1B10/Wnt signaling pathway. A novel four-gene signature is established for the prognosis prediction of smoking CRC patients. These findings have important translational implications given the continued use of tobacco and the difficulty in smoking cessation worldwide, which can be applied to alleviate the adverse effects induced by tobacco dependence on colorectal cancer patients.
Chemical composition and digestible and metabolizable energy contents in cold-pressed canola expellers fed to growing pigs
Authors: Omotosho Oluwakemi Y , Slominski Bogdan A , Niu Yanxing , Nyachoti Charles M , Rogiewicz Anna 
Published: April 2024

Abstract
Cold-pressed canola expellers (CPCE) are a byproduct of canola oil production obtained using the pressing method without thermal and chemical treatment. While CPCE is a valuable source of dietary energy and protein in swine nutrition, the discrepancy in processing conditions leads to variability in the nutritional quality of CPCE from different sources. This study aimed to determine the chemical composition, and digestible energy (DE) and metabolizable energy (ME) values of CPCE when fed to growing pigs. Samples of CPCE were collected from five processing facilities across Western Canada. The physical appearance of the CPCE samples hinted at a potential quality variation. Samples were subjected to a complete chemical characterization. Variations (P &lt; 0.05) were observed in the chemical composition, with the exception of non-phytate phosphorus, xylose, mannose, and galactose. On a g/kg dry matter (DM) basis, CPCE samples ranged as follows: ether extract from 85 to 177; crude protein (CP) from 351 to 419; neutral detergent fiber 231 to 300; total dietary fiber from 326 to 373; glycoproteins from 30 to 76; non-starch polysaccharides from 188 to 204, non-phytate phosphorus from 5.5 to 6.4, and gross energy (GE) in kcal/kg 5,027 to 5,635. The total glucosinolates (GLS) ranged from 5.0 to 9.7 µmol/g DM. Thirty-six (36) growing barrows, with an average initial body weight of 19.2 ± 1.0 kg, were individually housed in metabolism crates and assigned to one of the six experimental diets in a completely randomized design, with six pigs per diet. The diets included a corn–soybean meal (SBM)-based basal diet (100%) and five (5) experimental diets in which 18% of the basal diet was substituted with CPCE from different producers. Pigs were fed the experimental diets for 10 d, with 5-d adaptation period, followed by a 5-d period for the total, but separate, collection of feces and urine. Significant differences (P &lt; 0.05) among processing plants were observed in the DE and ME contents of CPCE, which averaged 3,531 and 3,172 kcal/kg DM, respectively. Differences (P &lt; 0.05) were noted in the apparent total tract digestibility of GE, nitrogen (N), as well as in the retention of DM, GE, and N in CPCE samples. In conclusion, while the chemical composition and values of DE and ME in CPCE vary among processors, the byproduct obtained through cold pressing process can be a valuable source of energy and protein for pig nutrition.
DIFFERENTIAL SIGNALING EFFECTS OF ESCHERICHIA COLI AND STAPHYLOCOCCUS AUREUS IN HUMAN WHOLE BLOOD INDICATE DISTINCT REGULATION OF THE NRF2 PATHWAY
Authors: Pourquoi Allison , Miller Michael R. , Koch Stephen R. , Boyle Katharine , Surratt Victoria , Nguyen Hong , Panja Sourav , Cartailler Jean-Philippe , Shrestha Shristi , Stark Ryan J. 
Published: April 2024

ABSTRACTEscherichia coliandStaphylococcus aureusare two of the most common bacterial species responsible for sepsis. While it is observed that they have disparate clinical phenotypes, the signaling differences elicited by each bacteria that drive this variance remain unclear. Therefore, we used human whole blood exposed to heat-killedE. coliorS. aureusand measured the transcriptomic signatures. Relative to unstimulated control blood, heat-killed bacteria exposure led to significant dysregulation (upregulated and downregulated) of >5,000 genes for each experimental condition, with a slight increase in gene alterations byS. aureus. While there was significant overlap regarding proinflammatory pathways, Gene Ontology overrepresentation analysis of the most altered genes suggested biological processes like macrophage differentiation and ubiquinone biosynthesis were more unique to heat-killedS. aureus, compared with heat-killedE. coliexposure. Using Ingenuity Pathway Analysis, it was demonstrated that nuclear factor erythroid 2-related factor 2 signaling, a main transcription factor in antioxidant responses, was predominately upregulated inS. aureusexposed blood relative toE. coli. Furthermore, the use of pharmacologics that preferentially targeted the nuclear factor erythroid 2-related factor 2 pathway led to differential cytokine profiles depending on the type of bacterial exposure. These findings reveal significant inflammatory dysregulation betweenE. coliandS. aureusand provide insight into the targeting of unique pathways to curb bacteria-specific responses.
Postoperative Complications in Living Donors for Lung Transplantation
Authors: Tanaka Shin , Fujii Kento , Ishihara Megumi , Choshi Haruki , Matsubara Kei , Hashimoto Kohei , Okahara Shuji , Shien Kazuhiko , Suzawa Ken , Miyoshi Kentaroh , Yamamoto Hiromasa , Okazaki Mikio , Sugimoto Seiichiro , Toyooka Shinichi 
Published: April 2024

Background.
Living donor lobar lung transplantation is a life-saving procedure for critically ill patients. This requires 2 healthy donors exposed to risks and without medical benefit. Therefore, the donor’s safety and minimal postoperative complications are crucial. This study aimed to investigate the short-term outcomes and identify the risk factors affecting these outcomes.

Methods.
The data of 175 living donors enrolled between 1998 and 2022 were analyzed. Donors were divided into era 1 (1998–2009) and era 2 (2010–2022).

Results.
The overall incidence of postoperative complications was 39%, of which 7% were major complications. Donors who underwent surgery on the right side had a higher incidence of delayed pulmonary fistulae (P = 0.01) and elevated liver enzyme levels (P = 0.028). Living donor surgery on the right side (P = 0.01), era 2 (P = 0.01), and the need for plasty (P = 0.04) were predictors of postoperative complications.

Conclusions.
Updated data on complications and their correlation with postoperative quality of life from this study could aid in the selection of potential donors and facilitate informed consent.
Population genomics reveals demographic history and climate adaptation in JapaneseArabidopsis halleri
Authors: Suda Ryo A , Kubota Shosei , Kumar Vinod , Castric Vincent , Krämer Ute , Morinaga Shin-Ichi , Tsuchimatsu Takashi 
Published: April 2024

AbstractClimate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history, and signatures of climate-driven selection based on genome-wide polymorphism data of 141 JapaneseArabidopsis halleriindividuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (∼50 kya). The ecological niche modeling predicted the range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans, and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.
Regional Variations in Live Proportions of Southwest Pacific Cold-Water CoralSolenosmilia variabilisReefs
Authors: Barnhill Kelsey Archer , Chin Caroline , Tracey Di , Clark Malcolm , De Clippele Laurence H. , Henley Sian F. , Wolfram Uwe , Hennige Sebastian 
Published: April 2024

AbstractReef-building cold-water-corals (CWC) form deep-sea habitats that can create biodiversity hotspots. As live coral and dead intact framework provide disparate ecosystem services and are vulnerable to different anthropogenic stressors, it is important to quantify the proportions of each on CWC reefs. We analysed 1,160 images ofSolenosmilia variabilisreefs at four sites off New Zealand (Valerie and Forde Guyots at the Louisville Seamount Chain & Ghoul and Gothic Seamounts at the Graveyard Seamount Complex) to determine the ratio of live coral to the whole reef area (termed live:reef). We found live:reef ratios are significantly different between sites at the offshore Louisville Seamount Chain and onshore Graveyard Seamount Complex. This could be driven by reef position relative to the aragonite saturation horizon (ASH) as corals in the Louisville Seamount Chain live below the ASH in colder and deeper waters than those at the Graveyard Seamount Complex, which live above the ASH. In the southwest Pacific, depth is a driver of live:reef ratios, with a larger proportion of live coral at shallow depths and dead intact framework at deeper depths. The live:reef ratios at Gothic Seamount within the Graveyard Seamount Complex remained stable between 2015 and 2020 despite significant differences in live coral, dead intact framework, and reef structure surface area. Our results indicate live:reef ratios can be used to estimate the amount of dead intact framework threatened by shoaling ASH due to ocean acidification at each site, which can help inform which sites could be protected as possible climate change refugia.
Comparative transcriptome reprogramming in oak galls containing asexual or sexual generations of gall wasps
Authors: Bellows Eleanor , Heatley Matthew , Shah Nirja , Archer Nathan , Giles Tom , Fray Rupert 
Published: April 2024

AbstractOak gall wasps have evolved strategies to manipulate the developmental pathways of their host to induce gall formation. This provides shelter and nutrients for the developing larva. Galls are entirely host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. The underlying molecular mechanisms of gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path, are poorly understood. In this study, we sought a deeper insight into the molecular underpinnings of this process.Oak gall wasps have two generations each year, one sexual, and one asexual. Galls formed by these two generations exhibit a markedly different appearance. We sequenced transcriptomes of both the asexual and sexual generations ofNeuroterus quercusbaccarumandNeuroterus numismalis. We then deployed Nanopore sequencing to generate long-read sequences to test the hypothesis that gall wasps introduce DNA insertions to determine gall development.We detected potential genome rearrangements, but did not uncover any non-host DNA insertions. Transcriptome analysis revealed that the transcriptomes of the sexual generations of distinct species of wasp are more similar than inter-generational comparisons from the same species of wasp.Our results highlight the intricate interplay between the host leaves and gall development, suggesting that season and requirements of the gall structure play a larger role than species in controlling gall development and structure.Summary StatementOak gall wasps,Neuroterus quercusbaccarumandNeuroterus numismalis, induce species-specific galls onQuercus roburleaves. We demonstrate that the sexual generation of distinct species of wasps induce more similar changes in the host than different generation galls from the same species.
Isolation of proteins on chromatin (iPOC) reveals signaling pathway-dependent alterations in the DNA-bound proteome
Authors: Wang Huiyu , Krijgsveld Jeroen , Sigismondo Gianluca 
Published: April 2024

AbstractSignaling pathways often convergence on transcription factors (TFs) and other DNA-binding proteins (DBPs) that regulate chromatin structure and gene expression, thereby governing a broad range of essential cellular functions. However, the repertoire of DBPs is incompletely understood even for the best-characterized pathways. Here, we optimized a strategy for the isolation of Proteins on Chromatin (iPOC) exploiting tagged nucleoside analogues to label the DNA and capture associated proteins, thus enabling the comprehensive, sensitive, and unbiased characterization of the DNA-bound proteome. We then applied iPOC to investigate chromatome changes upon perturbation of the cancer-relevant PI3K/AKT/mTOR pathway. Our results show distinct dynamics of the DNA-bound proteome upon selective inhibition of PI3K, AKT, or mTOR, and we provide evidence how this signaling cascade regulates the DNA-bound status of SUZ12, thereby modulating H3K27me3 levels. Collectively, iPOC is a powerful approach to study the composition of the DNA-bound proteome operating downstream of signaling cascades, thereby both expanding our knowledge of the mechanism of action of the pathway, and unveiling novel chromatin modulators that can potentially be targeted pharmacologically.
Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern
Authors: Jiang Wei , Deng Fenglin , Babla Mohammad , Chen Chen , Yang Dongmei , Tong Tao , Qin Yuan , Chen Guang , Marchant D. Blaine , Soltis Pamela S. , Soltis Douglas E. , Zeng Fanrong , Chen Zhong-Hua 
Published: April 2024

AbstractThe clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-related nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species due to the complex characteristics of fern genomes, genetics and physiology. Here, we established, for the first time, a protocol for gametophyte-based screening single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas-mediated gene editing in a model fern species,Ceratopteris richardii. We utilized theC. richardii Actinpromoter to drive sgRNA expression and enhanced CaMV 35S promoter to drive the expression ofStreptococcus pyogenesCas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes (e.g.,nucleotidase/phosphatase 1, CrSAL1;Cryptochrome 4, CRY4) andCrPDS, encoding a phytoene desaturase protein that resulted in an albino phenotype inC. richardii. Knockout ofCrSAL1resulted in significantly reduced stomatal conductance (gs), leaf transpiration rate (E), stomatal/pore length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover,CrSAL1overexpressing plants showed significantly increased net photosynthetic rate (A),gs, Eand intrinsic water use efficiency (iWUE) as well as most of the stomatal traits and ROS production in guard cells compared to those in the wild-type (WT) plants. Taken together, the optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery and agricultural applications.
Investigation of the mass spectra of singly heavy baryons
ΣQ
,
ΞQ′
, and
ΩQ(Q=c,b)
in the Regge trajectory model
Authors: Pan Ji-Hai , Pan Jisi 
Published: April 2024

Very recently, LHCb Collaboration observed that two new Ωc0 states decay into Ξc+K− with masses of about 3185 MeV and 3327 MeV. However, their spin-parity quantum numbers JP have not been determined. In this paper, we exploit the quark-diquark model, the linear Regge trajectory and the perturbation treatment method to analyze the mass spectra of the discovered experimental data for the singly heavy baryons Σc/Σb, Ξc′/Ξb′, and Ωc/Ωb. In addition, we further predict the mass spectra of several unobserved Σc/Σb, Ξc′/Ξb′, and Ωc/Ωb baryons. In the case of the Ωc(3185)0 and Ωc(3327)0 states, we determine Ωc(3185)0 as 2S state and Ωc(3327)0 as 1D state with JP=1/2+ and JP=3/2+, respectively. An overall good agreement of the obtained predictions with available experimental data are found.

Published by the American Physical Society
2024