bluuebunny/crossref_metadata_2025_split huggingface dataset:
1-Methylcyclopropene retards pak choi (Brassica rapasubsp. chinensis) yellowing via BcNAC055-, BcMYB44-, and BcOBF1-mediated regulation of the key chlorophyll degrading geneBcNYC1during storage at 20 °C
Authors: Song Liuli , Wang Junping , Yu Haitao , Yu Zhifang 
Published: December 2022

AbstractThe objective of this study was to investigate the molecular regulatory mechanism of 1-methylcyclopropene (1-MCP) treatment on leaf yellowing of pak choi during storage at 20 °C. In the present study, compared with the control and 10 μL/L ethylene-treated pak choi, 5.0 μL/L 1-MCP fumigation alleviated the yellowing process of pak choi as proved by the maintenance of higher levels of colour, chlorophyll content, and appearance. 1-MCP treatment decreased chlorophyll breakdown by downregulating the activity of chlorophyll-degrading enzymes (chlorophyll b reductase (CBR) and pheophytinase (PPH)) and the expression of their related genes (BcNYC1 and BcPPH). The application of 1-MCP also inhibited the transcript abundance of ethylene biosynthesis and signal transduction genes (BcACO, BcEIN3, and BcERF) and reduced ethylene production, thus helping to maintain the green colour of pak choi; however, ethylene treatment exerted the opposite function. Meanwhile, three transcription factors (BcNAC055, BcMYB44, and BcOBF1) were successfully cloned. Experiments performed using yeast one-hybrid assay, dual-luciferase reporter system and in vivo bioluminescence imaging assay, confirmed that BcNAC055, BcMYB44, and BcOBF1 directly bound to the BcNYC1 promoter. 1-MCP inhibited the expression levels of BcNAC055, BcMYB44, BcOBF1, and BcNYC1 during storage, while the application of ethylene activated their expression. In conclusion, 1-MCP downregulated the expression of the key chlorophyll degradation gene BcNYC1 by inhibiting the transcript level of its three positive regulators (BcNAC055, BcMYB44, and BcOBF1) and lowered the activity of chlorophyll-degrading enzyme CBR, thereby helping mitigate chlorophyll breakdown to retard leaf yellowing in pak choi. The results of this work extend our understanding of 1-MCP-delayed yellowing in postharvest pak choi.
Comparing Transgenic Production to Supplementation of ω-3 PUFA Reveals Distinct But Overlapping Mechanisms Underlying Protection Against Metabolic and Hepatic Disorders
Authors: Daniel Noëmie , Le Barz Mélanie , Mitchell Patricia L , Varin Thibault V , Julien Isabelle Bourdeau , Farabos Dominique , Pilon Geneviève , Gauthier Josée , Garofalo Carole , Kang Jing X , Trottier Jocelyn , Barbier Olivier , Roy Denis , Chassaing Benoit , Levy Emile , Raymond Frédéric , Lamaziere Antonin , Flamand Nicolas , Silvestri Cristoforo , Jobin Christian , Di Marzo Vincenzo , Marette André 
Published: December 2022

Abstract
We compared endogenous ω-3 PUFA production to supplementation for improving obesity-related metabolic dysfunction. Fat-1 transgenic mice, who endogenously convert exogenous ω-6 to ω-3 PUFA, and wild-type littermates were fed a high-fat diet and a daily dose of either ω-3 or ω-6 PUFA-rich oil for 12 wk. The endogenous ω-3 PUFA production improved glucose intolerance and insulin resistance but not hepatic steatosis. Conversely, ω-3 PUFA supplementation fully prevented hepatic steatosis but failed to improve insulin resistance. Both models increased hepatic levels of ω-3 PUFA-containing 2-monoacylglycerol and N-acylethanolamine congeners, and reduced levels of ω-6 PUFA-derived endocannabinoids with ω-3 PUFA supplementation being more efficacious. Reduced hepatic lipid accumulation associated with the endocannabinoidome metabolites EPEA and DHEA, which was causally demonstrated by lower lipid accumulation in oleic acid-treated hepatic cells treated with these metabolites. While both models induced a significant fecal enrichment of the beneficial Allobaculum genus, mice supplemented with ω-3 PUFA displayed additional changes in the gut microbiota functions with a significant reduction of fecal levels of the proinflammatory molecules lipopolysaccharide and flagellin. Multiple-factor analysis identify that the metabolic improvements induced by ω-3 PUFAs were accompanied by a reduced production of the proinflammatory cytokine TNFα, and that ω-3 PUFA supplementation had a stronger effect on improving the hepatic fatty acid profile than endogenous ω-3 PUFA. While endogenous ω-3 PUFA production preferably improves glucose tolerance and insulin resistance, ω-3 PUFA intake appears to be required to elicit selective changes in hepatic endocannabinoidome signaling that are essential to alleviate high-fat diet-induced hepatic steatosis.
Spatial change in differential stress magnitudes around the source fault before intraplate earthquakes
Authors: Iio Yoshihisa , Matsumoto Satoshi , Yamashita Yusuke , Sakai Shin'ichi , Tomisaka Kazuhide , Sawada Masayo , Iidaka Takashi , Iwasaki Takaya , Kamizono Megumi , Katao Hiroshi , Kato Aitaro , Kurashimo Eiji , Teguri Yoshiko , Tsuda Hiroo , Ueno Takashi 
Published: December 2022

SUMMARYHow are the sizes of the earthquakes determined? To solve this important problem, we analysed the data from a dense temporary seismic observation network installed in the aftershock area of the 2016 Mw 6.2 Central Tottori earthquake, which occurred in an intraplate region in Japan. We compared the stress field estimated from approximately 10 000 accurate focal mechanisms of aftershocks with the calculated post-earthquake stress field and found that the differential stress before the earthquake was very small near both horizontal edges. These results did not depend significantly on the modeled slip distribution and the orientation of the principal stress before the earthquake. Similar results were obtained for the 2000 Mw 6.7 Western Tottori earthquake, which also occurred in the same intraplate region in Japan. These results suggest that the fault size of large intraplate earthquakes can be determined by the region of small differential stress surrounding future earthquake faults.
Seismic tremor location of 10 large paroxysmal eruptions of Tungurahua volcano, Ecuador
Authors: Palacios Pablo B , Mader Heidy M , Kendall J-Michael , Yepes Hugo A 
Published: December 2022

SUMMARYThe most recent eruptive period of Tungurahua volcano lasted 17 yr (1999–2016), generating strong eruptive phases with the release of large amounts of seismic and acoustic energies. We have selected 10 large eruptions and located their seismic sources. The location method involves applying a new method for correcting for site effects in the seismic records and identifying, in the frequency domain, the signals from the ground-coupled airwaves and pyroclastic flows. The locations are computed by minimizing the differences of the source energy rates in the [0.4, 2.5] Hz range. The results suggest that the first three eruptions have locations mainly concentrated at the [−1, 2] km depth range (asl), and the locations of the fourth eruption are mainly coincident with depths of a possible reservoir estimated from petrological studies. This fact strongly suggests that this eruption was responsible of changes in the dynamics of Tungurahua, making the volcano prone to produce Vulcanian eruptions.
Citrusβ-carotene hydroxylase 2 (BCH2) participates in xanthophyll synthesis by catalyzing the hydroxylation ofβ-carotene and compensates for BCH1 in citrus carotenoid metabolism
Authors: Zhang Yingzi , Jin Jiajing , Zhu Shenchao , Sun Quan , Zhang Yin , Xie Zongzhou , Ye Junli , Deng Xiuxin 
Published: December 2022

AbstractAs an essential horticultural crop, Citrus has carotenoid diversity, which affects its aesthetic and nutritional values. β,β-Xanthophylls are the primary carotenoids accumulated in citrus fruits, and non-heme di-iron carotene hydroxylase (BCH) enzymes are mainly responsible for β,β-xanthophyll synthesis. Previous studies have focused on the hydroxylation of BCH1, but the role of its paralogous gene in citrus, BCH2, remains largely unknown. In this study, we revealed the β-hydroxylation activity of citrus BCH2 (CsBCH2) for the first time through the functional complementation assay using Escherichia coli, although CsBCH2 exhibited a lower activity in hydroxylating β-carotene into β-cryptoxanthin than citrus BCH1 (CsBCH1). Our results showed that overexpression of CsBCH2 in citrus callus increased xanthophyll proportion and plastoglobule size with feedback regulation of carotenogenic gene expression. This study revealed the distinct expression patterns and functional characteristics of two paralogous genes, CsBCH1 and CsBCH2, and illustrated the backup compensatory role of CsBCH2 for CsBCH1 in citrus xanthophyll biosynthesis. The independent function of CsBCH2 and its cooperative function with CsBCH1 in β-cryptoxanthin biosynthesis suggested the potential of CsBCH2 to be employed for expanding the synthetic biology toolkit in carotenoid engineering.
On the robustness to adversarial corruption and to heavy-tailed data of the Stahel–Donoho median of means
Authors: Depersin Jules , Lecué Guillaume 
Published: December 2022

AbstractWe consider median of means (MOM) versions of the Stahel–Donoho outlyingness (SDO) [ 23, 66] and of the Median Absolute Deviation (MAD) [ 30] functions to construct subgaussian estimators of a mean vector under adversarial contamination and heavy-tailed data. We develop a single analysis of the MOM version of the SDO which covers all cases ranging from the Gaussian case to the $L_2$ case. It is based on isomorphic and almost isometric properties of the MOM versions of SDO and MAD. This analysis also covers cases where the mean does not even exist but a location parameter does; in those cases we still recover the same subgaussian rates and the same price for adversarial contamination even though there is not even a first moment. These properties are achieved by the classical SDO median and are therefore the first non-asymptotic statistical bounds on the Stahel–Donoho median complementing the $\sqrt{n}$-consistency [ 58] and asymptotic normality [ 74] of the Stahel–Donoho estimators. We also show that the MOM version of MAD can be used to construct an estimator of the covariance matrix only under the existence of a second moment or of a scatter matrix if a second moment does not exist.
Preparing for Colonoscopy in People with Diabetes: A Review with Suggestions for Clinical Practice
Authors: Chirila Alexandra , Nguyen Mary E , Tinmouth Jill , Halperin Ilana J 
Published: December 2022

Abstract
People with diabetes have an increased risk of adverse events during the peri-colonoscopy period, including hypoglycemia, lactic acidosis, diabetic ketoacidosis and acute kidney injury. This is secondary to inadequate dietary modification, the bowel preparation and antihyperglycemic agent modification. With the availability of many new diabetes agents, endoscopists need updated guidance. This review of current literature provides a practical approach to antihyperglycemic agent modification in the context of colonoscopy preparation, as well as guidelines on dietary changes, the bowel preparation itself and glucose monitoring.
Survival in male breast cancer over the past 3 decades
Authors: Leone José P , Freedman Rachel A , Leone Julieta , Tolaney Sara M , Vallejo Carlos T , Leone Bernardo A , Winer Eric P , Lin Nancy U , Hassett Michael J 
Published: December 2022

AbstractBackgroundBreast cancer mortality in women has declined statistically significantly over the past several years. In men, it is unclear whether survival has changed over time. We evaluated changes in breast cancer–specific survival (BCSS) and overall survival (OS) in male breast cancer over the past 3 decades.MethodsWe evaluated men diagnosed with breast cancer between 1988 and 2017, reported in the Surveillance, Epidemiology, and End Results registry. Patients were categorized into 3 groups by year of diagnosis: 1988-1997, 1998-2007, and 2008-2017. BCSS and OS were estimated by Kaplan-Meier, and differences between groups were compared by log-rank test. Multivariable Cox regression evaluated the independent association of year of diagnosis with BCSS and OS. All tests were 2-sided.ResultsWe included 8481 men. Overall, BCSS at 5 years was 83.69%, 83.78%, and 84.41% in groups 1988-1997, 1998-2007, and 2008-2017, respectively (P = .86). There was no statistically significant difference in BCSS between the 3 groups within each stage of disease. Among all patients, OS at 5 years was 64.61%, 67.31%, and 69.05% in groups 1988-1997, 1998-2007, and 2008-2017, respectively (P = .01). In adjusted Cox models, each additional year of diagnosis had no statistically significant association with BCSS (hazard ratio = 1.00, 95% confidence interval = 0.99 to 1.01, P = .75), but there was statistically significant improvement in OS (hazard ratio = 0.99, 95% CI = 0.98 to 0.99, P = .009).ConclusionsOver the past 3 decades, there has been no statistically significant improvement in BCSS in male breast cancer. Changes in OS over time are consistent with increasing life expectancy. Efforts to improve BCSS in male breast cancer are warranted.
Particle acceleration in shearing flows: the self-generation of turbulent spine-sheath structures in relativistic magnetohydrodynamic jet simulations
Authors: Wang Jie-Shuang , Reville Brian , Mizuno Yosuke , Rieger Frank M , Aharonian Felix A 
Published: December 2022

ABSTRACT
X-ray observations of kiloparsec-scale extragalactic jets favour a synchrotron origin. The short cooling times of the emitting electrons require a distributed acceleration of electrons up to sub-PeV energies. In a previous paper, we found that this can be self-consistently explained by a shear acceleration model, where particles are accelerated to produce power-law spectra, with the spectral index being determined mainly by the velocity profile and turbulence spectrum. In this paper, we perform 3D relativistic magnetohydrodynamic simulations to investigate the formation of a spine-sheath structure and the development of turbulence for a relativistic jet propagating into a static cocoon. We explore different spine velocities and magnetic field profiles, with values being chosen to match typical Fanaroff–Riley type I/II jets. We find that in all cases a sheath is generated on the interface of the spine and the cocoon mainly as a result of the Kelvin–Helmholtz instability. The large-scale velocity profile in the sheath is close to linear. Turbulence develops in both the spine and the sheath, with a turbulent velocity spectrum consistent with Kolmogorov scaling. The implications for shear particle acceleration are explored, with a focus on the particle spectral index.
Improved radius determinations for the transiting brown dwarf population in the era of Gaia and TESS
Authors: Carmichael Theron W 
Published: December 2022

ABSTRACT
I report updates to the substellar mass–radius diagram for 11 transiting brown dwarfs (BDs) and low-mass stars published before the third data release from the Gaia mission (Gaia DR3). I re-analyse these transiting BD systems whose physical parameters were published between 2008 and 2019 and find that when using the parallax measurements from Gaia DR3, seven BDs show significant differences in their radius estimate or an improvement in the radius uncertainty. This has important implications for how these BDs are used to test substellar evolutionary models in the mass–radius diagram. The remaining four BDs show mass–radius estimates that are consistent with their previous pre-Gaia DR3 measurements. The seven BDs that show significant deviation from the original mass–radius measurements are AD 3116b, CoRoT-3b, CoRoT-15b, EPIC 201702477b, Kepler-39b, KOI-205b, and KOI-415b. Of these, AD 3116b is a known member of the Praesepe cluster at an age of 600 Myr. Additionally, some of the previously smallest known transiting BDs, KOI-205b and KOI-415b, are not as small as once thought, leaving the mass–radius region for the very oldest BDs relatively sparse as a result of this work.
Tracer-field cross-correlations with k-nearest neighbour distributions
Authors: Banerjee Arka , Abel Tom 
Published: December 2022

ABSTRACT
In astronomy and cosmology significant effort is devoted to characterizing and understanding spatial cross-correlations between points – e.g galaxy positions, high energy neutrino arrival directions, X-ray and AGN sources, and continuous fields – e.g. weak lensing meiand Cosmic Microwave Background maps. Recently, we introduced the k-nearest neighbour (kNN) formalism to better characterize the clustering of discrete (point) data sets. Here, we extend it to the point – field cross-correlations analysis. It combines kNN measurements of the point data set with measurements of the field smoothed at many scales. The resulting statistics are sensitive to all orders in the joint clustering of the points and the field. We demonstrate that this approach, unlike the 2-pt cross-correlation, can measure the statistical dependence of two data sets even when there are no linear (Gaussian) correlations between them. We further demonstrate that this framework is far more effective than the two point function in detecting cross-correlations when the continuous field is contaminated by high levels of noise. For a particularly high level of noise, the cross-correlation between haloes and the underlying matter field in a cosmological simulation, between 10 h−1 Mpc and 30 h−1 Mpc, is detected at &gt;5σ significance using the technique presented here, when the two-point cross-correlation significance is ∼1σ. Finally, we show that kNN cross-correlations of haloes and the matter field can be well modelled on quasi-linear scales using the Hybrid Effective Field Theory (HEFT) framework, with the same set of bias parameters as are used for 2-pt cross-correlations. The substantial improvement in the statistical power of detecting cross-correlations using this method makes it a promising tool for various cosmological applications.
The interaction between transport-segment DNA and topoisomerase IA—crystal structure of MtbTOP1 in complex with both G- and T-segments
Authors: Ferdous Shomita , Dasgupta Tumpa , Annamalai Thirunavukkarasu , Tan Kemin , Tse-Dinh Yuk-Ching 
Published: December 2022

Abstract
Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain–domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain–domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase–DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.
Polyribosomes of circular topology are prevalent in mammalian cells
Authors: Baymukhametov Timur N , Lyabin Dmitry N , Chesnokov Yury M , Sorokin Ivan I , Pechnikova Evgeniya V , Vasiliev Alexander L , Afonina Zhanna A 
Published: December 2022

Abstract
Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been shown to possess various spatial conformations, including a ring-shaped configuration which was considered to be functionally important. However, a recent in situ cryo-ET analysis of predominant regular inter-ribosome contacts did not confirm the abundance of ring-shaped polyribosomes in a cell cytoplasm. To address this discrepancy, here we analyzed the cryo-ET structure of polyribosomes in diluted lysates of HeLa cells. It was shown that the vast majority of the ribosomes were combined into polysomes and were proven to be translationally active. Tomogram analysis revealed that circular polyribosomes are indeed very common in the cytoplasm, but they mostly possess pseudo-regular structures without specific inter-ribosomal contacts. Although the size of polyribosomes varied widely, most circular polysomes were relatively small in size (4–8 ribosomes). Our results confirm the recent data that it is cellular mRNAs with short ORF that most commonly form circular structures providing an enhancement of translation.
High-throughput quantitative binding analysis of DNA aptamers using exonucleases
Authors: Canoura Juan , Alkhamis Obtin , Liu Yingzhu , Willis Connor , Xiao Yi 
Published: December 2022

AbstractAptamers are nucleic acid bioreceptors that have been used in various applications including medical diagnostics and as therapeutic agents. Identifying the most optimal aptamer for a particular application is very challenging. Here, we for the first time have developed a high-throughput method for accurately quantifying aptamer binding affinity, specificity, and cross-reactivity via the kinetics of aptamer digestion by exonucleases. We demonstrate the utility of this approach by isolating a set of new aptamers for fentanyl and its analogs, and then characterizing the binding properties of 655 aptamer–ligand pairs using our exonuclease digestion assay and validating the results with gold-standard methodologies. These data were used to select optimal aptamers for the development of new sensors that detect fentanyl and its analogs in different analytical contexts. Our approach dramatically accelerates the aptamer characterization process and streamlines sensor development, and if coupled with robotics, could enable high-throughput quantitative analysis of thousands of aptamer–ligand pairs.
Microbiota-Based Live Biotherapeutic RBX2660 for the Reduction of Recurrent Clostridioides difficile Infection in Older Adults With Underlying Comorbidities
Authors: Tillotson Glenn , Archbald-Pannone Laurie , Johnson Stuart , Ng Samson , Ando Masakazu , Harvey Adam , Bancke Lindy , Feuerstadt Paul 
Published: December 2022

Abstract

Background
Advanced age and underlying comorbidities are associated with greater rates of recurrence in patients with Clostridioides difficile infection (CDI). Reducing the likelihood of recurrence through treatment with an antimicrobial followed by a microbiota replacement therapy can decrease the burden of this infection and improve patient outcomes. We report the efficacy and safety of RBX2660, a microbiota-based live biotherapeutic, in older adults with recurrent CDI, grouped by comorbidities.

Methods
In this post hoc subgroup analysis of the PUNCH CD3 trial, we assessed outcomes in older adults (age ≥65 years) grouped by Charlson Comorbidity Index severity scores at screening (moderate [3–4] and severe [≥5]) and by the presence of underlying cardiac, renal, or gastrointestinal disorders.

Results
RBX2660 treatment success rates in older adults with comorbidities were consistent across subgroups and similar to those in the total RBX2660-treated population. A greater percentage of RBX2660-treated older adults remained free of CDI recurrence through 8 weeks following treatment compared with placebo-treated participants in all but 2 subgroups assessed. Across all subgroups, most treatment-emergent adverse events (TEAEs) were mild or moderate in severity and related to a preexisting condition. None of the serious or life-threatening TEAEs that occurred were related to RBX2660 or its administration. Occurrence of TEAEs did not cluster in any subgroup.

Conclusions
RBX2660 is efficacious and safe in older adults with recurrent CDI and underlying comorbidities.