bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of farmland abandonment on anthropogenic-alluvial soil microbiota and contaminant residues in Lycium barbarum fields
Authors: Zhang Junhua , He Mengyuan , Jia Keli , Shen Cong
Published: September 2023

Aims

There has been an increasing tendency to abandon crop cultivation and farming in old Lycium barbarum (wolfberry) stands to allow for natural restoration. However, little research has been dedicated to deciphering how soil quality changes in L. barbarum fields following abandonment from a physicochemical and microbiological perspective. Here we assessed the effects of farmland abandonment on anthropogenic-alluvial soil microbiota and contaminant residues in L. barbarum fields in Ningxia, China.

Methods and results

Soil microbiota, heavy metal, and neonicotinoid pesticide profiles in L. barbarum fields abandoned for one to four years were characterized. Microbial community analysis was performed by high-throughput sequencing of the bacterial 16S ribosomal RNA genes and the fungal nuclear ribosomal internal transcribed spacer region. Soil bacterial diversity increased from before abandonment to year three after abandonment, and fungal diversity peaked in year one after abandonment. Enrichment of potentially beneficial taxa (e.g. Limnobacter, Cavicella) as well as pathogenic taxa (e.g. Ilyonectria) was observed in the abandoned field soils, along with depletion of other taxa (e.g. Planococcus, Bipolaris). Soil copper, zinc, cadmium, imidacloprid, and acetamiprid concentrations all decreased with increasing time since abandonment and had varied correlations with soil quality, microbial diversity, and the relative abundances of major phyla. Soil available phosphorus, nitrate-nitrogen, and pH were the key factors shaping bacterial communities. The structuring of fungal communities was strongly influenced by soil pH, available phosphorus, and available nitrogen contents.

Conclusions

There were positive consequences of farmland abandonment in L. barbarum fields, such as optimized microbial community structure, reduced heavy metal accumulation, and enhanced pesticide degradation.
The participation of vacuoles and the regulation of various metabolic pathways under acid stress promote the differentiation of chlamydospore inTrichoderma harzianumT4
Authors: Zhu Xiaochong , Wang Yaping , Shen Chao , Zhang Songhan , Wang Wei
Published: September 2023

Aims

Chlamydospores are a special, differentiated type with high environmental resistance. Consequently, the chlamydospores of Trichoderma harzianum T4 can used to industrialize the latter. This study aimed to investigate the key factors affecting the sporulation type of T. harzianum T4 and the mechanisms underlying this effect.

Methods and results

In the liquid fermentation of T. harzianum T4, ammonium sulfate (AS) inhibited conidia formation and chlamydospore production. Fermentation tests revealed that acid stress induced sporulation type alteration. Transcriptomic analysis was used to evaluate the adaptation strategy and mechanism underlying spore type alteration under acid stress. The fermentation experiments involving the addition of amino acids revealed that branched-chain amino acids benefited conidia production, whereas β-alanine benefited chlamydospore production. Confocal microscope fluorescence imaging and chloroquine intervention demonstrated that vacuole function was closely related to chlamydospore production.

Conclusion

The sporulation type of T. harzianum T4 can be controlled by adjusting the fermentation pH. T. harzianum T4 cells employ various self-protection measures against strong acid stress, including regulating their metabolism to produce a large number of chlamydospores for survival.
A 2-component blend of coconut oil-derived fatty acids as an oviposition deterrent against Drosophila suzukii (Drosophilidae: Diptera)
Authors: Roh Gwang Hyun , Meier Linnea , Shrestha Binita , Hesler Stephen P , Zhu Junwei J , Kendra Paul E , Loeb Gregory M , Tay Jia-Wei , Cha Dong H
Published: September 2023

Coconut free fatty acid (CFFA), a mixture of 8 fatty acids derived from coconut oil, is an effective repellent and deterrent against a broad array of hematophagous insects. In this study, we evaluated the oviposition deterrent activity of CFFA on spotted-wing drosophila (SWD; Drosophila suzukii), a destructive invasive pest of berries and cherries, and identified bioactive key-deterrent compounds. In laboratory 2-choice tests, CFFA deterred SWD oviposition in a dose-dependent manner with the greatest reduction (99%) observed at a 20-mg dose compared with solvent control. In a field test, raspberries treated with 20-mg CFFA received 64% fewer SWD eggs than raspberries treated with the solvent control. In subsequent laboratory bioassays, 2 of CFFA components, caprylic and capric acids, significantly reduced SWD oviposition by themselves, while 6 other components had no effect. In choice and no-choice assays, we found that a blend of caprylic acid and capric acid, at equivalent concentrations and ratio as in CFFA, was as effective as CFFA, while caprylic acid or capric acid individually were not as effective as the 2-component blend or CFFA at equivalent concentrations, indicating the 2 compounds as the key oviposition deterrent components for SWD. The blend was also as effective as CFFA for other nontarget drosophilid species in the field. Given that CFFA compounds are generally regarded as safe for humans, CFFA and its bioactive components have potential application in sustainably reducing SWD damage in commercial fruit operations, thereby reducing the sole reliance on insecticides.
The ‘Fair Share’ of Climate Mitigation: Can Litigation Increase National Ambition for Brazil?
Authors: Tigre Maria Antonia
Published: September 2023

Several years after the adoption of the Paris Agreement, the world is still far from achieving its emission reduction target. Despite the scientific certainty of the devastating effects of climate change on human rights, countries’ ‘nationally determined contributions’ (NDCs) still fall short of the 1.5 °C goal. Compared to developed countries and their historical contributions, the Global South’s role in climate mitigation may appear insignificant. However, the magnitude of the human rights effects of climate change are enormous. Any increase above 1.5 °C would endanger human well-being and the ecosystems on which human life depends. Therefore, all parties must cooperate to adopt more ambitious NDCs. This imperative—while falling mainly on the Global North, which holds significant historical responsibility for emissions—also extends beyond the Global North, to, for example, a country like Brazil. This article assesses how fair share has played a role in climate litigation cases in the Global North (primarily in Europe) and discusses the possibilities and challenges of bringing similar cases in Brazil. It relies on the fair share methodology used to substantiate the argument of increased ambition in cases in the Global North, discussing whether a similar argument could be brought in Brazil.
The fixed points of belief and knowledge
Authors: Schuster Daniela
Published: September 2023

Self-referential sentences have troubled our understanding of language for centuries. The most famous self-referential sentence is probably the Liar, a sentence that says of itself that it is false. The Liar Paradox has encouraged many philosophers to establish theories of truth that manage to give a proper account of the truth predicate in a formal language. Kripke’s Fixed Point Theory from 1975 is one famous example of such a formal theory of truth that aims at giving a plausible notion of truth by allowing truth value gaps. However, not only the concept of truth gives rise to paradoxes. A syntactical treatment of epistemic notions like belief and knowledge leads to contradictions that very much resemble the Liar Paradox. Therefore, it seems to be fruitful to apply the established theories of truth to epistemic concepts. In this paper, I will present one such attempt of solving the epistemic paradoxes: I adapt Kripke’s Fixed Point Theory and interpret truth, knowledge and belief within the framework of a partial logic. Thereby I find not only the fixed point of truth but also the fixed points of knowledge and belief. In this fixed point, the predicates of truth, belief and knowledge find their definite interpretation and the paradoxes are avoided.
Perkinsus marinus in bioreactor: growth and a cost-reduced growth medium
Authors: Murphy Caitlin , Fernández Robledo José A , van Walsum G Peter
Published: September 2023

Perkinsus marinus (Perkinsea) is an osmotrophic facultative intracellular marine protozoan responsible for “Dermo” disease in the eastern oyster, Crassostrea virginica. In 1993 in vitro culture of P. marinus was developed in the absence of host cells. Compared to most intracellular protozoan parasites, the availability of P. marinus to grow in the absence of host cells has provided the basis to explore its use as a heterologous expression system. As the genetic toolbox is becoming available, there is also the need for larger-scale cultivation and lower-cost media formulations. Here, we took an industrial approach to scaled-up growth from a small culture flask to bioreactors, which required developing new cultivation parameters, including aeration, mixing, pH, temperature control, and media formulation. Our approach also enabled more real-time data collection on growth. The bioreactor cultivation method showed similar or accelerated growth rates of P. marinus compared to culture in T-flasks. Redox measurements indicated sufficient oxygen availability throughout the cultivation. Replacing fetal bovine serum with chicken serum showed no differences in the growth rate and a 60% reduction in the medium cost. This study opens the door to furthering P. marinus as a valid heterologous expression system by showing the ability to grow in bioreactors.

One-Sentence Summary

Perkinsus marinus, a microbial parasite of oysters that could be useful for developing vaccines for humans, has been shown to grow well in laboratory equipment that can be expanded to commercial scale using a less expensive growth formula than usual laboratory practice.
High-resolution global precipitation downscaling with latent Gaussian models and non-stationary stochastic partial differential equation structure
Authors: Zhang Jiachen , Bonas Matthew , Bolster Diogo , Fuglstad Geir-Arne , Castruccio Stefano
Published: September 2023

Obtaining high-resolution maps of precipitation data can provide key insights to stakeholders to assess a sustainable access to water resources at urban scale. Mapping a non-stationary, sparse process such as precipitation at very high spatial resolution requires the interpolation of global datasets at the location where ground stations are available with statistical models able to capture complex non-Gaussian global space–time dependence structures. In this work, we propose a new approach based on capturing the spatially varying anisotropy of a latent Gaussian process via a locally deformed stochastic partial differential equation (SPDE) with a buffer allowing for a different spatial structure across land and sea. The finite volume approximation of the SPDE, coupled with integrated nested Laplace approximation ensures feasible Bayesian inference for tens of millions of observations. The simulation studies showcase the improved predictability of the proposed approach against stationary and no-buffer alternatives. The proposed approach is then used to yield high-resolution simulations of daily precipitation across the United States.
Enhancing surgical planning of distal splenopancreatectomy through 3D printed models: a case report
Authors: Arsenkov Stefan , Plavevski Ognen , Nikolovski Andrej , Arsenkov Ljuben , Shurlani Arben , Saliu Valon
Published: September 2023

The complex anatomy of the peripancreatic region was a challenge to many surgeons in the past. Up until recently, the only way to prepare and plan a surgery was through the use of traditional 2D images, obtained via computed tomography or magnetic resonance imaging. Recently, the advantages in the field of 3D printing (also called additive manufacturing, or rapid prototyping) allowed the creation of replicas of the patient’s anatomy which is to be used for preoperative planning and visual reference. We present the case of a 46-y.o. patient with a distal pancreatic lesion requiring a distal splenopancreatectomy, who benefited from the use of 3D printing technology. No intraoperative or postoperative complications were encountered, while the created model was used to plan and perform the needed resection.
Automatic and Quantitative Measurement of Spectrometer Aberrations
Authors: Guo Yueming , Lupini Andrew R
Published: September 2023

The performance of electron energy loss spectrometers can often be limited by their electron optical aberrations. Due to recent developments in high energy resolution and momentum-resolved electron energy loss spectroscopy (EELS), there is renewed interest in optimizing the performance of such spectrometers. For example, the “ω − q” mode of momentum-resolved EELS, which uses a small convergence angle and requires aligning diffraction spots with the slot aperture, presents a challenge in the realignments of the spectrometer required by the adjustment of the projection lenses. Automated and robust alignment can greatly benefit such a process. The first step toward this goal is automatic and quantitative measurement of spectrometer aberrations. We demonstrate the measurement of geometric aberrations and distortions in EELS within a monochromated scanning transmission electron microscope (STEM). To better understand the results, we present a wave mechanical simulation of the experiment. Using the measured aberration and distortion coefficients as inputs to the simulation, we find a good match between the simulation and experiment, verifying formulae used in the simulation. From verified simulations with known aberration coefficients, we can assess the accuracy of measurements. Understanding the errors and inaccuracies in the procedure can guide further progress in aberration measurement and correction for new spectrometer developments.
Ground-based calibration and characterization of LaBr3-SiPM-based gamma-ray detector on GECAM satellite: 8–160 keV
Authors: He Jian-Jian , An Zheng-Hua , Peng Wen-Xi , Li Xin-Qiao , Xiong Shao-Lin , Zhang Da-Li , Qiao Rui , Guo Dong-Ya , Cai Ce , Chang Zhi , Chen Can , Chen Gang , Du Yuan-Yuan , Gao Min , Gao Rui , Gong Ke , Hou Dong-Jie , Li Chao-Yang , Li Gang , Li Lu , Li Mao-Shun , Li Xiao-Bo , Li Xu-Fang , Li Yan-Guo , Liang Xiao-Hua , Liu Jia-Cong , Liu Xiao-Jing , Liu Ya-Qing , Lu Hong , Ma Xiang , Meng Bin , Shi Feng , Song Li-Ming , Sun Xi-Lei , Wang Chen-Wei , Wang Hui , Wang Hui-Zhen , Wang Jin-Zhou , Wang Yu-Sa , Wen Xing , Wen Xiang-Yang , Xiao Shuo , Xu Yan-Bing , Xu Yu-Peng , Xue Wang-Chen , Yang Jia-Wei , Yang Sheng , Yi Qi-Bin , Zhang Cheng-Mo , Zhang Chao-Yue , Zhang Fan , Zhang Fei , Zhang Peng , Zhang Shuang-Nan , Zhang Yan-Qiu , Zhao Xiao-Yun , Zhao Yi , Zheng Chao , Zheng Shi-Jie , Zhou Xing , Zhu Yue
Published: September 2023

As the main detector of the Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor mission (GECAM), the calibration of the energy response and detection efficiency of the gamma-ray detector (GRD) is the main content of the ground-based calibration. This article mainly focuses on the calibration of the energy response and detection efficiency in the 8–160 keV with a refined measurement around the absorption edges of the lanthanum bromide crystal ($\rm {LaBr_3}$). The GRD performances for different crystal types, data acquisition modes, working modes, and incident positions are also analysed in detail. We show that the calibration campaign is comprehensive, the detector performance meets the flight requirements, and the calibration results generally agree with simulations as expected. The detector’s model was corrected by the ground-based calibration, which led to the establishment of the calibration data base.
Painting baryons on to N-body simulations of galaxy clusters with image-to-image deep learning
Authors: Chadayammuri Urmila , Ntampaka Michelle , ZuHone John , Bogdán Ákos , Kraft Ralph P
Published: September 2023

Galaxy cluster mass functions are a function of cosmology, but mass is not a direct observable, and systematic errors abound in all its observable proxies. Mass-free inference can bypass this challenge, but it requires large suites of simulations spanning a range of cosmologies and models for directly observable quantities. In this work, we devise a U-net – an image-to-image machine learning algorithm – to ‘paint’ the illustristng model of baryons on to dark matter-only (DMO) simulations of galaxy clusters. Using 761 galaxy clusters with M200c ≳ 1014 M⊙ from the TNG300 simulation at z < 1, we train the algorithm to read in maps of projected dark matter mass and output maps of projected gas density, temperature, and X-ray flux. Despite being trained on individual images, the model reproduces the true scaling relation and scatter for the MDM–LX, as well as the distribution functions of the cluster X-ray luminosity and gas mass. For just one decade in cluster mass, the model reproduces three orders of magnitude in LX. The model is biased slightly high when using dark matter maps from the DMO simulation. The model performs well on inputs from TNG300-2, whose mass resolution is eight times coarser; further degrading the resolution biases the predicted luminosity function high. We conclude that U-net-based baryon painting is a promising technique to build large simulated cluster catalogues, which can be used to improve cluster cosmology by combining existing full-physics and large N-body simulations.
An FUV and optical study of star formation in closely interacting galaxies: star-forming rings, tidal arms, and nuclear outflows
Authors: Yadav Jyoti , Das Mousumi , Barway Sudhanshu , Combes Francoise
Published: September 2023

We present a study of the morphology of star formation and the associated nuclear activity in a sample of eight closely interacting southern galaxies, which are in different stages of interaction, starting with nearly merged nuclei that have one prominent bulge to more widely spaced interacting galaxies. We have used far-ultraviolet (FUV) observations from the Ultraviolet Imaging Telescope (UVIT), near-Infrared observations from the Infrared Survey Facility (IRSF) telescope, and archival optical data from the Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) integral field spectrograph. Analysing resolved stellar populations across the disc of the interacting galaxies can provide unique insights into how interactions affect galaxy properties, such as morphology, star formation rates, and chemical composition. We take advantage of the unprecedented capabilities of MUSE and UVIT to carry out a highly detailed spatially and spectrally resolved study of star formation rate, star formation histories, metallicity, and active galactic nucleus activity in the sample of eight interacting galaxies that are in different stages of interaction. Most of our sample galaxies are gas-rich and show evidence of recent, massive star formation in tidal tails, rings, and spiral arms. This is evident from their FUV and Hα emissions, which trace young, massive star-forming regions. We compared the star formation rate in the barred and unbarred galaxies in our sample and found that the barred galaxies do not show significant enhancement in star formation rate or large-scale difference in star formation morphology compared to unbarred galaxies. IC5250 and NGC7733N show extended nuclear outflows of sizes ∼5 and 8 kpc, respectively.
The intrinsic alignment of red galaxies in DES Y1 redMaPPer galaxy clusters
Authors: Zhou C , Tong A , Troxel M A , Blazek J , Lin C , Bacon D , Bleem L , Chang C , Costanzi M , DeRose J , Dietrich J P , Drlica-Wagner A , Gruen D , Gruendl R A , Hoyle B , Jarvis M , MacCrann N , Mawdsley B , McClintock T , Melchior P , Prat J , Pujol A , Rozo E , Rykoff E S , Samuroff S , Sheldon E , Shin T , Rosell A Carnero , Yanny B , Sánchez C , Tucker D L , Sevilla-Noarbe I , Zuntz J , Varga T N , Zhang Y , Alves O , Amon A , Bertin E , Brooks D , Burke D L , Kind M Carrasco , da Costa L N , Davis T M , De Vicente J , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Flaugher B , Frieman J , Gerdes D W , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Jeltema T , Kuehn K , Lahav O , Lima M , Marshall J L , Mena-Fernández J , Menanteau F , Miquel R , Palmese A , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Porredon A , Raveri M , Romer A K , Sanchez E , Smith M , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , To C , Weaverdyck N , Weller J , Wiseman P
Published: September 2023

Clusters of galaxies trace the most non-linear peaks in the cosmic density field. The weak gravitational lensing of background galaxies by clusters can allow us to infer their masses. However, galaxies associated with the local environment of the cluster can also be intrinsically aligned due to the local tidal gradient, contaminating any cosmology derived from the lensing signal. We measure this intrinsic alignment in Dark Energy Survey (DES) Year 1 redMaPPer clusters. We find evidence of a non-zero mean radial alignment of galaxies within clusters between redshifts 0.1–0.7. We find a significant systematic in the measured ellipticities of cluster satellite galaxies that we attribute to the central galaxy flux and other intracluster light. We attempt to correct this signal, and fit a simple model for intrinsic alignment amplitude (AIA) to the measurement, finding AIA = 0.15 ± 0.04, when excluding data near the edge of the cluster. We find a significantly stronger alignment of the central galaxy with the cluster dark matter halo at low redshift and with higher richness and central galaxy absolute magnitude (proxies for cluster mass). This is an important demonstration of the ability of large photometric data sets like DES to provide direct constraints on the intrinsic alignment of galaxies within clusters. These measurements can inform improvements to small-scale modelling and simulation of the intrinsic alignment of galaxies to help improve the separation of the intrinsic alignment signal in weak lensing studies.
Evolution in the orbital structure of quiescent galaxies from MAGPI, LEGA-C, and SAMI surveys: direct evidence for merger-driven growth over the last 7 Gyr
Authors: D’Eugenio Francesco , van der Wel Arjen , Piotrowska Joanna M , Bezanson Rachel , Taylor Edward N , van de Sande Jesse , Baker William M , Bell Eric F , Bellstedt Sabine , Bland-Hawthorn Joss , Bluck Asa F L , Brough Sarah , Bryant Julia J , Colless Matthew , Cortese Luca , Croom Scott M , Derkenne Caro , van Dokkum Pieter , Fisher Deanne , Foster Caroline , Gallazzi Anna , de Graaff Anna , Groves Brent , van Houdt Josha , del P. Lagos Claudia , Looser Tobias J , Maiolino Roberto , Maseda Michael , Mendel J Trevor , Nersesian Angelos , Pacifici Camilla , Poci Adriano , Remus Rhea-Silvia , Sweet Sarah M , Thater Sabine , Tran Kim-Vy , Übler Hannah , Valenzuela Lucas M , Wisnioski Emily , Zibetti Stefano
Published: September 2023

We present the first study of spatially integrated higher-order stellar kinematics over cosmic time. We use deep rest-frame optical spectroscopy of quiescent galaxies at redshifts z = 0.05, 0.3, and 0.8 from the SAMI, MAGPI, and LEGA-C surveys to measure the excess kurtosis h4 of the stellar velocity distribution, the latter parametrized as a Gauss-Hermite series. Conservatively using a redshift-independent cut in stellar mass ($M_\star = 10^{11}\, \mathrm{M_\odot }$) and matching the stellar-mass distributions of our samples, we find 7σ evidence of h4 increasing with cosmic time, from a median value of 0.019 ± 0.002 at z = 0.8 to 0.059 ± 0.004 at z = 0.06. Alternatively, we use a physically motivated sample selection based on the mass distribution of the progenitors of local quiescent galaxies as inferred from numerical simulations; in this case, we find 10σ evidence. This evolution suggests that, over the last 7 Gyr, there has been a gradual decrease in the rotation-to-dispersion ratio and an increase in the radial anisotropy of the stellar velocity distribution, qualitatively consistent with accretion of gas-poor satellites. These findings demonstrate that massive galaxies continue to accrete mass and increase their dispersion support after becoming quiescent.
Relaxation of Natural Selection in the Evolution of the Giant Lungfish Genomes
Authors: Fuselli Silvia , Greco Samuele , Biello Roberto , Palmitessa Sergio , Lago Marta , Meneghetti Corrado , McDougall Carmel , Trucchi Emiliano , Rota Stabelli Omar , Biscotti Assunta Maria , Schmidt Daniel J , Roberts David T , Espinoza Thomas , Hughes Jane Margaret , Ometto Lino , Gerdol Marco , Bertorelle Giorgio
Published: September 2023

Nonadaptive hypotheses on the evolution of eukaryotic genome size predict an expansion when the process of purifying selection becomes weak. Accordingly, species with huge genomes, such as lungfish, are expected to show a genome-wide relaxation signature of selection compared with other organisms. However, few studies have empirically tested this prediction using genomic data in a comparative framework. Here, we show that 1) the newly assembled transcriptome of the Australian lungfish, Neoceratodus forsteri, is characterized by an excess of pervasive transcription, or transcriptional leakage, possibly due to suboptimal transcriptional control, and 2) a significant relaxation signature in coding genes in lungfish species compared with other vertebrates. Based on these observations, we propose that the largest known animal genomes evolved in a nearly neutral scenario where genome expansion is less efficiently constrained.
RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures
Authors: Malhotra Sony , Mulvaney Thomas , Cragnolini Tristan , Sidhu Haneesh , Joseph Agnel P , Beton Joseph G , Topf Maya
Published: September 2023

Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for identifying rigid bodies in protein structures exist, however an equivalent for nucleic acid structures is lacking. With the increase in cryo-EM maps containing RNA and progress in RNA structure prediction, there is a need for such tools. We previously developed RIBFIND, a program for clustering protein secondary structures into rigid bodies. In RIBFIND2, this approach is extended to nucleic acid structures. RIBFIND2 can identify biologically relevant rigid bodies in important groups of complex RNA structures, capturing a wide range of dynamics, including large rigid-body movements. The usefulness of RIBFIND2-assigned rigid bodies in cryo-EM model refinement was demonstrated on three examples, with two conformations each: Group II Intron complexed IEP, Internal Ribosome Entry Site and the Processome, using cryo-EM maps at 2.7–5 Å resolution. A hierarchical refinement approach, performed on progressively smaller sets of RIBFIND2 rigid bodies, was clearly shown to have an advantage over classical all-atom refinement. RIBFIND2 is available via a web server with structure visualization and as a standalone tool.
Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP
Authors: Lyu Zhihui , Villanueva Patricia , O’Malley Liam , Murphy Parker , Augenstreich Jacques , Briken Volker , Singh Abhyudai , Ling Jiqiang
Published: September 2023

Translational fidelity is critical for microbial fitness, survival and stress responses. Much remains unknown about the genetic and environmental control of translational fidelity and its single-cell heterogeneity. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified over 20 genes critical for stop-codon readthrough. Most of these identified genes were not previously known to affect translational fidelity. Intriguingly, we show that several genes controlling metabolism, including cyaA and crp, enhance stop-codon readthrough. CyaA catalyzes the synthesis of cyclic adenosine monophosphate (cAMP). Combining RNA sequencing, metabolomics and biochemical analyses, we show that deleting cyaA impairs amino acid catabolism and production of ATP, thus repressing the transcription of rRNAs and tRNAs to decrease readthrough. Single-cell analyses further show that cAMP is a major driver of heterogeneity in stop-codon readthrough and rRNA expression. Our results highlight that carbon metabolism is tightly coupled with stop-codon readthrough.
The Application of CT Radiomics in the Diagnosis of Vein Wall Invasion in Patients With Renal Cell Carcinoma Combined With Tumor Thrombus
Authors: Zhao Xun , Yan Ye , Xie Wanfang , Zhao Litao , Zhang Shudong , Liu Jiangang , Liu Cheng , Ma Lulin
Published: September 2023

Objective

The objective of this study was to explore the application of radiomics combined with machine learning to establish different models to assist in the diagnosis of venous wall invasion in patients with renal cell carcinoma and venous tumor thrombus and to evaluate the diagnostic efficacy.

Materials and Methods

We retrospectively reviewed the data of 169 patients in Peking University Third Hospital from March 2015 to January 21, who was diagnosed as renal mass with venous invasion. According to the intraoperative findings, 111 patients were classified to the venous wall invasion group and 58 cases in the non-invasion group. ITK-snap was used for tumor segmentation and PyRadiomics 3.0.1 package was used for feature extraction. A total of 1598 features could be extracted from each CT image. The patients were divided into training set and testing set by time. The elastic-net regression with 4-fold cross-validation was used as a dimension-reduction method. After feature selection, a support vector machines (SVM) model, a logistic regression (LR) model, and an extra trees (ET) model were established. Then the sensitivity, specificity, accuracy, and the area under the curve (AUC) were calculated to evaluate the diagnostic performance of each model on the testing set.

Results

Patients before September 2019 were divided into the training set, of which 88 patients were in the invasion group and 42 patients were in the non-invasion group. The others were in the testing set, of which 32 patients were in the invasion group and 16 patients were in the non-invasion group. A total of 34 radiomics features were obtained by the elastic-net regression. The SVM model had an AUC value of 0.641 (95% CI, 0.463-0.769), a sensitivity of 1.000, and a specificity of 0.062. The LR model had an AUC value of 0.769 (95% CI, 0.620-0.877), a sensitivity of 0.913, and a specificity of 0.312. The ET model had an AUC value of 0.853 (95% CI, 0.734-0.948), a sensitivity of 0.783, and a specificity of 0.812. Among the 3 models, the ET model had the best diagnostic effect, with a good balance of sensitivity and specificity. And the higher the tumor thrombus grade, the better the diagnostic efficacy of the ET model. In inferior vena cava tumor thrombus, the sensitivity, specificity, accuracy, and AUC of ET model can be improved to 0.889, 0.800, 0.857, 0.878 (95% CI, 0.745-1.000).

Conclusion

Machine learning combined with radiomics method can effectively identify whether venous wall was invaded by tumor thrombus and has high diagnostic efficacy with an AUC of 0.853 (95% CI, 0.734-0.948).
Impact of dark energy on the equation of state in light of the latest cosmological data
Authors: Myrzakulov N , Koussour M , Alfedeel Alnadhief H A , Hassan E I
Published: September 2023

We reconstruct the effective equation of state (EoS) within the framework of the general theory of relativity in a homogeneous and isotropic Friedmann–Lemaître–Robertson–Walker universe, which is assumed to be composed of matter and dark energy (DE). Our analysis employs a dataset consisting of 31 cosmic chronometer data points, six data points of baryon acoustic oscillations, and 1048 type Ia supernovae from the Pantheon sample, and we determine the best-fitting values of the model parameters through Markov chain Monte Carlo simulation. We then use these parameter values to calculate various cosmological parameters, such as the DE EoS parameter, the energy density, the deceleration parameter, the state-finder parameters, and the Om(z) diagnostic. All the analyzed cosmological parameters show behavior consistent with the accelerated universe scenario.
Systematic Development of Standards for Mixed Methods Reporting in Rehabilitation Health Sciences Research
Authors: Tovin Melissa M , Wormley Michelle E
Published: September 2023

Objective

Mixed methods research (MMR) integrates quantitative and qualitative methods throughout the research process to answer complex research questions. MMR designs align with the guiding frameworks of patient-centered care and social determinants of health by effectively examining the role of contextual factors and human experiences in influencing health and rehabilitation outcomes. Reporting standards and critical appraisal tools ensure the quality and transparency of the research process. MMR standards exist; yet, there is a need for reporting guidelines and an appraisal tool that meets field standards, is applicable across rehabilitation fields of study, and can accommodate the range of possibilities for combining research approaches and methods.

Methods

Mixed Methods Reporting in Rehabilitation & Health Sciences (MMR-RHS) was developed using a systematic consensus-building process in accordance with published guidance and was preregistered with the Enhancing the Quality and Transparency of Health Research Network. MMR-RHS evolved through a sequence of steps, including extensive literature review, expert consultation, stakeholder feedback, pilot testing, and tool refinement.

Results

MMR-RHS consists of 20 criteria that align with field standards for rigor and transparency, with an emphasis on integration throughout the research process, a key component of MMR.

Conclusions

A systematic process was utilized to develop the reporting standards and an appraisal tool for MMR in rehabilitation and health science. The tool is comprehensive, includes a set of criteria grounded in MMR literature, and is flexible for application to a range of MMR designs commonly seen in rehabilitation research.

Impact

The MMR-RHS may improve the quality and transparency of MMR by supporting investigators, authors, reviewers, and editors during project development, manuscript preparation, and critical review. The tool may assist readers in critical appraisal, knowledge translation, and application of published MMR findings. Ultimately, the MMR-RHS may help legitimize mixed methods in rehabilitation and health research, an important step toward understanding the complexities of health care, patient outcomes, and evolving societal health needs.
Outcomes following switching from etanercept originator to etanercept biosimilar in 1024 patients with RA: a matched-analysis of the BSRBR-RA
Authors: Kearsley-Fleet Lianne , Rokad Aasiyah , Tsoi Man-Fung , Zhao Sizheng Steven , Lunt Mark , Watson Kath D ,   BSRBR-RA Contributors Group, Hyrich Kimme L
Published: September 2023

Objectives

Adults with RA are being switched from etanercept originator to biosimilar in non-medical/cost-saving switching. This analysis aims to investigate outcomes in these patients, including (i) drug survival and (ii) disease activity at 6 months and 12 months, compared with those who remain on the originator.

Methods

Using BSRBR-RA, those who switched directly from etanercept originator to biosimilar were identified and matched to patients receiving the originator, based on gender, age, disease duration and originator start year. Drug survival was calculated; Cox-proportional hazard models assessed differences in drug persistence between those who switched vs remaining on originator. Change in DAS28 after 6 months and 12 months was compared between cohorts. Multiple imputation was used.

Results

A total of 1024 adults with RA switching from etanercept originator to biosimilar were included, with a matched cohort of patients remaining on the originator. Patients who switched onto a biosimilar product were no more likely to discontinue etanercept treatment vs those who remained on the originator; hazard ratio 1.06 (95%CI 0.89–1.26), with 65% of patients remaining on treatment at three years. Ninety-five (9%) patients switched back to the originator within the first year. After 6 months and 12 months, biosimilar patients were no more likely to have a worsening of DAS28 (>0.6 units) compared with those who remained on the originator.

Conclusions

This is the largest matched comparative effectiveness analysis showing patients switching from etanercept originator to biosimilar appearing to do just as well with regard to disease activity and drug persistence compared with those who remained on the originator. These data will be reassuring to clinicians and patients regarding non-medical switching.
Labour market digitalization and social class: evidence of mobility and reproduction from a European survey of online platform workers
Authors: Martindale Nicholas , Lehdonvirta Vili
Published: September 2023

The type of work we do as adults is significantly influenced by our parents’ social class. However, digital technologies are transforming the way labour markets work. Candidates are screened using algorithmic decision-making systems. Skills are validated with online tests and feedback ratings. Communications take place online. Could these transformations undermine the advantages that have accrued to workers with privileged backgrounds or reproduce this privilege through digital divides? We examine this question with survey evidence from the online (remote) platform economy, a labour market segment where these digital transformations have progressed furthest (N = 1,001). The results reveal that online platform workers come predominantly from privileged class backgrounds, but we find less evidence of parental class shaping what types of online work they do. We conclude that digital transformations of labour markets may reproduce disparities in access to work but attenuate some class-based differences in the selection of workers by employers.
Sleep apnea, hypoxia, and late-onset epilepsy: the Atherosclerosis Risk in Communities study
Authors: Carosella Christopher M , Gottesman Rebecca F , Kucharska-Newton Anna , Lutsey Pamela L , Spira Adam P , Punjabi Naresh M , Schneider Andrea L C , Full Kelsie M , Johnson Emily L
Published: September 2023

Study Objective

Sleep apnea is associated with unexplained epilepsy in older adults in small studies. We sought to determine the relationship between sleep apnea and additional sleep characteristics and late-onset epilepsy (LOE), adjusting for comorbidities, using data from the large, prospective Atherosclerosis Risk in Communities (ARIC) Study cohort.

Methods

We used Medicare claims to identify cases of LOE in ARIC participants. We used polysomnography data from 1309 ARIC participants who also participated in the Sleep Heart Health Study in 1995–1998, and demographic and comorbidity data from ARIC. Later risk of LOE was evaluated using survival analysis with a competing risk of death. We also used survival analysis in 2672 ARIC participants to identify the association between self-reported obstructive sleep apnea (2011–2013), and the risk of subsequent LOE.

Results

Late-midlife oxygen desaturation to less than 80% during sleep was associated with subsequent development of LOE, adjusted subhazard ratio 3.28 (1.18–9.08), but the apnea–hypopnea index was not related. Participant report of diagnosis of sleep apnea in 2011–2013 was also associated with subsequent LOE, adjusted subhazard ratio 2.59 (1.24–5.39).

Conclusions

Sleep apnea and oxygen saturation nadir during sleep are associated with LOE, independently of hypertension and other comorbidities. These potentially modifiable risk factors could have large clinical implications for LOE.
Tree-ring δ15N as an indicator of nitrogen dynamics in stands with N2-fixing Alnus rubra
Authors: Nehring L , Kranabetter J M , Harper G J , Hawkins B J
Published: September 2023

Tree-ring δ15N may depict site-specific, long-term patterns in nitrogen (N) dynamics under N2-fixing species, but field trials with N2-fixing tree species are lacking and the relationship of temporal patterns in tree-ring δ15N to soil N dynamics is controversial. We examined whether the tree-ring δ15N of N2-fixing red alder (Alnus rubra Bong.) would mirror N accretion rates and δ15N of soils and whether the influence of alder-fixed N could be observed in the wood of a neighboring conifer. We sampled a 27-year-old replacement series trial on south-eastern Vancouver Island, with red alder and coastal Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) planted in five proportions (0/100, 11/89, 25/75, 50/50 and 100/0) at a uniform stem density. An escalation in forest floor N content was evident with an increasing proportion of red alder, equivalent to a difference of ~750 kg N ha−1 between 100% Douglas-fir versus 100% alder. The forest floor horizon also had high δ15N values in treatments with more red alder. Red alder had a consistent quadratic fit in tree-ring δ15N over time, with a net increase of $\sim$1.5‰, on average, from initial values, followed by a plateau or slight decline. Douglas-fir tree-ring δ15N, in contrast, was largely unchanged over time (in three of four plots) but was significantly higher in the 50/50 mix. The minor differences in current leaf litter N content and δ15N between alder and Douglas-fir, coupled with declining growth in red alder, suggests the plateau or declining trend in alder tree-ring δ15N could coincide with lower N2-fixation rates, potentially by loss in alder vigor at canopy closure, or down-regulation via nitrate availability.
Identification of Clinically Significant Cytokine Signature Clusters in Patients With Septic Shock
Authors: Zhao Jack O. , Patel Bhakti K. , Krishack Paulette , Stutz Matthew R. , Pearson Steven D. , Lin Julie , Lecompte-Osorio Paola A. , Dugan Karen C. , Kim Seoyoen , Gras Nicole , Pohlman Anne , Kress John P. , Hall Jesse B. , Sperling Anne I. , Adegunsoye Ayodeji , Verhoef Philip A. , Wolfe Krysta S.
Published: September 2023

OBJECTIVES:

To identify cytokine signature clusters in patients with septic shock.

DESIGN:

Prospective observational cohort study.

SETTING:

Single academic center in the United States.

PATIENTS:

Adult (≥ 18 yr old) patients admitted to the medical ICU with septic shock requiring vasoactive medication support.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

One hundred fourteen patients with septic shock completed cytokine measurement at time of enrollment (t1) and 24 hours later (t2). Unsupervised random forest analysis of the change in cytokines over time, defined as delta (t2–t1), identified three clusters with distinct cytokine profiles. Patients in cluster 1 had the lowest initial levels of circulating cytokines that decreased over time. Patients in cluster 2 and cluster 3 had higher initial levels that decreased over time in cluster 2 and increased in cluster 3. Patients in clusters 2 and 3 had higher mortality compared with cluster 1 (clusters 1–3: 11% vs 31%; odds ratio [OR], 3.56 [1.10–14.23] vs 54% OR, 9.23 [2.89–37.22]). Cluster 3 was independently associated with in-hospital mortality (hazard ratio, 5.24; p = 0.005) in multivariable analysis. There were no significant differences in initial clinical severity scoring or steroid use between the clusters. Analysis of either t1 or t2 cytokine measurements alone or in combination did not reveal clusters with clear clinical significance.

CONCLUSIONS:

Longitudinal measurement of cytokine profiles at initiation of vasoactive medications and 24 hours later revealed three distinct cytokine signature clusters that correlated with clinical outcomes.
Experience With the Crescent• Right Atrial Jugular Dual Lumen Catheter for Pediatric Venovenous Extracorporeal Membrane Oxygenation: A Case Series
Authors: Walczak Ashley B. , Bigelow Amee M. , Schneider Brian , Deitemyer Matthew , Duffy Vicky , Lloyd Eric A. , Frazier W. Joshua , Seabrook Ruth B. , Halaweish Ihab F. , McConnell Patrick I.
Published: September 2023

The Crescent dual lumen right atrial (RA) cannula has recently been introduced for the support of pediatric patients in need of venovenous extracorporeal membrane oxygenation (VV ECMO) support. We present the first pediatric case series illustrating utility of the Crescent RA cannula in the pediatric patient population at a single institution over a 10 month period. From December 2021 to August 2022, six pediatric patients were adequately supported on seven VV ECMO runs at our institution with the Crescent RA cannula. ECMO cannulation, circuit design, anticoagulation management, ECMO circuit pressures, flow rates, and recirculation were similar to our standard of care for VV ECMO. The Crescent RA cannula can be used safely and effectively to provide adequate support for pediatric patients requiring VV ECMO.
Predictors of manual dexterity at 3 and 6 months after stroke: integration of clinical, neurophysiological, and neuroimaging factors
Authors: Jeong Eui Jin , Kang Mun Jeong , Lee Sekwang , Hwang Yeji , Park Ju Seob , Kim Ki Min , Pyun Sung-Bom
Published: September 2023

This retrospective study aimed to predict dexterity at 3 and 6 months post-stroke by integrating clinical, neurophysiological, and neuroimaging factors. We included 126 patients with first-ever, unilateral, and supratentorial stroke. Demographic, stroke characteristics, and initial clinical assessment variables [Mini-mental state examination and Fugl–Meyer Assessment Upper Extremity (FMA-UE)] were evaluated 2 weeks after stroke. Dexterity, measured using the Manual Function Test (MFT) hand subscore, was the primary outcome. The neurophysiological variables, upper limb somatosensory evoked potential (SEP) and motor evoked potential (MEP), were assessed 2 weeks post-stroke. The neuroimaging variable, fractional anisotropy (FA) of the corticospinal tract (CST), was assessed 3 weeks post-stroke. Multiple regression analysis revealed significant predictors for improved dexterity at 3 and 6 months post-stroke, including younger age, higher FMA-UE score, presence of waveforms in the SEP and MEP, and higher FA values in the CST (adjusted R2 = 0.776, P < 0.001 at 3 months; adjusted R2 = 0.668, P < 0.001 at 6 months; where MEP, SEP, and FA accounted together for an additional 0.079 and 0.166 of variance beyond age and FMA-UE, respectively). Subgroup analysis was conducted by categorizing the participants based on their initial hand function: those with no hand function (MFT hand subscore = 0) (N = 60) and those with a score >0 (N = 51). Initial FMA-UE was a primary predictive factor regardless of the time point or initial severity, whereas the presence of MEP was a significant predictor only in the group with no initial hand dexterity.