bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling the green dialogue: advancements in omics technologies for deciphering plant–microbe interactions in soil
Authors: Bhimani Priyanka , Mahavar Parul , Rajguru Bhumi , Bhatt Vaibhav D. , Nathani Neelam M. , Shri Manju 
Published: June 2024

AbstractThe complex interactions that exist between soil bacteria and plants have a significant impact on agricultural sustainability. These relationships, which can be pathogenic or symbiotic, are essential to comprehending and improving the health and productivity of plants. It has not been possible to fully understand the intricacies of these relationships using traditional methodologies. But the development of multi-omics technologies—genomics, transcriptomics, proteomics, and metabolomics—along with next-generation sequencing has completely changed our capacity to analyze and comprehend the dynamics between plants and microbes. With an emphasis on the use of various omics techniques, this brief overview investigates the complex mechanisms governing the interactions between microorganisms and plants. Researchers can create detailed interaction networks and identify regulatory pathways by combining multi-omics data. These revelations shed important light on the interactions, symbiosis, and disease that occur between microorganisms and plants. In the end, understanding these complex interactions has a great deal of potential to advance sustainable agricultural methods and guarantee global food security in the face of environmental difficulties.
Constraints and Drivers of Dissolved Fluxes of Pyrogenic Carbon in Soil and Freshwater Systems: A Global Review and Meta‐Analysis
Authors: Abney R. B. , Barnes M. E. , Moss A. , Santos F. 
Published: June 2024

AbstractPyrogenic carbon (PyC) is a significant component of the global soil carbon pool due to its longer environmental persistence than other soil organic matter components. Despite PyC's persistence in soil, recent work has indicated that it is susceptible to loss processes such as mineralization and leaching, with the significance and magnitude of these largely unknown at the hillslope and watershed scales. We present a review of the work concerning dissolved PyC transport in soil and freshwater. Our analysis found that the primary environmental controls on dissolved PyC (dPyC) transport are the formation conditions and quality of the PyC itself, with longer and higher temperature charring conditions leading to less transport of dPyC. While correlations between dPyC and dissolved organic carbon in rivers and other pools are frequently reported, the slope of these correlations was pool‐dependent (i.e., soil‐water, precipitation, lakes, streams, rivers), suggesting site‐specific environmental controls. However, the lack of consistency in analytical techniques and sample preparation remains a major challenge to quantifying environmental controls on dPyC fluxes. We propose that future research should focus on the following: (a) consistency in methodological approaches, (b) more quantitative measures of dPyC in pools and fluxes from soils to streams, (c) turnover times of dPyC in soils and aquatic systems, and (d) improved understanding of how mechanisms controlling the fate of dPyC in dynamic post‐fire landscapes interact. With more refined quantitative information about the controls on dPyC transport at the hillslope and landscape scale, we can increase the accuracy and utility of global carbon models.
Mitochondrial metabolic reprogramming in diabetic kidney disease
Authors: Fan Xiaoting , Yang Meilin , Lang Yating , Lu Shangwei , Kong Zhijuan , Gao Ying , Shen Ning , Zhang Dongdong , Lv Zhimei 
Published: June 2024

AbstractDiabetic kidney disease, known as a glomerular disease, arises from a metabolic disorder impairing renal cell function. Mitochondria, crucial organelles, play a key role in substance metabolism via oxidative phosphorylation to generate ATP. Cells undergo metabolic reprogramming as a compensatory mechanism to fulfill energy needs for survival and growth, attracting scholarly attention in recent years. Studies indicate that mitochondrial metabolic reprogramming significantly influences the pathophysiological progression of DKD. Alterations in kidney metabolism lead to abnormal expression of signaling molecules and activation of pathways, inducing oxidative stress-related cellular damage, inflammatory responses, apoptosis, and autophagy irregularities, culminating in renal fibrosis and insufficiency. This review delves into the impact of mitochondrial metabolic reprogramming on DKD pathogenesis, emphasizing the regulation of metabolic regulators and downstream signaling pathways. Therapeutic interventions targeting renal metabolic reprogramming can potentially delay DKD progression. The findings underscore the importance of focusing on metabolic reprogramming to develop safer and more effective therapeutic approaches.
VHL suppresses UBE3B-mediated breast tumor growth and metastasis
Authors: Wang Shuo , Li Huiyan , Liu Xiong , Yin Tingting , Li Tingru , Zheng Miaomiao , Liu Min , Meng Xiaoqian , Zhou Jun , Wang Yijie , Chen Yan 
Published: June 2024

AbstractProtein homeostasis is predominantly governed through post-translational modification (PTM). UBE3B, identified as an oncoprotein, exhibits elevated protein levels in breast cancer. However, the impact of PTM on UBE3B remains unexplored. In this study, we show that VHL is a bona fide E3 ligase for UBE3B. Mechanistically, VHL directly binds to UBE3B, facilitating its lysine 48 (K48)-linked polyubiquitination at K286 and K427 in a prolyl hydroxylase (PHD)-independent manner. Consequently, this promotes the proteasomal degradation of UBE3B. The K286/427R mutation of UBE3B dramatically abolishes the inhibitory effect of VHL on breast tumor growth and lung metastasis. Additionally, the protein levels of UBE3B and VHL exhibit a negative correlation in breast cancer tissues. These findings delineate an important layer of UBE3B regulation by VHL.
Projected loss of brown macroalgae and seagrasses with global environmental change
Authors: Manca Federica , Benedetti-Cecchi Lisandro , Bradshaw Corey J. A. , Cabeza Mar , Gustafsson Camilla , Norkko Alf M. , Roslin Tomas V. , Thomas David N. , White Lydia , Strona Giovanni 
Published: June 2024

AbstractAlthough many studies predict extensive future biodiversity loss and redistribution in the terrestrial realm, future changes in marine biodiversity remain relatively unexplored. In this work, we model global shifts in one of the most important marine functional groups—ecosystem-structuring macrophytes—and predict substantial end-of-century change. By modelling the future distribution of 207 brown macroalgae and seagrass species at high temporal and spatial resolution under different climate-change projections, we estimate that by 2100, local macrophyte diversity will decline by 3–4% on average, with 17 to 22% of localities losing at least 10% of their macrophyte species. The current range of macrophytes will be eroded by 5–6%, and highly suitable macrophyte habitat will be substantially reduced globally (78–96%). Global macrophyte habitat will shift among marine regions, with a high potential for expansion in polar regions.
Dynamic restructuring of nickel sulfides for electrocatalytic hydrogen evolution reaction
Authors: Ding Xingyu , Liu Da , Zhao Pengju , Chen Xing , Wang Hongxia , Oropeza Freddy E. , Gorni Giulio , Barawi Mariam , García-Tecedor Miguel , de la Peña O’Shea Víctor A. , Hofmann Jan P. , Li Jianfeng , Kim Jongkyoung , Cho Seungho , Wu Renbing , Zhang Kelvin H. L. 
Published: June 2024

AbstractTransition metal chalcogenides have been identified as low-cost and efficient electrocatalysts to promote the hydrogen evolution reaction in alkaline media. However, the identification of active sites and the underlying catalytic mechanism remain elusive. In this work, we employ operando X-ray absorption spectroscopy and near-ambient pressure X-ray photoelectron spectroscopy to elucidate that NiS undergoes an in-situ phase transition to an intimately mixed phase of Ni3S2 and NiO, generating highly active synergistic dual sites at the Ni3S2/NiO interface. The interfacial Ni is the active site for water dissociation and OH* adsorption while the interfacial S acts as the active site for H* adsorption and H2 evolution. Accordingly, the in-situ formation of Ni3S2/NiO interfaces enables NiS electrocatalysts to achieve an overpotential of only 95 ± 8 mV at a current density of 10 mA cm−2. Our work highlighted that the chemistry of transition metal chalcogenides is highly dynamic, and a careful control of the working conditions may lead to the in-situ formation of catalytic species that boost their catalytic performance.
Environmental versus phylogenetic controls on leaf nitrogen and phosphorous concentrations in vascular plants
Authors: Tian Di , Yan Zhengbing , Schmid Bernhard , Kattge Jens , Fang Jingyun , Stocker Benjamin D. 
Published: June 2024

AbstractGlobal patterns of leaf nitrogen (N) and phosphorus (P) stoichiometry have been interpreted as reflecting phenotypic plasticity in response to the environment, or as an overriding effect of the distribution of species growing in their biogeochemical niches. Here, we balance these contrasting views. We compile a global dataset of 36,413 paired observations of leaf N and P concentrations, taxonomy and 45 environmental covariates, covering 7,549 sites and 3,700 species, to investigate how species identity and environmental variables control variations in mass-based leaf N and P concentrations, and the N:P ratio. We find within-species variation contributes around half of the total variation, with 29%, 31%, and 22% of leaf N, P, and N:P variation, respectively, explained by environmental variables. Within-species plasticity along environmental gradients varies across species and is highest for leaf N:P and lowest for leaf N. We identified effects of environmental variables on within-species variation using random forest models, whereas effects were largely missed by widely used linear mixed-effect models. Our analysis demonstrates a substantial influence of the environment in driving plastic responses of leaf N, P, and N:P within species, which challenges reports of a fixed biogeochemical niche and the overriding importance of species distributions in shaping global patterns of leaf N and P.
Unravelling the operation of organic artificial neurons for neuromorphic bioelectronics
Authors: Belleri Pietro , Pons i Tarrés Judith , McCulloch Iain , Blom Paul W. M. , Kovács-Vajna Zsolt M. , Gkoupidenis Paschalis , Torricelli Fabrizio 
Published: June 2024

AbstractOrganic artificial neurons operating in liquid environments are crucial components in neuromorphic bioelectronics. However, the current understanding of these neurons is limited, hindering their rational design and development for realistic neuronal emulation in biological settings. Here we combine experiments, numerical non-linear simulations, and analytical tools to unravel the operation of organic artificial neurons. This comprehensive approach elucidates a broad spectrum of biorealistic behaviors, including firing properties, excitability, wetware operation, and biohybrid integration. The non-linear simulations are grounded in a physics-based framework, accounting for ion type and ion concentration in the electrolytic medium, organic mixed ionic-electronic parameters, and biomembrane features. The derived analytical expressions link the neurons spiking features with material and physical parameters, bridging closer the domains of artificial neurons and neuroscience. This work provides streamlined and transferable guidelines for the design, development, engineering, and optimization of organic artificial neurons, advancing next generation neuronal networks, neuromorphic electronics, and bioelectronics.
Re-thinking all-cause COVID-19 hospitalizations as a surrogate measure for severe illness in observational surveillance studies
Authors: Kelly J. Daniel , Leonard Samuel , Boscardin W. John , Hoggatt Katherine J. , Lum Emily N. , Austin Charles C. , Byers Amy L. , Tien Phyllis C. , Bravata Dawn M. , Keyhani Salomeh 
Published: June 2024

AbstractAll-cause COVID-19 hospitalization ≤ 30 days of infection is a common outcome for severe illness in observational/surveillance studies. Milder COVID-19 disease and COVID-19-specific measurements calls for an evaluation of this endpoint. This was a descriptive, retrospective cohort study of adults ≥ 18 who were established in primary care at Veteran Health Administration (VHA) facilities. The outcome was hospitalization within 30 days of a laboratory-confirmed, symptomatic SARS-CoV-2 infection. Between December 15, 2021 and May 1, 2022, a simple random sample of all VA facilities, excluding Puerto Rico or Philippines, was drawn to identify these hospitalized cases and determine whether hospitalization was due to COVID-19-specific causes. A chart review was conducted to record the inpatient clinical team’s diagnosis and whether the inpatient team classified the diagnosis as COVID-19 related or not. These data were used to classify hospitalizations as either due to COVID-19-specific causes (direct manifestations of SARS-CoV-2 infection) or non-COVID-19-specific hospitalizations (incidental SARS-CoV-2 infection), A simple random sample of 9966 (12.3%) all-cause hospitalizations (95% CI: 12.1%, 12.5%) was used to select 300 representative patients. Of these, 226/300 (75.3%) were determined to be COVID-19-specific. COVID-19 pneumonia was most common (147/226, 65.0%). The highest proportion of COVID-19-specific hospitalizations occurred among unvaccinated (85.0%), followed by vaccinated but not boosted (73.7%) and boosted (59.4%) (p < 0.001). The proportion of non-COVID-19-specific hospitalizations was higher in the later period (15–30 days: 55.0%) than the early (0–15 days: 22.5%) (p = 0.003). This study supports the outcome of COVID-19-specific hospitalization instead of all-cause hospitalization in observational studies. The earlier outcome period (0–15 days) was less susceptible to potential measurement bias.
Kit foxes demonstrate adaptive compromise characteristics under intraguild predation pressure by coyotes in the Great Basin desert
Authors: Pershyn Nadine A. , Gese Eric M. , Stuber Erica F. , Kluever Bryan M. 
Published: June 2024

AbstractCoyotes (Canis latrans) are believed to contribute to declining kit fox (Vulpes macrotis) numbers in the Great Basin desert through intraguild predation. Intraguild prey have been shown to exhibit adaptive compromise, whereby an animal increases selection for risky, but food-rich areas during times of food stress (i.e. winter). We evaluated the habitat selection of kit foxes in the Great Basin desert to elucidate if they demonstrated adaptive compromise as a method of coexisting with coyotes. We created 2nd order resource selection functions to analyze kit fox habitat selection associated with coyote relative probability of use (RPU), prey abundance, and type of soil substrate. In the summer, we found that kit fox selection for areas of relatively more abundant prey was not significant, and there was a small positive selection for coyote RPU. In the winter, we found a positive relationship between kit fox selection and prey abundance as well as a stronger selection for coyote RPU. These findings do follow the pattern of adaptive compromise. We also found kit foxes selected for silty and sandy soils, which are conducive to den construction, as they use dens seasonally for breeding but also year-round for multiple uses, including refugia from predators and extreme heat. Soil substrate appeared to be an important factor impacting kit fox habitat selection.
Comparative analysis of light storage in antirelaxation-coated and buffer-gas-filled alkali vapor cells
Authors: Đujić M. , Buhin D. , Šantić N. , Aumiler D. , Ban T. 
Published: June 2024

AbstractWe explore light storage in antirelaxation-coated and buffer-gas-filled alkali vapor cells, employing electromagnetically induced transparency (EIT) in warm rubidium vapor. We conduct a comparative study of light storage performance under identical experimental conditions for these two cell types. Using a buffer-gas-filled cell resulted in approximately a tenfold improvement in memory efficiency and storage time compared to antirelaxation-coated cells. Moreover, we demonstrate that memory efficiency can be further enhanced by choosing a near-resonant EIT $$\Lambda$$
Λ
-scheme over a resonant one. Our findings provide valuable insights for optimizing light storage, thereby contributing to the development of field-deployable quantum memories.
Paleoseismological evidence for segmentation of the Main Himalayan Thrust in the Darjeeling-Sikkim Himalaya
Authors: Brice Atul , Jayangondaperumal R. , Priyanka Rao Singh , Pandey Arjun , Mishra Rajeeb Lochan , Singh Ishwar , Sati Madhusudan , Kumar Pankaj , Dash Sandipta Prasad 
Published: June 2024

AbstractWhether the Main Himalayan Thrust can host a single surface-rupturing event in the Himalaya with a rupture length of > 700 km remains controversial. Previous paleoseismological studies in the Darjeeling-Sikkim Himalaya (DSH) suggested medieval surface-rupturing earthquakes, correlating them with the eleventh–thirteenth century events from Nepal and Bhutan and extending the coseismic rupture length > 700 km. Conversely, there is no rupture evidence of the 1714 Bhutan and 1934 Bihar–Nepal earthquakes in the DSH, resulting in a discrepancy in the rupture extent of the great earthquakes. Consequently, we conducted a paleoseismological investigation across a ~ 10 m-high fault scarp on the Himalayan Frontal Thrust at Chenga village, DSH, revealing a surface-faulting event during 1313–395 BCE. We suggest that the DSH is a 150 km-long independent segment bounded by a transverse ridge and fault and has a recurrence interval of ~ 949–1963 years, which is significantly larger than Nepal (~ 700–900 years) and Bhutan Himalaya (~ 339–761 years).
The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species
Authors: Burzyński Artur , Śmietanka Beata , Fernández-Pérez Jenyfer , Lubośny Marek 
Published: June 2024

AbstractBivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
On body and off body communication using a compact wideband and high gain wearable textile antenna
Authors: Sharma Deepti , Kumar Sachin , Tiwari Rakesh Nath , Choi Hyun Chul , Kim Kang Wook 
Published: June 2024

AbstractIn this paper, a compact low-profile dual-band wearable textile antenna is proposed for on-body and off-body communications. The presented antenna works efficiently in the 5G n79 frequency band (4.4 − 5 GHz) and the ISM band (5.725 − 5.875 GHz). The designed antenna has an ultra-wide impedance bandwidth of 2.01 GHz and peak realized gains of 10.5 dBi and 12 dBi at 4.5 GHz and 5.8 GHz, respectively. The antenna has a small footprint (π × 0.3λ02), which is inspired by circular fractal geometry. The performance of the presented wearable antenna is evaluated at various body parts, including the arm, wrist, and chest. The link margin is evaluated in the on-body and off-body communication scenarios, i.e., communication with the implantable antenna and the outside-body antenna, which is 80 dB and 65 dB at 4.5 GHz and 5.8 GHz, respectively. The 1 gm/10 gm specific absorption rate values at 4.5 GHz and 5.8 GHz are 0.12/0.098 and 0.11/0.082, respectively, which are significantly lower than the standard values, making the proposed antenna suitable for modern wearable applications.
Oxidative stress induced by hydrogen peroxide disrupts zebrafish visual development by altering apoptosis, antioxidant and estrogen related genes
Authors: Saputra Febriyansyah , Kishida Mitsuyo , Hu Shao-Yang 
Published: June 2024

AbstractHydrogen peroxide is considered deleterious molecule that cause cellular damage integrity and function. Its key redox signaling molecule in oxidative stress and exerts toxicity on a wide range of organisms. Thus, to understand whether oxidative stress alters visual development, zebrafish embryos were exposed to H2O2 at concentration of 0.02 to 62.5 mM for 7 days. Eye to body length ratio (EBR) and apoptosis in retina at 48 hpf, and optomotor response (OMR) at 7 dpf were all measured. To investigate whether hydrogen peroxide-induced effects were mediated by oxidative stress, embryos were co-incubated with the antioxidant, glutathione (GSH) at 50 μM. Results revealed that concentrations of H2O2 at or above 0.1 mM induced developmental toxicity, leading to increased mortality and hatching delay. Furthermore, exposure to 0.1 mM H2O2 decreased EBR at 48 hpf and impaired OMR visual behavior at 7 dpf. Additionally, exposure increased the area of apoptotic cells in the retina at 48 hpf. The addition of GSH reversed the effects of H2O2, suggesting the involvement of oxidative stress. H2O2 decreased the expression of eye development-related genes, pax6α and pax6β. The expression of apoptosis-related genes, tp53, casp3 and bax, significantly increased, while bcl2α expression decreased. Antioxidant-related genes sod1, cat and gpx1a showed decreased expression. Expression levels of estrogen receptors (ERs) (esr1, esr2α, and esr2β) and ovarian and brain aromatase genes (cyp19a1a and cyp19a1b, respectively) were also significantly reduced. Interestingly, co-incubation of GSH effectivity reversed the impact of H2O2 on most parameters. Overall, these results demonstrate that H2O2 induces adverse effects on visual development via oxidative stress, which leads to alter apoptosis, diminished antioxidant defenses and reduced estrogen production.
Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline
Authors: Norton-Baker Brenna , Denton Mackenzie C. R. , Murphy Natasha P. , Fram Benjamin , Lim Samuel , Erickson Erika , Gauthier Nicholas P. , Beckham Gregg T. 
Published: June 2024

AbstractAs genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.