bluuebunny/crossref_metadata_2025 huggingface dataset:
Distant relatives of a eukaryotic cell-specific toxin family evolved a complement-like mechanism to kill bacteria
Authors: Abrahamsen Hunter L. , Sanford Tristan C. , Collamore Casie E. , Johnstone Bronte A. , Coyne Michael J. , García-Bayona Leonor , Christie Michelle P. , Evans Jordan C. , Farrand Allison J. , Flores Katia , Morton Craig J. , Parker Michael W. , Comstock Laurie E. , Tweten Rodney K.
Published: June 2024

Cholesterol-dependent cytolysins (CDCs) comprise a large family of pore-forming toxins produced by Gram-positive bacteria, which are used to attack eukaryotic cells. Here, we functionally characterize a family of 2-component CDC-like (CDCL) toxins produced by the Gram-negative Bacteroidota that form pores by a mechanism only described for the mammalian complement membrane attack complex (MAC). We further show that the Bacteroides CDCLs are not eukaryotic cell toxins like the CDCs, but instead bind to and are proteolytically activated on the surface of closely related species, resulting in pore formation and cell death. The CDCL-producing Bacteroides is protected from the effects of its own CDCL by the presence of a surface lipoprotein that blocks CDCL pore formation. These studies suggest a prevalent mode of bacterial antagonism by a family of two-component CDCLs that function like mammalian MAC and that are wide-spread in the gut microbiota of diverse human populations.
Mechanistic understanding of speciated oxide growth in high entropy alloys
Authors: Gwalani Bharat , Martin Andrew , Kautz Elizabeth , Guo Boyu , Lambeets S. V. , Olszta Matthew , Battu Anil Krishna , Malakar Aniruddha , Yang Feipeng , Guo Jinghua , Thevuthasan Suntharampillai , Li Ruipeng , Amassian Aram , Thuo Martin , Devaraj Arun
Published: June 2024

Complex multi-element alloys are gaining prominence for structural applications, supplementing steels, and superalloys. Understanding the impact of each element on alloy surfaces due to oxidation is vital in maintaining material integrity. This study investigates oxidation mechanisms in these alloys using a model five-element equiatomic CoCrFeNiMn alloy, in a controlled oxygen environment. The oxidation-induced surface changes correlate with each element’s interactive tendencies with the environment, guided by thermodynamics. Initial oxidation stages follow atomic size and redox potential, with the latter becoming dominant over time, causing composition inversion. The study employs in-situ atom probe tomography, transmission electron microscopy, and X-ray absorption near-edge structure techniques to elucidate the oxidation process and surface oxide structure evolution. Our findings deconvolute the mechanism for compositional and structural changes in the oxide film and will pave the way for a predictive design of complex alloys with improved resistance to oxidation under extreme conditions.
Single-gold etching at the hypercarbon atom of C-centred hexagold(I) clusters protected by chiral N-heterocyclic carbenes
Authors: Pei Xiao-Li , Zhao Pei , Ube Hitoshi , Lei Zhen , Ehara Masahiro , Shionoya Mitsuhiko
Published: June 2024

Chemical etching of nano-sized metal clusters at the atomic level has a high potential for creating metal number-specific structures and functions that are difficult to achieve with bottom-up synthesis methods. In particular, precisely etching metal atoms one by one from nonmetallic element-centred metal clusters and elucidating the relationship between their well-defined structures, and chemical and physical properties will facilitate future materials design for metal clusters. Here we report the single-gold etching at a hypercarbon centre in gold(I) clusters. Specifically, C-centred hexagold(I) clusters protected by chiral N-heterocyclic carbenes are etched with bisphosphine to yield C-centred pentagold(I) (CAuI5) clusters. The CAuI5 clusters exhibit an unusually large bathochromic shift in luminescence, which is reproduced theoretically. The etching mechanism is experimentally and theoretically suggested to be a tandem dissociation-association-elimination pathway. Furthermore, the vacant site of the central carbon of the CAuI5 cluster can accommodate AuCl, allowing for post-functionalisation of the C-centred gold(I) clusters.
CHIT1 at diagnosis predicts faster disability progression and reflects early microglial activation in multiple sclerosis
Authors: Beliën Jarne , Swinnen Stijn , D’hondt Robbe , Verdú de Juan Laia , Dedoncker Nina , Matthys Patrick , Bauer Jan , Vens Celine , Moylett Sinéad , Dubois Bénédicte
Published: June 2024

Multiple sclerosis (MS) is characterized by heterogeneity in disease course and prediction of long-term outcome remains a major challenge. Here, we investigate five myeloid markers – CHIT1, CHI3L1, sTREM2, GPNMB and CCL18 – in the cerebrospinal fluid (CSF) at diagnostic lumbar puncture in a longitudinal cohort of 192 MS patients. Through mixed-effects and machine learning models, we show that CHIT1 is a robust predictor for faster disability progression. Integrative analysis of 11 CSF and 26 central nervous system (CNS) parenchyma single-cell/nucleus RNA sequencing samples reveals CHIT1 to be predominantly expressed by microglia located in active MS lesions and enriched for lipid metabolism pathways. Furthermore, we find CHIT1 expression to accompany the transition from a homeostatic towards a more activated, MS-associated cell state in microglia. Neuropathological evaluation in post-mortem tissue from 12 MS patients confirms CHIT1 production by lipid-laden phagocytes in actively demyelinating lesions, already in early disease stages. Altogether, we provide a rationale for CHIT1 as an early biomarker for faster disability progression in MS.
Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution
Authors: Zhang Xiao , Blaxter Mark , Wood Jonathan M. D. , Tracey Alan , McCarthy Shane , Thorpe Peter , Rayner Jack G. , Zhang Shangzhe , Sikkink Kirstin L. , Balenger Susan L. , Bailey Nathan W.
Published: June 2024

Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population’s transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how ‘adaptation begets adaptation’; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation.
Towards extending the aircraft flight envelope by mitigating transonic airfoil buffet
Authors: Lagemann Esther , Brunton Steven L. , Schröder Wolfgang , Lagemann Christian
Published: June 2024

In the age of globalization, commercial aviation plays a central role in maintaining our international connectivity by providing fast air transport services for passengers and freight. However, the upper limit of the aircraft flight envelope, i.e., its operational limit in the high-speed (transonic) regime, is usually fixed by the occurrence of transonic aeroelastic effects. These harmful structural vibrations are associated with an aerodynamic instability called transonic buffet. It refers to shock wave oscillations occurring on the aircraft wings, which induce unsteady aerodynamic loads acting on the wing structure. Since the structural response can cause severe structural damage endangering flight safety, the aviation industry is highly interested in suppressing transonic buffet to extend the flight envelope to higher aircraft speeds. In this contribution, we demonstrate experimentally that the application of porous trailing edges substantially attenuates the buffet phenomenon. Since porous trailing edges have the additional benefit of reducing acoustic aircraft emissions, they could prospectively provide faster air transport with reduced noise emissions.
Allostatic load as a predictor of postoperative complications in patients with breast cancer
Authors: Chen J. C. , Elsaid Mohamed I. , Handley Demond , Anderson Lisa , Andersen Barbara L. , Carson William E. , Beane Joal D. , Kim Alex , Skoracki Roman , Pawlik Timothy M. , Obeng-Gyasi Samilia
Published: June 2024

Allostatic load (AL) is a biological measure of cumulative exposure to socioenvironmental stressors (e.g., poverty). This study aims to examine the association between allostatic load (AL) and postoperative complications (POC) among patients with breast cancer. Females ages 18+ with stage I-III breast cancer who received surgical management between 01/01/2012-12/31/2020 were identified in the Ohio State Cancer registry. The composite AL measure included biomarkers from the cardiovascular, metabolic, immune, and renal systems. High AL was defined as composite scores greater than the cohort’s median (2.0). POC within 30 days of surgery were examined. Univariable and multivariable regression analysis examined the association between AL and POC. Among 4459 patients, 8.2% had POC. A higher percentage of patients with POC were unpartnered (POC 44.7% vs no POC 35.5%), government-insured (POC 48.2% vs no POC 38.3%) and had multiple comorbidities (POC 32% vs no POC 20%). Patients who developed POC were more likely to have undergone sentinel lymph node biopsy followed by axillary lymph node dissection (POC 51.2% vs no POC 44.6%). High AL was associated with 29% higher odds of POC (aOR 1.29, 95% CI 1.01–1.63). A one-point increase in AL was associated with 8% higher odds of POC (aOR 1.08, 95% CI 1.02-1.16) and a quartile increase in AL was associated with 13% increased odds of POC (aOR 1.13, 95% CI 1.01–1.26). Among patients undergoing breast cancer surgery, increased exposure to adverse socioenvironmental stressors, operationalized as AL, was associated with higher odds of postoperative complications.
Gaps and opportunities in modelling human influence on species distributions in the Anthropocene
Authors: Frans Veronica F. , Liu Jianguo
Published: June 2024

Understanding species distributions is a global priority for mitigating environmental pressures from human activities. Ample studies have identified key environmental (climate and habitat) predictors and the spatial scales at which they influence species distributions. However, regarding human influence, such understandings are largely lacking. Here, to advance knowledge concerning human influence on species distributions, we systematically reviewed species distribution modelling (SDM) articles and assessed current modelling efforts. We searched 12,854 articles and found only 1,429 articles using human predictors within SDMs. Collectively, these studies of >58,000 species used 2,307 unique human predictors, suggesting that in contrast to environmental predictors, there is no ‘rule of thumb’ for human predictor selection in SDMs. The number of human predictors used across studies also varied (usually one to four per study). Moreover, nearly half the articles projecting to future climates held human predictors constant over time, risking false optimism about the effects of human activities compared with climate change. Advances in using human predictors in SDMs are paramount for accurately informing and advancing policy, conservation, management and ecology. We show considerable gaps in including human predictors to understand current and future species distributions in the Anthropocene, opening opportunities for new inquiries. We pose 15 questions to advance ecological theory, methods and real-world applications.
Ancient genomes reveal insights into ritual life at Chichén Itzá
Authors: Barquera Rodrigo , Del Castillo-Chávez Oana , Nägele Kathrin , Pérez-Ramallo Patxi , Hernández-Zaragoza Diana Iraíz , Szolek András , Rohrlach Adam Benjamin , Librado Pablo , Childebayeva Ainash , Bianco Raffaela Angelina , Penman Bridget S. , Acuña-Alonzo Victor , Lucas Mary , Lara-Riegos Julio César , Moo-Mezeta María Ermila , Torres-Romero Julio César , Roberts Patrick , Kohlbacher Oliver , Warinner Christina , Krause Johannes
Published: June 2024

The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (ad 600–1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1–4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population’s genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around ad 500–900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
Inner core backtracking by seismic waveform change reversals
Authors: Wang Wei , Vidale John E. , Pang Guanning , Koper Keith D. , Wang Ruoyan
Published: June 2024

The solid inner core, suspended within the liquid outer core and anchored by gravity, has been inferred to rotate relative to the surface of Earth or change over years to decades based on changes in seismograms from repeating earthquakes and explosions1,2. It has a rich inner structure3–6 and influences the pattern of outer core convection and therefore Earth’s magnetic field. Here we compile 143 distinct pairs of repeating earthquakes, many within 16 multiplets, built from 121 earthquakes between 1991 and 2023 in the South Sandwich Islands. We analyse their inner-core-penetrating PKIKP waves recorded on the medium-aperture arrays in northern North America. We document that many multiplets exhibit waveforms that change and then revert at later times to match earlier events. The matching waveforms reveal times at which the inner core re-occupies the same position, relative to the mantle, as it did at some time in the past. The pattern of matches, together with previous studies, demonstrates that the inner core gradually super-rotated from 2003 to 2008, and then from 2008 to 2023 sub-rotated two to three times more slowly back through the same path. These matches enable precise and unambiguous tracking of inner core progression and regression. The resolved different rates of forward and backward motion suggest that new models will be necessary for the dynamics between the inner core, outer core and mantle.
Global variability in atmospheric new particle formation mechanisms
Authors: Zhao Bin , Donahue Neil M. , Zhang Kai , Mao Lizhuo , Shrivastava Manish , Ma Po-Lun , Shen Jiewen , Wang Shuxiao , Sun Jian , Gordon Hamish , Tang Shuaiqi , Fast Jerome , Wang Mingyi , Gao Yang , Yan Chao , Singh Balwinder , Li Zeqi , Huang Lyuyin , Lou Sijia , Lin Guangxing , Wang Hailong , Jiang Jingkun , Ding Aijun , Nie Wei , Qi Ximeng , Chi Xuguang , Wang Lin
Published: June 2024

A key challenge in aerosol pollution studies and climate change assessment is to understand how atmospheric aerosol particles are initially formed1,2. Although new particle formation (NPF) mechanisms have been described at specific sites3–6, in most regions, such mechanisms remain uncertain to a large extent because of the limited ability of atmospheric models to simulate critical NPF processes1,7. Here we synthesize molecular-level experiments to develop comprehensive representations of 11 NPF mechanisms and the complex chemical transformation of precursor gases in a fully coupled global climate model. Combined simulations and observations show that the dominant NPF mechanisms are distinct worldwide and vary with region and altitude. Previously neglected or underrepresented mechanisms involving organics, amines, iodine oxoacids and HNO3 probably dominate NPF in most regions with high concentrations of aerosols or large aerosol radiative forcing; such regions include oceanic and human-polluted continental boundary layers, as well as the upper troposphere over rainforests and Asian monsoon regions. These underrepresented mechanisms also play notable roles in other areas, such as the upper troposphere of the Pacific and Atlantic oceans. Accordingly, NPF accounts for different fractions (10–80%) of the nuclei on which cloud forms at 0.5% supersaturation over various regions in the lower troposphere. The comprehensive simulation of global NPF mechanisms can help improve estimation and source attribution of the climate effects of aerosols.
Mental navigation in the primate entorhinal cortex
Authors: Neupane Sujaya , Fiete Ila , Jazayeri Mehrdad
Published: June 2024

A cognitive map is a suitably structured representation that enables novel computations using previous experience; for example, planning a new route in a familiar space1. Work in mammals has found direct evidence for such representations in the presence of exogenous sensory inputs in both spatial2,3 and non-spatial domains4–10. Here we tested a foundational postulate of the original cognitive map theory1,11: that cognitive maps support endogenous computations without external input. We recorded from the entorhinal cortex of monkeys in a mental navigation task that required the monkeys to use a joystick to produce one-dimensional vectors between pairs of visual landmarks without seeing the intermediate landmarks. The ability of the monkeys to perform the task and generalize to new pairs indicated that they relied on a structured representation of the landmarks. Task-modulated neurons exhibited periodicity and ramping that matched the temporal structure of the landmarks and showed signatures of continuous attractor networks12,13. A continuous attractor network model of path integration14 augmented with a Hebbian-like learning mechanism provided an explanation of how the system could endogenously recall landmarks. The model also made an unexpected prediction that endogenous landmarks transiently slow path integration, reset the dynamics and thereby reduce variability. This prediction was borne out in a reanalysis of firing rate variability and behaviour. Our findings link the structured patterns of activity in the entorhinal cortex to the endogenous recruitment of a cognitive map during mental navigation.
Oligomerization-mediated autoinhibition and cofactor binding of a plant NLR
Authors: Ma Shoucai , An Chunpeng , Lawson Aaron W. , Cao Yu , Sun Yue , Tan Eddie Yong Jun , Pan Jinheng , Jirschitzka Jan , Kümmel Florian , Mukhi Nitika , Han Zhifu , Feng Shan , Wu Bin , Schulze-Lefert Paul , Chai Jijie
Published: June 2024

Nucleotide-binding leucine-rich repeat (NLR) proteins play a pivotal role in plant immunity by recognizing pathogen effectors1,2. Maintaining a balanced immune response is crucial, as excessive NLR expression can lead to unintended autoimmunity3,4. Unlike most NLRs, the plant NLR required for cell death 2 (NRC2) belongs to a small NLR group characterized by constitutively high expression without self-activation5. The mechanisms underlying NRC2 autoinhibition and activation are not yet understood. Here we show that Solanum lycopersicum (tomato) NRC2 (SlNRC2) forms dimers and tetramers and higher-order oligomers at elevated concentrations. Cryo-electron microscopy shows an inactive conformation of SlNRC2 in these oligomers. Dimerization and oligomerization not only stabilize the inactive state but also sequester SlNRC2 from assembling into an active form. Mutations at the dimeric or interdimeric interfaces enhance pathogen-induced cell death and immunity in Nicotianabenthamiana. The cryo-electron microscopy structures unexpectedly show inositol hexakisphosphate (IP6) or pentakisphosphate (IP5) bound to the inner surface of the C-terminal leucine-rich repeat domain of SlNRC2, as confirmed by mass spectrometry. Mutations at the inositol phosphate-binding site impair inositol phosphate binding of SlNRC2 and pathogen-induced SlNRC2-mediated cell death in N. benthamiana. Our study indicates a negative regulatory mechanism of NLR activation and suggests inositol phosphates as cofactors of NRCs.
Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression
Authors: Lobo Vivian , Shcherbinina Evgeniia , Westholm Jakub O. , Nowak Iwona , Huang Hsiang-Chi , Angeletti Davide , Anastasakis Dimitrios G. , Sarshad Aishe A.
Published: June 2024

In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.
Microbial imbalance in Chinese children with diarrhea or constipation
Authors: Ren Jing , Ren Yi , Mu Yu , Zhang Lanying , Chen Binghan , Li Sisi , Fang Qinyi , Zhang Zhiming , Zhang Kejian , Li Sabrina , Liu Wei , Cui Yutao , Li Xu
Published: June 2024

Diarrhea and constipation are common health concerns in children. Numerous studies have identified strong association between gut microbiota and digestive-related diseases. But little is known about the gut microbiota that simultaneously affects both diarrhea and constipation or their potential regulatory mechanisms. Stool samples from 618 children (66 diarrhea, 138 constipation, 414 healthy controls) aged 0–3 years were collected to investigate gut microbiota changes using 16S rRNA sequencing. Compared with healthy, children with diarrhea exhibited a significant decrease in microbial diversity, while those with constipation showed a marked increase (p < 0.05). Significantly, our results firstly Ruminococcus increased in constipation (p = 0.03) and decreased in diarrhea (p < 0.01) compared to healthy controls. Pathway analysis revealed that Ruminococcus highly involved in the regulation of five common pathways (membrane transport, nervous system, energy metabolism, signal transduction and endocrine system pathways) between diarrhea and constipation, suggesting a potential shared regulatory mechanism. Our finding firstly reveals one core microorganisms that may affect the steady balance of the gut in children with diarrhea or constipation, providing an important reference for potential diagnosis and treatment of constipation and diarrhea.
Solitonic solutions and stability analysis of Benjamin Bona Mahony Burger equation using two versatile techniques
Authors: Hussain Ejaz , Shah Syed Asif Ali , Bariq Abdul , Li Zhao , Ahmad Muhammad Riaz , Ragab Adham E. , Az-Zo’bi Emad A.
Published: June 2024

This study aims to explore the precise resolution of the nonlinear Benjamin Bona Mahony Burgers (BBMB) equation, which finds application in a variety of nonlinear scientific disciplines including fluid dynamics, shock generation, wave transmission, and soliton theory. Within this paper, we employ two versatile methodologies, specifically the extended $$\exp (-\Psi (\chi ))$$

exp
(
-
Ψ
(
χ
)
)

expansion technique and the novel Kudryashov method, to identify the exact soliton solutions of the nonlinear BBMB equation. The solutions we discovered involve trigonometric functions, hyperbolic functions, and rational functions. The uniqueness of this research lies in uncovering the bright soliton, kink wave solution, and periodic wave solution, and conducting stability analysis. Furthermore, the solutions’ graphical characteristics were explored through the utilization of the mathematical software Maple 2022 (https://maplesoft.com/downloads/selectplatform.aspx?hash=61ab59890f2313b2241fde3423fd975e). The system’s physical interpretation is defined through various types of graphs, including contour graphs, 3D-surface graphs, and line graphs, which use appropriate parameter values. These recommended techniques hold significant importance and are applicable in diverse nonlinear evolutionary equations found in the field of nonlinear sciences for illustrating nonlinear physical models.
Haliskia peterseni, a new anhanguerian pterosaur from the late Early Cretaceous of Australia
Authors: Pentland Adele H. , Poropat Stephen F. , Duncan Ruairidh J. , Kellner Alexander W. A. , Bantim Renan A. M. , Bevitt Joseph J. , Tait Alan M. , Grice Kliti
Published: June 2024

Pterosaur remains have been reported from every continent; however, pterosaur skeletons remain rare. A new pterosaur is presented here,Haliskia petersenigen. et sp. nov., constituting the most complete specimen from Australia from the upper Albian Toolebuc Formation of the Eromanga Basin (Queensland, Australia). A combination of features, including the presence of a premaxillary crest and curved teeth, and the morphology of the scapulocoracoid, support its referral to Anhangueria.Haliskiacan be distinguished from all other anhanguerian pterosaurs based on two dental characters: the 4th and 5th tooth pairs are smaller than the 3rd and 6th, and the 2nd and 5th alveoli are smaller than 3–4 and 6–8. Moreover, the hyoid is 70% the total length of the mandible. The phylogenetic analyses presented here placeHaliskiawithin Anhangueria. In one analysis,HaliskiaandFerrodracoare resolved as sister taxa, withTropeognathus mesembrinussister to that clade. The other resolvesHaliskia,MythungaandFerrodracoin a polytomy within Tropeognathinae. The new Australian pterosaur attests to the success of Anhangueria during the latest Early Cretaceous and suggests that the Australian forms were more taxonomically diverse and palaeobiogeographically complex than previously recognized.
MPXV DNA kinetics in bloodstream and other body fluids samples
Authors: Meschi Silvia , Colavita Francesca , Carletti Fabrizio , Mazzotta Valentina , Matusali Giulia , Specchiarello Eliana , Ascoli Bartoli Tommaso , Mondi Annalisa , Minosse Claudia , Giancola Maria Letizia , Pinnetti Carmela , Valli Maria Beatrice , Lapa Daniele , Mizzoni Klizia , Sullivan David J. , Ou Jiangda , Focosi Daniele , Girardi Enrico , Nicastri Emanuele , Antinori Andrea , Maggi Fabrizio
Published: June 2024

Since spring 2022, the global epidemiology of the monkeypox virus (MPXV) has changed. The unprecedented increase of human clade II MPXV cases worldwide heightened concerns about this emerging zoonotic disease. We analysed the positivity rates, viral loads, infectiousness, and persistence of MPXV DNA for up to 4 months in several biological samples from 89 MPXV-confirmed cases. Our data showed that viral loads and positivity rates were higher during the first two weeks of symptoms for all sample types. Amongst no-skin-samples, respiratory specimens showed higher MPXV DNA levels and median time until viral clearance, suggesting their usefulness in supporting MPXV diagnosis, investigating asymptomatic patients, and monitoring viral shedding. Infectious virus was cultured from respiratory samples, semen, and stools, with high viral loads and collected within the first 10 days. Notably, only one saliva and one semen were found positive for viral DNA after 71 and 31 days from symptoms, respectively. The focus on bloodstream samples showed the best testing sensitivity in plasma, reporting the overall highest MPXV DNA detection rate and viral loads during the 3-week follow-up as compared to serum and whole-blood. The data here presented can be useful for MPXV diagnostics and a better understanding of the potential alternative routes of its onward transmission.
Inclusive study of peanut shells derived activated carbon as an adsorbent for removal of lead and methylene blue from water
Authors: Hashem Heba M. , El-Maghrabey Mahmoud , El-Shaheny Rania
Published: June 2024

Green and efficient agro-waste-based activated carbon has been prepared utilizing peanut shells for adsorptive elimination of an industrial dye, methylene blue, and lead from polluted water. The carbonaceous biomass obtained from peanut shells was chemically activated using either NaOH, ZnCl2, or steam and characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, and N2 adsorption and desorption studies. The adsorption process was optimal for methylene blue at alkaline pH, while pH 4.5 was optimal for Pb (II) adsorption. The adsorption takes place through pseudo-second-order kinetic, and the rate-governing step of the adsorption procedure are intraparticle diffusion and film diffusion. Furthermore, the thermodynamics of the adsorption process has been studied, and the obtained Gibbs free energy (ΔG°) values are negative (− 35.90 to − 43.59 kJ mol−1) indicating the spontaneous adsorption of the investigated pollutants on the prepared activated carbon. As per the correlation coefficient, the obtained results were best fit by the Langmuir isotherm with maximum adsorption capacity of 303.03 mg g−1 for methylene blue and 130.89 mg g−1 for Pb (II). The activated carbon successfully removed methylene blue and Pb (II) with %removal exceeding 95%. The mechanisms of interaction of Pb (II) with the activated carbon is a combination of electrostatic interaction and ion exchange, while methylene blue interacts with the activated carbon via π–π interaction, hydrogen bonds, and electrostatic interaction. Thus, the prepared activated carbon has been employed to decontaminate wastewater and groundwater samples. The developed agro-waste-based activated carbon is a promising, cost-efficient, green, and accessible tool for water remediation.
Unraveling the hepatic stellate cells mediated mechanisms in aging's influence on liver fibrosis
Authors: Wahid Reham M. , Hassan Nancy Husseiny , Samy Walaa , Abdelhadi Amina A. , Saadawy Sara F. , Elsayed Sherein F. , Seada Sara G. , Mohamed Sara Refaee Abdo
Published: June 2024

Aging enhances numerous processes that compromise homeostasis and pathophysiological processes. Among these, activated HSCs play a pivotal role in advancing liver fibrosis. This research delved into how aging impacts liver fibrosis mechanisms. The study involved 32 albino rats categorized into four groups: Group I (young controls), Group II (young with liver fibrosis), Group III (old controls), and Group IV (old with liver fibrosis). Various parameters including serum ALT, adiponectin, leptin, and cholesterol levels were evaluated. Histopathological analysis was performed, alongside assessments of TGF-β, FOXP3, and CD133 gene expressions. Markers of fibrosis and apoptosis were the highest in group IV. Adiponectin levels significantly decreased in Group IV compared to all other groups except Group II, while cholesterol levels were significantly higher in liver fibrosis groups than their respective control groups. Group III displayed high hepatic expression of desmin, α-SMA, GFAP and TGF- β and in contrast to Group I. Increased TGF-β and FOXP3 gene expressions were observed in Group IV relative to Group II, while CD133 gene expression decreased in Group IV compared to Group II. In conclusion, aging modulates immune responses, impairs regenerative capacities via HSC activation, and influences adipokine and cholesterol levels, elevating the susceptibility to liver fibrosis.
Investigating the potential of X chromosome shredding for mouse genetic biocontrol
Authors: Bunting Mark D. , Godahewa Gelshan I. , McPherson Nicole O. , Robertson Louise J. , Gierus Luke , Piltz Sandra G. , Edwards Owain , Tizard Mark , Thomas Paul Q.
Published: June 2024

CRISPR-Cas9 technology has facilitated development of strategies that can potentially provide more humane and effective methods to control invasive vertebrate species, such as mice. One promising strategy is X chromosome shredding which aims to bias offspring towards males, resulting in a gradual and unsustainable decline of females. This method has been explored in insects with encouraging results. Here, we investigated this strategy in Mus musculus by targeting repeat DNA sequences on the X chromosome with the aim of inducing sufficient DNA damage to specifically eliminate X chromosome-bearing sperm during gametogenesis. We tested three different guide RNAs (gRNAs) targeting different repeats on the X chromosome, together with three male germline-specific promoters for inducing Cas9 expression at different stages of spermatogenesis. A modest bias towards mature Y-bearing sperm was detected in some transgenic males, although this did not translate into significant male-biasing of offspring. Instead, cleavage of the X chromosome during meiosis typically resulted in a spermatogenic block, manifest as small testes volume, empty tubules, low sperm concentration, and sub/infertility. Our study highlights the importance of controlling the timing of CRISPR-Cas9 activity during mammalian spermatogenesis and the sensitivity of spermatocytes to X chromosome disruption.
Virtual/augmented reality-based human–machine interface and interaction modes in airport control towers
Authors: Bagassi Sara , Corsi Marzia , De Crescenzio Francesca , Santarelli Ramona , Simonetti Aurora , Moens Laura , Terenzi Michela
Published: June 2024

The concept of an innovative human–machine interface and interaction modes based on virtual and augmented reality technologies for airport control towers has been developed with the aim of increasing the human performances and situational awareness of air traffic control operators. By presenting digital information through see-through head-mounted displays superimposed over the out-of-the-tower view, the proposed interface should stimulate controllers to operate in a head-up position and, therefore, reduce the number of switches between a head-up and a head-down position even in low visibility conditions. This paper introduces the developed interface and describes the exercises conducted to validate the technical solutions developed, focusing on the simulation platform and exploited technologies, to demonstrate how virtual and augmented reality, along with additional features such as adaptive human–machine interface, multimodal interaction and attention guidance, enable a more natural and effective interaction in the control tower. The results of the human-in-the-loop real-time validation exercises show that the prototype concept is feasible from both an operational and technical perspective, the solution proves to support the air traffic controllers in working in a head-up position more than head-down even with low-visibility operational scenarios, and to lower the time to react in critical or alerting situations with a positive impact on the human performances of the user. While showcasing promising results, this study also identifies certain limitations and opportunities for refinement, aimed at further optimising the efficacy and usability of the proposed interface.
CircZNF609 and circNFIX as possible regulators of glioblastoma pathogenesis via miR-145-5p/EGFR axis
Authors: Ghadami Elham , Gorji Ali , Pour-Rashidi Ahmad , Noorbakhsh Farshid , Kabuli Majid , Razipour Masoumeh , Choobineh Hamid , Maghsudlu Mohaddese , Damavandi Elia , Ghadami Mohsen
Published: June 2024

Glioblastoma is a rare and deadly malignancy with a low survival rate. Emerging evidence has shown that aberrantly expressed circular RNAs (circRNAs) play a critical role in the initiation and progression of GBM tumorigenesis. The oncogenic function of circZNF609 and circNFIX is involved in several types of cancer, but the role and underlying mechanism of these circRNAs in glioblastoma remain unclear. In this study, we hypothesized that circZNF609 and circNFIX may regulate EGFR through sponging miR-145-5p. Herein, we assessed the expression levels of circZNF609, circNFIX, miR-145-5p, and EGFR using quantitative polymerase chain reaction in glioblastoma patients and normal brain samples. The results showed that circZNF609, circNFIX, and EGFR expression levels were upregulated and miR145-5p was downregulated (p = 0.001, 0.06, 0.002, and 0.0065, respectively), while there was no significant association between clinicopathological features of the patients and the level of these genes expression. We also found a significant inverse correlation between miR145-5p and the expression of cZNF609, cNFIX and EGFR (p = 0.0003, 0.0006, and 0.009, respectively). These findings may open a new window for researchers to better understand the potential pathways involved in GBM pathogenesis. In conclusion, it may provide a new potential pathway for the development of effective drugs for the treatment of GBM patients.
Arsenic uptake by Agrostis capillaris, as related to its genotypic diversity in the area of historical ore mining and processing
Authors: Dradrach Agnieszka , Nowosad Kamila , Kozak Bartosz , Karczewska Anna
Published: June 2024

Common bentgrass Agrostis capillaris L. is known as tolerant to toxic elements. A hypothesis was examined that its ecotypes growing in historically polluted sites show a limited arsenic uptake and have genetic features that distinguish them from commercially available cultivars. The study was conducted in Złoty Stok, a historical area of arsenic mining. Additionally, two commercial cultivars were grown in pots with arsenic-rich soils. Based on arsenic concentrations in plant roots and shoots, bioconcentration and translocation factors BCF and TF were calculated. Commercial cultivars indicated many times higher BCF shoots and TF values compared to field plants. DNA analysis of leaf blades showed a clear distinction between the plants growing in some sites and patches in the field, and also a gene overlap between the plants in the field and commercial forms. The research did not allow for identification of ecotypes with exceptionally limited arsenic uptake. Moreover, there were no significant differences between the genotypic characteristics of plants growing in polluted sites and those poorly tolerant grown from commercially available seeds. Apparently, other factors, and not genetically determined features, are responsible for A. capillaris tolerance to arsenic in Złoty Stok.
Neuroprotective effects of naltrexone in a mouse model of post-traumatic seizures
Authors: Rodriguez Saul , Sharma Shaunik , Tiarks Grant , Peterson Zeru , Jackson Kyle , Thedens Daniel , Wong Angela , Keffala-Gerhard David , Mahajan Vinit B. , Ferguson Polly J. , Newell Elizabeth A. , Glykys Joseph , Nickl-Jockschat Thomas , Bassuk Alexander G.
Published: June 2024

Traumatic Brain Injury (TBI) induces neuroinflammatory response that can initiate epileptogenesis, which develops into epilepsy. Recently, we identified anti-convulsive effects of naltrexone, a mu-opioid receptor (MOR) antagonist, used to treat drug addiction. While blocking opioid receptors can reduce inflammation, it is unclear if post-TBI seizures can be prevented by blocking MORs. Here, we tested if naltrexone prevents neuroinflammation and/or seizures post-TBI. TBI was induced by a modified Marmarou Weight-Drop (WD) method on 4-week-old C57BL/6J male mice. Mice were placed in two groups: non-telemetry assessing the acute effects or in telemetry monitoring for interictal events and spontaneous seizures both following TBI and naltrexone. Molecular, histological and neuroimaging techniques were used to evaluate neuroinflammation, neurodegeneration and fiber track integrity at 8 days and 3 months post-TBI. Peripheral immune responses were assessed through serum chemokine/cytokine measurements. Our results show an increase in MOR expression, nitro-oxidative stress, mRNA expression of inflammatory cytokines, microgliosis, neurodegeneration, and white matter damage in the neocortex of TBI mice. Video-EEG revealed increased interictal events in TBI mice, with 71% mice developing post-traumatic seizures (PTS). Naltrexone treatment ameliorated neuroinflammation, neurodegeneration, reduced interictal events and prevented seizures in all TBI mice, which makes naltrexone a promising candidate against PTS, TBI-associated neuroinflammation and epileptogenesis in a WD model of TBI.
3D video tracking analysis reveals that mosquitoes pass more likely through holes in permethrin-treated than in untreated nets
Authors: Fatou Mathurin , Müller Pie
Published: June 2024

In addition to killing, mosquito nets treated with permethrin have been claimed to repel mosquitoes, reducing their success in passing through a holed net. We have tested this hypothesis by tracking mosquitoes in a modified World Health Organization tunnel test. In the original assay, mosquitoes are released at one end of the tunnel and have to pass through a holed piece of net to reach the bait at the other end. The mosquitoes are left in the tunnel overnight, while mortality and feeding rates are scored the following morning. Since the original test does not reveal how mosquitoes move within the tunnel, we combined the tunnel with a 3D video camera system. We tracked susceptible and permethrin-resistant Anopheles gambiae s.s. as they moved in the tunnel and interacted with an untreated or a permethrin-treated net (Olyset Net®). Surprisingly, while permethrin increased the mortality and reduced blood-feeding rates, twice as many mosquitoes passed through the holes of the permethrin-treated net. The flight trajectories reveal that upon exposure to the permethrin-treated net, both mosquito colonies showed increased ‘excitation’, thereby augmenting their chance of getting through the holes in the net. The study underlines the complexity of behavioural modes of action of insecticides.
Disturbance of hibernating bats due to researchers entering caves to conduct hibernacula surveys
Authors: Whiting Jericho C. , Doering Bill , Aho Ken , Bybee Bryan F.
Published: June 2024

Estimating population changes of bats is important for their conservation. Population estimates of hibernating bats are often calculated by researchers entering hibernacula to count bats; however, the disturbance caused by these surveys can cause bats to arouse unnaturally, fly, and lose body mass. We conducted 17 hibernacula surveys in 9 caves from 2013 to 2018 and used acoustic detectors to document cave-exiting bats the night following our surveys. We predicted that cave-exiting flights (i.e., bats flying out and then back into caves) of Townsend’s big-eared bats (Corynorhinus townsendii) and western small-footed myotis (Myotis ciliolabrum) would be higher the night following hibernacula surveys than on nights following no surveys. Those two species, however, did not fly out of caves more than predicted the night following 82% of surveys. Nonetheless, the activity of bats flying out of caves following surveys was related to a disturbance factor (i.e., number of researchers × total time in a cave). We produced a parsimonious model for predicting the probability of Townsend’s big-eared bats flying out of caves as a function of disturbance factor and ambient temperature. That model can be used to help biologists plan for the number of researchers, and the length of time those individuals are in a cave to minimize disturbing bats.
A biogenic geodesic dome of the silica skeleton in Phaeodaria
Authors: Yamaguchi Momoka , Nakamura Yasuhide , Watanabe Hiroto , Kimoto Katsunori , Oaki Yuya , Shimode Shinji , Imai Hiroaki
Published: June 2024

Unique architectures of microbial skeletons are viewed as a model for the architectural design of artificial structural materials. In particular, the specific geometric arrangement of a spherical skeleton 0.5–1.5 mm in diameter of shell-bearing protists, Phaeodaria (Aulosphaera sp.), is remarkably interesting because of its similarity to a geodesic polyhedron, which is a hollow framework with 6-branched nodes that requires minimal building material for maximal strength. A phaeodarian skeleton composed of silica rods 5–10 µm in diameter was characterized as a distorted dome that is based on an icosahedron sectioned with a 7-frequency subdivision. The major difference of the biogenic architecture from the ideal geodesic dome is the coexistence of 7- and 5-branched nodes with the distortion of the frames and the presence of radial spines. From a microscopic perspective, the frames and radial spines were revealed to be hollow tubes having inner fibers and lamellar walls consisting of silica nanoparticles 4–8 nm in diameter with interlayer organic matter. The high degradability of the silica skeleton in seawater after cell mortality is ascribed to the specific nanometric composite structure. The biological architectonics sheds light on the production of environmentally friendly, lightweight structural materials and microdevices.
Proteomic analysis of plasma at the preterminal stage of rhesus nonhuman primates exposed to a lethal total-body dose of gamma-radiation
Authors: Carpenter Alana D. , Fatanmi Oluseyi O. , Wise Stephen Y. , Tyburski John B. , Cheema Amrita K. , Singh Vijay K.
Published: June 2024

The identification and validation of radiation biomarkers is critical for assessing the radiation dose received in exposed individuals and for developing radiation medical countermeasures that can be used to treat acute radiation syndrome (ARS). Additionally, a fundamental understanding of the effects of radiation injury could further aid in the identification and development of therapeutic targets for mitigating radiation damage. In this study, blood samples were collected from fourteen male nonhuman primates (NHPs) that were exposed to 7.2 Gy ionizing radiation at various time points (seven days prior to irradiation; 1, 13, and 25 days post-irradiation; and immediately prior to the euthanasia of moribund (preterminal) animals). Plasma was isolated from these samples and was analyzed using a liquid chromatography tandem mass spectrometry approach in an effort to determine the effects of radiation on plasma proteomic profiles. The primary objective was to determine if the radiation-induced expression of specific proteins could serve as an early predictor for health decline leading to a preterminal phenotype. Our results suggest that radiation induced a complex temporal response in which some features exhibit upregulation while others trend downward. These statistically significantly altered features varied from pre-irradiation levels by as much as tenfold. Specifically, we found the expression of integrin alpha and thrombospondin correlated in peripheral blood with the preterminal stage. The differential expression of these proteins implicates dysregulation of biological processes such as hemostasis, inflammation, and immune response that could be leveraged for mitigating radiation-induced adverse effects.