bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectral Analysis of the Morphology of Fresh Lunar Craters I: Rim Crest, Floor, and Rim Flank Outlines
Authors: Du Jun , Minton David A. , Blevins Austin M. , Fassett Caleb I. , Huang Ya‐Huei
Published: November 2024

The morphology of fresh lunar craters contains information about the physical properties of both the impactors and the lunar surface, and is therefore crucial to our knowledge of the impact cratering process. Spectral analysis is a powerful tool to study crater morphology, as it can reveal the topographic variation on different scales. In this study, we calculate the power spectral densities of the radial distance and elevation of the rim crest, floor, and rim flank outlines of fresh lunar craters. The resulting power spectral density can be decomposed into an average component and a natural variability component. For the average component, we derive the classic morphometric parameter‐crater diameter relations that are consistent with previous studies. For the natural variability component, we find that in general the spectral power increases with wavelength, which can be fitted by a piecewise function with four breakpoints. Among the four breakpoints, the power of the third breakpoint (i.e., the degree‐2 power) is of particular interest, as it determines the ellipticity of the outline. The power of the third breakpoint is found to have a diameter dependence with a peak at 20 km, which indicates that transitional craters are more elliptical than simple and complex craters. The diameter dependence of the power spectral density enables us to generate the synthetic outlines of a crater of a particular size, which can be used to develop a preliminary 3‐dimensional shape model for fresh lunar craters that is useful for improving Monte Carlo modeling of cratered surfaces on the Moon.
A Better Understanding of Atmospheric Methane Sources Using 13CH3D and 12CH2D2 Clumped Isotopes
Authors: Haghnegahdar Mojhgan A. , Hultquist Nicole , Hamovit Nora D. , Yarwood Stephanie A. , Bouyon Amaury , Kaufman Alan J. , Sun Jiayang , Magen Cedric , Farquhar James
Published: November 2024

We evaluate the use of clumped isotopes of methane (CH4) to fingerprint local atmospheric sources of methane. We focus on a regenerative stormwater conveyance (RSC) stream wetland site running through the University of Maryland campus, which emits methane due to its engineering. Air samples in the RSC were collected at different heights above the surface and at different times of the day including both early in the morning, after methane accumulated below the nocturnal boundary layer, and late in the afternoon when convection mixed air to the cloud layer. Measured Δ12CH2D2 values of air samples record mixing between locally produced methane with low D/H and ambient air. The Δ12CH2D2 of the near surface air collected at the RSC during the early morning ranges from ∼+23‰ to ∼+35‰ which is lower than the ∼+50‰ values of tropospheric air. Mixing between background air (with Δ12CH2D2 ∼+50‰) and methane captured from chamber and bubble samples, as well as produced in incubation (all with negative Δ12CH2D2), explains the observed values of Δ12CH2D2 and Δ13CH3D of near surface RSC air samples. The effect of mixing with biogenic sources on Δ13CH3D is much smaller. The findings demonstrate how methane isotopologues can be used as a tool not only to fingerprint local contributions to these greenhouse gas emissions but also to identify sources of near‐surface methane hot spots.
Monitoring of Ionospheric Variability Using the Low lAtitude Long Range Ionospheric raDar (LARID): Capabilities, Advantages and Limitations
Authors: Sun Wenjie , Li Guozhu , Ning Baiqi , Hu Lianhuan , Otsuka Yuichi , Dai Guofeng , Xie Haiyong , Zhao Xiukuan , Li Yi , Shinbori Atsuki , Nishioka Michi , Perwitasari Septi , Wang Chi
Published: November 2024

A Low lAtitude long Range Ionospheric raDar (LARID), which was built recently at Dongfang (19.2°N, 108.8°E, magnetic latitude 13.9°), Hainan Is., China, is employed to study the ionospheric variability over a large region. The LARID consists of two high frequency (HF) coherent backscatter radars, looking toward east and west, respectively, with a field‐of‐view covering a wide longitude from Africa to Pacific. Here we report some results by the LARID, with main focus on its capabilities, advantages and limitations in monitoring ionospheric variability. The results show that the LARID can detect various ionospheric variations at low latitudes, including (a) sequentially generated equatorial plasma bubbles over a longitude span of ∼80°, (b) near‐range E region irregularities drifting across more than 1,000 km, (c) ionospheric background information retrieved from ground scatters, (d) traveling ionospheric disturbances, and (e) sporadic E structures reflecting HF radio waves at low elevation angles. It is demonstrated that the LARID provides an important tool for investigating different types of ionospheric variability over a broad region, especially over the Indian Ocean and west Pacific, and will contribute significantly to the regional ionospheric weather forecasting.
Measuring River Surface Velocity Using UAS‐Borne Doppler Radar
Authors: Zhou Zhen , Riis‐Klinkvort Laura , Jørgensen Emilie Ahrnkiel , Lindenhoff Christine , Frías Monica Coppo , Vesterhauge Alexander Rietz , Olesen Daniel Haugård , Lavish Makar , Dobrovolskiy Alexey , Kadek Alexey , Orlic Niksa , Grubesa Tomislav , Drmić Luka , Grosen Henrik , Nielsen Sune , Wennerberg Daniel , Fagerström Viktor , Axén Jenny , Gustafsson David , Bauer‐Gottwein Peter
Published: November 2024

Using Unoccupied Aerial Systems (UAS) equipped with optical RGB cameras and Doppler radar, surface velocity can be efficiently measured at high spatial resolution. UAS‐borne Doppler radar is particularly attractive because it is suitable for real‐time velocity determination, because the measurement is contactless, and because it has fewer limitations than image velocimetry techniques. In this paper, five cross‐sections (XSs) were surveyed within a 10 km stretch of Rönne River in Sweden. Ground‐truth surface velocity observations were retrieved with an electromagnetic velocity sensor (OTT MF Pro) along the XS at one m spacing. Videos from a UAS RGB camera were analyzed using both Particle Image Velocimetry (PIV) and Space‐Time Image Velocimetry (STIV) techniques. Furthermore, we recorded full waveform signal data using a Doppler radar at multiple waypoints across the river. An algorithm fits two alternative models to the average amplitude curve to derive the correct river surface velocity based on Gaussian models with: (a) one peak, and (b) two peaks. Results indicate that river flow velocity and propwash velocity caused by the drone can be found in XS where the flow velocity is low, while the drone‐induced propwash velocity can be neglected in fast and highly turbulent flows. To verify the river flow velocity derived from Doppler radar, a mean PIV value within the footprint of the Doppler radar at each waypoint was calculated. Finally, quantitative comparisons of OTT MF Pro data with STIV, mean PIV and Doppler radar revealed that UAS‐borne Doppler radar could reliably measure the river surface velocity.
Environmental public health research at the U.S. Environmental Protection Agency: A blueprint for exposure science in a connected world
Authors: Stanek Lindsay W. , Cascio Wayne E. , Barzyk Timothy M. , Breen Michael S. , DeLuca Nicole M. , Griffin Shannon M. , Melnyk Lisa Jo , Minucci Jeffrey M. , Thomas Kent W. , Tulve Nicolle S. , Weaver Christopher P. , Cohen Hubal Elaine A.
Published: November 2024

Exposure science plays an essential role in the U.S. Environmental Protection Agency’s (U.S. EPA) mission to protect human health and the environment. The U.S. EPA’s Center for Public Health and Environmental Assessment (CPHEA) within the Office of Research and Development (ORD) provides the exposure science needed to characterize the multifaceted relationships between people and their surroundings in support of national, regional, local and individual-level actions. Furthermore, exposure science research must position its enterprise to tackle the most pressing public health challenges in an ever-changing environment. These challenges include understanding and confronting complex human disease etiologies, disparities in the social environment, and system-level changes in the physical environment. Solutions will sustainably balance and optimize the health of people, animals, and ecosystems. Our objectives for this paper are to review the role of CPHEA exposure science research in various recent decision-making contexts, to present current challenges facing U.S. EPA and the larger exposure science field, and to provide illustrative case examples where CPHEA exposure science is demonstrating the latest methodologies at the intersection of these two motivations. This blueprint provides a foundation for applying exposomic tools and approaches to holistically understand real-world exposures so optimal environmental public health protective actions can be realized within the broader context of a One Health framework.

Impact statement

The U.S. EPA’s Center for Public Health and Environmental Assessment exposure research priorities reside at the intersection of environmental decision contexts and broad public health challenges. The blueprint provides a foundation for advancing the tools and approaches to holistically understand real-world exposures so optimal environmental protection actions can be realized. A One Health lens can help shape exposure research for maximum impact to support solutions that are transdisciplinary and must engage multiple sectors.
Association of polygenic liabilities for schizophrenia and bipolar disorder with educational attainment and cognitive aging
Authors: Wu Chi-Shin , Hsu Chia-Lin , Lin Mei-Chen , Su Mei-Hsin , Lin Yen-Feng , Chen Chia-Yen , Hsiao Po-Chang , Pan Yi-Jiun , Chen Pei-Chun , Huang Yen-Tsung , Wang Shi-Heng
Published: November 2024

To elucidate the specific and shared genetic background of schizophrenia (SCZ) and bipolar disorder (BPD), this study explored the association of polygenic liabilities for SCZ and BPD with educational attainment and cognitive aging. Among 106,806 unrelated community participants from the Taiwan Biobank, we calculated the polygenic risk score (PRS) for SCZ (PRSSCZ) and BPD (PRSBPD), shared PRS between SCZ and BPD (PRSSCZ+BPD), and SCZ-specific PRS (PRSSCZvsBPD). Based on the sign-concordance of the susceptibility variants with SCZ/BPD, PRSSCZ was split into PRSSCZ_concordant/PRSSCZ_discordant, and PRSBPD was split into PRSBPD_concordant/PRSBPD_discordant. Ordinal logistic regression models were used to estimate the association with educational attainment. Linear regression models were used to estimate the associations with cognitive aging (n = 27,005), measured by the Mini-Mental State Examination (MMSE), and with MMSE change (n = 6194 with mean follow-up duration of 3.9 y) in individuals aged≥ 60 years. PRSSCZ, PRSBPD, and PRSSCZ+BPD were positively associated with educational attainment, whereas PRSSCZvsBPD was negatively associated with educational attainment. PRSSCZ was negatively associated with MMSE, while PRSBPD was positively associated with MMSE. The concordant and discordant parts of polygenic liabilities have contrasting association, PRSSCZ_concordant and PRSBPD_concordant mainly determined these effects mentioned above. PRSSCZvsBPD predicted decreases in the MMSE scores. Using a large collection of community samples, this study provided evidence for the contrasting effects of polygenic architecture in SCZ and BPD on educational attainment and cognitive aging and suggested that SCZ and BPD were not genetically homogeneous.
UK guidelines for the management of bone sarcomas
Authors: Gerrand Craig , Amary Fernanda , Anwar Hanny A. , Brennan Bernadette , Dileo Palma , Kalkat Maninder Singh , McCabe Martin G. , McCullough Anna Louise , Parry Michael C. , Patel Anish , Seddon Beatrice M. , Sherriff Jennifer M. , Tirabosco Roberto , Strauss Sandra J.
Published: November 2024

This document is an update of the British Sarcoma Group guidelines (2016) and provides a reference standard for the clinical care of UK patients with primary malignant bone tumours (PMBT) and giant cell tumours (GCTB) of bone. The guidelines recommend treatments that are effective and should be available in the UK, and support decisions about management and service delivery. The document represents a consensus amongst British Sarcoma Group members in 2024. Key recommendations are that bone pain, or a palpable mass should always lead to further investigation and that patients with clinical or radiological findings suggestive of a primary bone tumour at any anatomic site should be referred to a specialist centre and managed by an accredited bone sarcoma multidisciplinary team. Treatment recommendations are provided for the major tumour types and for localised, metastatic and recurrent disease. Follow-up schedules are suggested.
ACBP/DBI neutralization for the experimental treatment of fatty liver disease
Authors: Motiño Omar , Lambertucci Flavia , Joseph Adrien , Durand Sylvère , Anagnostopoulos Gerasimos , Li Sijing , Carbonnier Vincent , Nogueira-Recalde Uxía , Montégut Léa , Chen Hui , Aprahamian Fanny , Nirmalathasan Nitharsshini , Maiuri Maria Chiara , Pietrocola Federico , Valla Dominique , Laouénan Cédric , Gautier Jean-François , Castera Laurent ,   QUID NASH Investigators, Castera Laurent , Vallet-Pichard Anaïs , Vidal-Trécan Tiphaine , Manchon Pauline , Paradis Valérie , Roulot Dominique , Boitard Christian , Terris Benoit , Bihan Hélène , Julla Jean-Baptiste , Poynard Thierry , Bzrustowski Angélique , Larger Etienne , Czernichow Sébastien , Pol Stanislas , Bedossa Pierre , Junot Christophe , de Preville Nathalie , Zaleski Isabelle Durand , Rautou Pierre-Emmanuel , Van Beers Bernard , Dioguardi Marco , Vilgrain Valérie , Correas Jean-Marie , Garteiser Philippe , Riveline Jean-Pierre , Ibberson Mark , Martins Isabelle , Kroemer Guido
Published: November 2024

Acyl-CoA binding protein (ACBP), also known as diazepam-binding inhibitor (DBI), is an extracellular checkpoint of autophagy. Here, we report that patients with histologically confirmed metabolic-associated steatohepatitis (MASH) or liver fibrosis exhibit elevated levels of circulating ACBP/DBI protein as compared to non-affected controls. Plasma ACBP/DBI strongly correlated with the NAFLD and FIB4 scores in patients, and these correlations were independent of age and body mass index. We studied the capacity of a monoclonal antibody (mAb) neutralizing mouse ACBP/DBI to combat active liver disease in several mouse models, in which steatohepatitis had been induced by four different protocols, namely, (i) methionine/choline-deficient diet, (ii) Western style diet (WD) alone, (iii) WD combined with the hepatotoxic agent CCl4, and (iv) a combination of CCl4 injections and oral ethanol challenge. Injections of anti-ACBP/DBI mAb attenuated histological, enzymological, metabolomic and transcriptomic signs of liver damage in these four models, hence halting or reducing the progression of non-alcoholic and alcoholic liver disease. Steatosis, inflammation, ballooning and fibrosis responded to ACBP/DBI inhibition at the preclinical level. Altogether, these findings support a causal role of ACBP/DBI in MASH and liver fibrosis, as well as the possibility to therapeutically target ACBP/DBI.
A non-canonical mechanism of GPCR activation
Authors: Powers Alexander S. , Khan Aasma , Paggi Joseph M. , Latorraca Naomi R. , Souza Sarah , Di Salvo Jerry , Lu Jun , Soisson Stephen M. , Johnston Jennifer M. , Weinglass Adam B. , Dror Ron O.
Published: November 2024

The goal of designing safer, more effective drugs has led to tremendous interest in molecular mechanisms through which ligands can precisely manipulate the signaling of G-protein-coupled receptors (GPCRs), the largest class of drug targets. Decades of research have led to the widely accepted view that all agonists—ligands that trigger GPCR activation—function by causing rearrangement of the GPCR’s transmembrane helices, opening an intracellular pocket for binding of transducer proteins. Here we demonstrate that certain agonists instead trigger activation of free fatty acid receptor 1 by directly rearranging an intracellular loop that interacts with transducers. We validate the predictions of our atomic-level simulations by targeted mutagenesis; specific mutations that disrupt interactions with the intracellular loop convert these agonists into inverse agonists. Further analysis suggests that allosteric ligands could regulate the signaling of many other GPCRs via a similar mechanism, offering rich possibilities for precise control of pharmaceutically important targets.
De novo transcriptome analysis of the Indian squid Uroteuthis duvaucelii (Orbigny, 1848) from the Indian Ocean
Authors: Krishnan Nisha , Sukumaran Sandhya , Vysakh V. G. , Sebastian Wilson , Jose Anjaly , Raj Neenu , Gopalakrishnan A.
Published: November 2024

Cephalopods have dominated the oceans for hundreds of millions of years and are unquestionably at the peak of molluscan evolution. The development of the large brain and a well-sophisticated sensory system contributed significantly to its success. Therefore, it is considered the best example of convergent evolution and attracted the attention of scientists from various disciplines of biology. The aim of the present study is to construct a reference transcriptome in the Indian squid Uroteuthis duvaucelii to gain insights into cephalopod evolution and enrich the existing cephalopod database. Around 72 million short Illumina reads were generated from five different tissues, including the brain, eye, gill, heart and gonads, and assembled using the Trinity assembler. About 26230 protein-coding sequences were annotated from the assembled transcripts. The BUSCO completeness of the assembly was 71.71% compared to the Mollusca_Odb10 gene set. KEGG and REACTOME pathway analyzes revealed that U. duvaucelii shares many genes and pathways with higher vertebrates.
Embracing the informative missingness and silent gene in analyzing biologically diverse samples
Authors: Du Dongping , Bhardwaj Saurabh , Lu Yingzhou , Wang Yizhi , Parker Sarah J. , Zhang Zhen , Van Eyk Jennifer E. , Yu Guoqiang , Clarke Robert , Herrington David M. , Wang Yue
Published: November 2024

Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel. We developed the ABDS tool suite specifically for analyzing biologically diverse samples. Collectively, a mechanism-integrated group-wise pre-imputation scheme is proposed to retain informative missingness associated with signature genes, a cosine-based one-sample test is extended to detect group-silenced signature genes, and a unified heatmap is designed to display multiple sample groups. We describe the methodological principles and demonstrate the effectiveness of three analytics tools under targeted scenarios, supported by comparative evaluations and biomedical showcases. As an open-source R package, ABDS tool suite complements rather than replaces existing tools and will allow biologists to more accurately detect interpretable molecular signals among phenotypically diverse sample groups.
Collagen crosslinking-induced corneal morphological changes: a three-dimensional light sheet Microscopy-based evaluation
Authors: Stoecker Axel , Pinkert-Leetsch Diana , Koch Timea , Ackermann Roland , Nolte Stefan , van Oterendorp Christian , Russmann Christoph , Missbach-Guentner Jeannine
Published: November 2024

Stiffness-related eye diseases such as keratoconus require comprehensive visualization of the complex morphological matrix changes. The aim of this study was to use three-dimensional (3D) light sheet fluorescence microscopy (LSFM) to analyze unlabeled corneal tissue samples, qualitatively visualizing changes in corneal stiffness. Isolated porcine corneal tissue samples were treated with either NaCl or 0.1% glutaraldehyde (GTA) prior to clearing with benzyl alcohol/benzyl benzoate (BABB) and subsequently scanned with LSFM. After analysis of the LSFM data sets, the samples were embedded in paraffin to validate the results by conventional planar microscopy. In the unlabeled corneal tissue samples the 2D/3D morphology of the entire tissue volume was identified by specific autofluorescence signals. An enhancement of collagen crosslinking was induced by applying GTA to the corneal tissue. Subsequent LSFM scans showed specific morphological changes due to altered autofluorescence signals of the corneal stroma, which were confirmed by conventional histology. Therefore, LSFM analysis of corneal tissue samples allowed label-free 3D autofluorescence assessment of the corneal morphology in its anatomical context. It provides the technical basis for the examination of the pathologically altered cornea and facilitates ophthalmologic examinations of corneal diseases based on the altered tissue stiffness.
His-tag based supramolecular biopolymerization
Authors: Lal Mitra , Kesselman Ellina , Wachtel Ellen , Kleinerman Olga , Peleg Yoav , Albeck Shira , Majhi Koushik , Sheves Mordechai , Patchornik Guy
Published: November 2024

The term supramolecular polymer has been applied to polymeric materials in which the individual units, i.e., building blocks—are bound to each other via noncovalent interactions, including electrostatic or hydrogen bonding, as well as metal–ligand conjugation. The building blocks are generally low molecular weight amphiphiles. Methods for preparing biopolymers based on non-toxic, metal–ligand conjugation have been little studied; however, they offer significant potential for tuning the response of biologically relevant macromolecules. In this communication, we characterize the assembly and morphology of supramolecular biopolymers in which the building blocks are low- or medium-molecular weight globular proteins—ubiquitin and Cas9-interacting via metal–ligand conjugation. In each case, the protein gene was expressed in cell culture with the addition of hexa-His/linkers at both the N and C termini. Divalent cations investigated were Zn2+ and Ni2+. We observe in cryo-TEM imaging an absolute requirement for divalent cations for the formation of supramolecular biopolymers. In the presence of Ni2+, 1D assembled fibers are predominant, while with Zn2+, the more frequently detected structures are sheet-like. We use gel electrophoresis and CD spectroscopy to monitor possible secondary and tertiary structural changes in the protein building blocks during conjugation.
Fabrication of novel PVA loaded ZnO nanoparticles for anti-renal failure
Authors: Hassan Shawky M. , Tarek Mahmoud , Samra Salem , El-Dafrawy Shady M.
Published: November 2024

X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to investigate the structural, surface and particles properties of a series of zinc oxides (ZnO) doped with polyvinyl alcohol (PVA) that were prepared using the sol-gel method. The results demonstrated that the crystallinity of the catalysts decreased as the PVA content increased beyond 5 PVA/ZnO. However, on raising the calcination temperature up to 500 °C, the average crystal size of the PVA/ZnO nanoparticles increased. Next Pyridine adsorption was used to measure the surface acidity of the catalysts, and the results showed that doping ZnO with PVA and raising the calcination temperature to 500 °C increased the catalyst’s surface acidity. Furthermore, the data indicates that raising the ratio of the Brønsted to Lewis acid sites enhanced the catalytic activity for the synthesis of coumarin derivatives. We concluded that the structural and acidity characteristics of the catalysts under study had a significant impact on the catalytic activity. Furthermore, a study examining the biological activity of ZnO/PVA and pure ZnO revealed that 5PVA/ZnO performed the best in terms of improving the kidney functions of diabetic rats.
Starvation-induced metabolic rewiring affects mTORC1 composition in vivo
Authors: Kaade Edgar , Mausbach Simone , Erps Nina , Sylvester Marc , Shakeri Farhad , Jachimowicz Ron D. , Gieselmann Volkmar , Thelen Melanie
Published: November 2024

Lysosomes play a crucial role in metabolic adaptation to starvation, but detailed in vivo studies are scarce. Therefore, we investigated the changes of the proteome of liver lysosomes in mice starved short-term for 6h or long-term for 24h. We verified starvation-induced catabolism by weight loss, ketone body production, drop in blood glucose and an increase of 3-methylhistidine. Deactivation of mTORC1 in vivo after short-term starvation causes a depletion of mTORC1 and the associated Ragulator complex in hepatic lysosomes, resulting in diminished phosphorylation of mTORC1 target proteins. While mTORC1 lysosomal protein levels and activity in liver were restored after long-term starvation, the lysosomal levels of Ragulator remained constantly reduced. To determine whether this mTORC1 activity pattern may be organ-specific, we further investigated the key metabolic organs muscle and brain. mTORC1 inactivation, but not re-activation, occurred in muscle after a starvation of 12 h or longer. In brain, mTORC1 activity remained unchanged during starvation. As mTORC1 deactivation is known to induce autophagy, we further investigated the more than 150 non-lysosomal proteins enriched in the lysosomal fraction upon starvation. Proteasomal, cytosolic and peroxisomal proteins dominated after short-term starvation, while after long-term starvation, mainly proteasomal and mitochondrial proteins accumulated, indicating ordered autophagic protein degradation.
Biological control of nosemosis in Apis mellifera L. with Acacia nilotica extract
Authors: El-Sayed Ashraf S. A. , Fathy Nahla A. M. , Labib Mai , El-Baz Ashraf F. , El-Sheikh Aly A. , Moustafa Ahmed H.
Published: November 2024

Nosemosis is one of the most devastating diseases of Apis mellifera (Honey bees) caused by the single-celled spore-forming fungi Nosema apis, N. ceranae and N. neumanii, causing a severe loss on the colony vitality and productivity. Fumagillin, a MetAP2 inhibitor, was a certified treatment for controlling nosemosis, nevertheless, due to its deleterious effects on honey bees and humans, it is prohibited. So, searching for novel biological agents with affordable selectivity to target Nosema species infecting Apis mellifera, with nil toxicity to bees and humans is the main objective of this study. Nosema species were isolated from naturally infected honey bees. The methanolic extracts of Acacia nilotica, Elaeis guineensis, and Catharanthus roseus were tested to selectively control the growth of Nosema spp of honeybees. The spores of Nosema species were molecularly and morphologically identified. Among the tested plant extracts, the methanolic extracts (0.1%) of A. nilotica had the most activity towards Nosema spp causing about 37.8 and 32.5% reduction in the spores’ load at 5- and 9-days post-infection, respectively, compared to the untreated control. At 0.1%, the A. nilotica methanolic extract exhibited the highest inhibitory effect for Nosema spores, without any obvious bee mortality. Catharanthus roseus displayed a reduction of spores by 27.02%, with bee mortality rate of 27.02%. At 1% for 5 dpi, the A. nilotica extracts led to 18.18% bee mortality, while the C. roseus extracts resulted in 100% mortality, as revealed from the toxicity and quantification bioassays. So, the extracts of A. nilotica and C. roseus had a significant effect in controlling the N. apis and N. ceranae titer compared to the infected untreated control at both time points. The titer of N. apis and N. ceranae was noticeably decreased by more than 80% and 90%, in response to A. nilotica, compared to the control. From the metabolic profiling by GC–MS analysis, the most frequent active compounds of A. nilotica were 2,4,6-trihy-droxybenzoic acid, 1,2-dihydroxybenzene, myristic acid, and linoleic acid. These compounds were analyzed in silico to assess their binding affinity to the ATP binding protein, methionine aminopeptidase and polar tube protein of Nosema species as target enzymes. The compound 2,4,6-trihydroxybenzoic acid had the lowest energy to bind with ATP binding protein, methionine aminopeptidase and polar tube protein of Nosema, followed by 1,2-dihydroxybenzene and myristic acid, compared to fumagilin. So, from the experimental and molecular docking analysis, the extracts of A. nilotica had the highest activity to attack the cellular growth machinery of Nosema species without an obvious effect to the honeybees, ensuring their prospective promising application.
ZnO doped PAMAM for asphalt improvement as anti-corrosive coatings
Authors: Al-Gamal Abdalrahman G. , Gado Walaa S. , Abo El-Khair Muhammad A. , Zakaria Khaled , Ragab A. A. , Kabel Khalid I.
Published: November 2024

Asphalt is widely used as a coating resin due to its excellent adhesion strength and cost-effectiveness; however, its limited corrosion protection necessitates enhancement. In this study, poly(amidoamine) (PAMAM), combined with zinc oxide (ZnO) nanoparticles, was incorporated into the asphalt matrix to improve its anticorrosive properties. Various ratios of PAMAM-ZnO nanocomposite (1, 2, 4, and 6% by weight) were added to the asphalt binder, with the materials characterized using XRD, ¹H-NMR, and SEM techniques. The 2% PAMAM-ZnO/asphalt ratio exhibited the most significant improvement, achieving a corrosion protection efficiency (η%) of 97.93%, as confirmed by Tafel analysis, and a charge transport resistance (RCT) of 75.91 Ω cm² according to electrochemical impedance spectroscopy (EIS) data. A combination of barrier formation and sacrificial protection drives the corrosion inhibition mechanism. The PAMAM-ZnO nanocomposite forms a highly uniform layer on the carbon steel surface, creating an effective physical barrier that prevents the penetration of corrosive agents, thereby minimizing defects like pinholes. This barrier effect is complemented by the sacrificial protection provided by the ZnO nanoparticles, which are more reactive than the underlying steel and preferentially interact with corrosive ions (e.g., chloride ions). This interaction leads to the formation of stable ZnO corrosion products, which enhance the barrier and reduce the likelihood of corrosion on the steel surface. Additionally, PAMAM facilitates the even distribution and strong adhesion of ZnO within the asphalt matrix, ensuring a durable protective layer. The synergic impact between the polymer barrier and sacrificial ZnO protection results in the exceptional corrosion resistance observed in the 2% PAMAM-ZnO/asphalt formulation, offering a promising approach for advanced anticorrosive coatings.
Antibacterial efficacy of berry juices against Bacillus cereus relative to their phytochemical composition and antioxidant properties
Authors: Królak Kamil , Ścieszka Sylwia , Kordialik-Bogacka Edyta , Oracz Joanna , Ditrych Maciej , Szczygieł Tomasz , Dybka-Stępień Katarzyna , Otlewska Anna , Żyżelewicz Dorota
Published: November 2024

Ensuring the safety and stability of minimally processed foods using natural preservatives is of great scientific and commercial interest in modern biotechnology. Berry juice supplementation is increasingly recognized within this field. This study investigated the effectiveness of juices from four berry species Aronia melanocarpa, Ribes nigrum, Vaccinium macrocarpon, and Sambucus nigra, against the food pathogen Bacillus cereus. Overall, the antibacterial potency of juice supplements (up to 10% v/v in tryptic soy broth) followed the order of chokeberry > blackcurrant > cranberry > elderberry, with the latter showing no inhibitory effects. Notably, chokeberry and elderberry juices presented lower acidity and significantly greater phenolic contents (p < 0.05) than blackcurrant and cranberry juices did, suggesting that B. cereus susceptibility is not strictly dependent upon low extracellular pH or elevated anthocyanin levels. Instead, it is inferred to correlate with pro-oxidative effects induced directly at the intracellular level. Accordingly, this paper discusses the antioxidative, acidic, and lipophilic attributes of juices and their constituent fractions, including anthocyanins, to elucidate their biopreservative potential. The results of this study increase our understanding of the antibacterial susceptibility of B. cereus.
Bidirectional Mendelian randomization links gut microbiota to primary biliary cholangitis
Authors: Zhou Zhijia , Li Wenxuan , Wu Yuelan , Wang Tao , Zhang Jinghao , You Liping , Li Haoran , Zheng Chao , Gao Yueqiu , Sun Xuehua
Published: November 2024

Primary biliary cholangitis (PBC) and gut microbiota (GM) are epidemiologically correlated but the causal inter-relationships remain poorly understood. We aim to explore the causal relationships between GM and PBC. Using the MiBioGen consortium, GWAS data for GM at the species level and the largest publicly available PBC GWAS data to date, we performed a bidirectional two-sample Mendelian randomization by the inverse variance weighted, MR-Egger, weighted median, weighted model and MR-PRESSO to elucidate the potential causal role of GM in PBC. To measure the heterogeneity of instrumental variables (IV), Cochran’s Q statistic and MR-Egger intercept test were used. Genetically instrumented order Coriobacteriales (odds ratio [OR] = 2.18, 95% confidence interval [CI] 1.30–3.66, P = 0.004) significantly increased the risk for PBC, while genetically driven class Deltaproteobacteria (OR = 0.52, 95% CI 0.36–0.74, P = 0.002) causally decrease the NAFLD risk. Reverse MR analysis showed no significant association between PBC and the two specific GM. However, it indicated that PBC progression significantly increases the abundance of the class Bacteroidia, order Bacteroidales, and phylum Bacteroidetes (OR = 1.02, 95% CI 1.002–1.03, P = 0.026), while decreasing the abundance of the genus Lachnospiraceae UCG010 (OR = 0.98, 95% CI 0.96–0.995, P = 0.026). Our study demonstrated that genetically driven order Coriobacteriales and class Deltaproteobacteria were causally related to PBC risk. This causality provided a new perspective on ameliorating PBC by modulating GM. Our study demonstrated that genetically driven order Coriobacteriales and class Deltaproteobacteria were causally related to PBC risk. PBC was causally related to the abundance of four GM taxa(class Bacteroidia, order Bacteroidales, phylum Bacteroidetes and genus Lachnospiraceae UCG010). This causality provided a new perspective on ameliorating PBC by modulating GM.
Generating and validating renewable affimer protein binding reagents targeting SH2 domains
Authors: Heseltine Sophie J. , Billenness Gregory J. , Martin Heather L , Tiede Christian , Tang Anna A.S. , Foy Eleanor , Reddy Grace , Gibson Naomi , Johnson Matt , Webb Michael E. , McPherson Michael J. , Tomlinson Darren C.
Published: November 2024

Despite SH2 domains, being pivotal in protein interactions linked to various diseases like cancer, we lack specific research tools for intracellular assays. Understanding SH2-mediated interactions and creating effective inhibitors requires tools which target individual protein domains. Affimer reagents exhibit promise, yet their potential against the extensive SH2 domain family remains largely unexplored. Our study aimed to bridge this gap by identifying Affimer reagents that selectively bind to 22 out of 41 SH2 domains. These reagents enabled a medium-throughput screening approach resembling siRNA studies, shedding light on their functionality. Notably, select Affimers demonstrated the ability to curtail the nuclear translocation of pERK, with Grb2 being a prominent target. Further analyses revealed that these Grb2-specific Affimer reagents displayed competitive inhibition with impressive metrics: IC50s ranging from 270.9 nM to 1.22 µM, together with low nanomolar binding affinities. Moreover, they exhibited the ability to pull down endogenous Grb2 from cell lysates, illustrating their efficacy in binding the Grb2 SH2 domain. This comprehensive assessment underscores the potential of Affimer reagents as domain-specific inhibitors. Their viability for medium/high-throughput phenotypic screening presents a promising avenue via which to identify and characterize potential drug targets within the SH2 domain family.
Microfluidic qPCR for detection of 21 common respiratory viruses in children with influenza-like illness
Authors: Saville Thomas J. , Colton Hayley , Jarju Sheikh , Armitage Edwin P. , Drammeh Sainabou , Tazzyman Simon , Jagne Ya Jankey , Sallah Hadijatou J. , Senghore Elina , Evans Cariad M. , Darton Thomas C. , de Silva Thushan I.
Published: November 2024

Multiple respiratory viruses lead to high morbidity and mortality, yet global surveillance platforms focus primarily on seasonal influenza viruses. The COVID-19 pandemic and new RSV vaccines highlight the importance of a broader approach. Upper respiratory tract swabs from children aged 24–59 months presenting with influenza-like illness in The Gambia were collected during follow-up of a live-attenuated influenza vaccine randomised controlled trial in 2017–18. A microfluidic quantitative polymerase chain reaction (qPCR) assay was established and used to detect 21 respiratory viruses. 76.6% of samples had one or more viruses detected (n = 121/158). The viruses detected most frequently were rhinovirus (n = 37/158, 23.4%) and adenovirus (n = 34/158, 21.5%), followed by parainfluenza virus 3, influenza B and human metapneumovirus B. A third of positive samples had multiple viruses detected (two n = 31/121, 25.6%; three n = 9/121, 7.4%). Our data demonstrates how microfluidic qPCR is a useful tool for high-throughput, comprehensive detection of multiple respiratory viruses in surveillance platforms. Rapidly changing epidemiology exemplifies the need for new, broader approaches to virus surveillance in low-resource settings to respond to future epidemics and to guide the need for and use of new prevention and therapeutic measures.
Impact of molecular configuration on the photoluminescence and electrical characteristics of poly-pyrrol-thiazol-imine polymers films
Authors: Ghazy Ahmed R. , Kenawy El-Refaie , Darwesh Nourhan , Shendy S. , El-Shaer Abdelhamid , Ghazy R.
Published: November 2024

The optical, photoluminescence, and electrical properties of Poly(Z)-PTI and Poly(E)-PTI, two Poly-Pyrrol-Thiazol-Imine polymers with comparable chemical structures but distinct configurations, were examined. Using the dip-casting method, polymer films were deposited on ITO substrates. UV-VIS spectroscopy revealed that both polymers diverged between 500 and 800 nm, showing the impact of molecular arrangement, but showed similar absorption behavior for wavelengths shorter than 500 nm. For Poly(Z)-PTI, the direct optical energy gaps were 2.06 eV, while for Poly(E)-PTI, they were 1.78 eV. Poly(Z)-PTI displayed an emission peak at 610 nm (red) according to laser photoluminescence spectra, while Poly(E)-PTI peaked at 563 nm (green-yellow). The capacitance behavior was revealed by electrochemical impedance spectroscopy. Nyquist plots suggested an equivalent circuit model of Rs (CRct)(QR)(CR) for both polymers, and the relaxation times were 15.9 ns for Poly(Z)-PTI and 89.5 ns for Poly(E)-PTI. The Mott-Schottky analysis verified the n-type conductivity, revealing 2.18 × 1016 cm− 3 carrier densities for Poly(Z)-PTI and 1.78 × 1016 cm− 3 for Poly(E)-PTI. At lower frequencies, both polymers exhibited limited conductivity and large dielectric constants. Insights into the possible uses of Poly-Pyrrol-Thiazol-Imine polymers in electrical and optoelectronic devices are provided by this study, which emphasizes the influence of molecular configuration on these polymers’ characteristics.
Potential biological applications of environment friendly synthesized iron oxide nanoparticles using Sageretia thea root extract
Authors: Israeel Muhammad , Iqbal Javed , Abbasi Banzeer Ahsan , Ijaz Shumaila , Ullah Rafi , Zarshan Farishta , Yaseen Tabassum , Khan Gul , Murtaza Ghulam , Ali Iftikhar , Alarjani Khaloud Mohammed , Elshikh Mohamed S , Rizwan Muhammad , Khan Shoaib , Iqbal Rashid
Published: November 2024

The green synthesis of Iron oxide nanoparticles (IONPs) has shown numerous advantages over conventional physical and chemical synthesis methods as these methods non-ecofriendly and uses toxic chemicals and complicated equipments. In present study, Iron oxide nanoparticles (IONPs) were created using simple, sustainable, eco-friendly and green chemistry protocol. The roots of novel medicinal plant Sageretia thea was used as a bio-template for the preparation of IONPs. Further, the synthesis of IONPs was confirmed using different analytical tools like UV-Vis, FT-IR, XRD, EDX, and SEM. The average sizes of (NPs) were found to be 16.04 nm. Further, asynthesized IONPs were evaluated for several biological potentials including antibacterial, antifungal Anti-radical potentials (DPPH) and cytotoxicity assays. Antibacterial potencies were investigated using bacterial strains (in the concentration range of 1000–31.25 µg/mL) revealing significant antibacterial potentials. ABA and SAU was reported to be least susceptible while KPN was observed to be most susceptible strain in bactericidal studies. Further, different fungal strains were used to investigate the antifungal potentials of IONPs (in the concentration range of 1000–31.25 µg/mL) and revealed strong antifungal potencies against different pathogenic strains. Furthermore, MRA, FA and ANI were most susceptible and ABA was least susceptible in fungicidal examination. Significant cytotoxicity potential was examined using brine shrimps cytotoxicity assay, thus revealing the cytotoxic potential of asynthesized IONPs. The IC50 for S. thea based IONPs was recorded as 33.85 µg/mL. Strong anti-radical potentials (DPPH) assay was performed to evaluate the ROS scavenging potential of S.T@IONPs. The highest scavenging potential was noted as 78.06%, TRP as 81.92% and TAC as 84% on maximum concentration of 200 µg/mL. In summary, our experimental results concluded, that asynthesized IONPs have strong antibacterial, antifungal, DPPH scavenging and cytotoxic potentials and can be used in different biological applications. In nutshell, our as-prepared nanoparticles have shown potential bioactivities and we recommend, different other in vitro and in vivo biological and bioactivities to further analyze the biological potentials.
Water in peripheral TM-interfaces of Orai1-channels triggers pore opening
Authors: Hopl Valentina , Tiffner Adéla , Wutscher Armin , Sallinger Matthias , Grabmayr Herwig , Prantl Magdalena , Fröhlich Maximilian , Söllner Julia , Weiß Sarah , Najjar Hadil , Nazarenko Yuliia , Harant Selina , Kriško Natalia , Fahrner Marc , Humer Christina , Höglinger Carmen , Krobath Heinrich , Bonhenry Daniel , Derler Isabella
Published: November 2024

The activation of the Ca2+-channel Orai1 via the physiological activator stromal interaction molecule 1 (STIM1) requires structural rearrangements within the entire channel complex involving a series of gating checkpoints. Focusing on the gating mechanism operating along the peripheral transmembrane domain (TM) 3/TM4-interface, we report here that some charged substitutions close to the center of TM3 or TM4 lead to constitutively active Orai1 variants triggering nuclear factor of activated T-cell (NFAT) translocation into the nucleus. Molecular dynamics simulations unveil that this gain-of-function correlates with enhanced hydration at peripheral TM-interfaces, leading to increased local structural flexibility of the channel periphery and global conformational changes permitting pore opening. Our findings indicate that efficient dehydration of the peripheral TM-interfaces driven by the hydrophobic effect is critical for maintaining the closed state of Orai1. We conclude that a charge close to the center of TM3 or TM4 facilitates concomitant hydration and widening of peripheral TM interfaces to trigger constitutive Orai1 pore opening to a level comparable to or exceeding that of native activated Orai1.
Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA
Authors: Huang Zhuoli , Zheng Yuhui , Wang Weikai , Zhou Wenwen , Zhang Yanbo , Wei Chen , Zhang Xiuqing , Jin Xin , Yin Jianhua
Published: November 2024

Pathway analysis is a crucial analytical phase in disease research on single-cell RNA sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge. However, currently available tools for generating cell-level pathway activity scores (PAS) exhibit computational inefficacy in large-scale scRNA-seq datasets. Additionally, disease-related pathways are often identified through cross-condition comparisons within specific cell types, overlooking potential patterns that involve multiple cell types. Here, we present single-cell pathway activity factor analysis (scPAFA), a Python library designed for large-scale single-cell datasets allowing rapid PAS computation and uncovering biologically interpretable disease-related multicellular pathway modules, which are low-dimensional representations of disease-related PAS alterations in multiple cell types. Application on colorectal cancer (CRC) datasets and large-scale lupus atlas over 1.2 million cells demonstrated that scPAFA can achieve over 40-fold reductions in the runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the heterogeneity of CRC and transcriptional abnormalities in lupus patients, respectively. Overall, scPAFA presents a valuable addition to existing research tools in disease research, with the potential to reveal complex disease mechanisms and support biomarker discovery at the pathway level.
Thermoresponsive degradable hydrogels with renewable surfaces for protein removal
Authors: Komatsu Syuuhei , Kamei Naoki , Kikuchi Akihiko
Published: November 2024

In this paper, the synthesis of a thermoresponsive degradable gel that can effectively remove proteins by surface degradation was reported. The thermoresponsive shrinkage behavior caused decomposition near the surface, effectively removing proteins.
A review on solid–solid heterogeneous interfacial interactions in electrocatalytic conversion of inorganic molecules
Authors: Liang Wen-Xuan , Han Huimin , Zhen Chun-Hua , Hua Yingjie , Li Jun-Tao , Zhou Yao
Published: November 2024

A schematic depiction of the various solid–solid interfaces existing in a porous electrode.
Coverage-dependent stability of RuxSiy on Ru(0001): a comparative DFT and XPS study
Authors: Cottom Jonathon , van Vliet Stefan , Meyer Jörg , Bliem Roland , Olsson Emilia
Published: November 2024

This work investigates the coverage dependent stability of silicon and oxygen on ruthenium, extending from defect centers in ruthenium bulk to the adsorption on the Ru(0001) surface.
Highly efficient CO2 capture and chemical fixation of a microporous (3, 36)-connected txt-type Cu(ii)-MOF with multifunctional sites
Authors: Dong Wenyu , Wang Zhaoxu , Cai Zuxian , Deng Yiqiang , Wang Guanyu , Zheng Baishu
Published: November 2024

A microporous (3, 36)-connected txt-type Cu(ii)-MOF (HNUST-17) with multifunctional sites (open copper sites, acylamide and amine groups) exhibits high-performance for CO2 capture and chemical conversion.
Uptake of Ammonia by Ice Surfaces at Atmospheric Temperatures
Authors: Richter Clemens , Gholami Shirin , Manoharan Yanisha , Buttersack Tillmann , Longetti Luca , Artiglia Luca , Ammann Markus , Bartels-Rausch Thorsten , Bluhm Hendrik
Published: November 2024

We present an ambient pressure X-ray photoelectron spectroscopy investigation of the adsorption of ammonia on ice over the temperature range of −23 °C to −50 °C. Previous flow tube studies...