bluuebunny/crossref_metadata_2025 huggingface dataset:
Herbal Amara extract induces gastric fundus relaxation via inhibition of the M2 muscarinic receptor
Authors: Piqué‐Borràs Maria‐Riera , Röhrl Johann , Künstle Gerald
Published: September 2024

Background

Impaired gastric accommodation is one of the most frequent symptoms of functional dyspepsia. The safety and efficacy of conventional treatments remain to be proven and alternative herbal therapies have been proposed to alleviate gastrointestinal symptoms. This preclinical study examined the role of herbal Amara extract (containing Artemisia absinthium, Centaurium erythraea, Cichorium intybus, Gentiana lutea, Juniperus communis, Achillea millefolium, Peucedanum ostruthium, Salvia officinalis, and Taraxacum extracts) on gastric (fundus) accommodation and the possible implication of muscarinic receptors in its regulation.

Methods

The effect of Amara extract on fundus motility was investigated in organ baths of smooth muscle strips isolated from the fundus of guinea pigs, and the role of the muscarinic receptor pathway was evaluated using functional and radioligand binding assays in cell lines expressing the M2 or M3 muscarinic receptor.

Key Results

Amara extract inhibited carbachol‐induced contraction of guinea pig smooth muscle strips in a dose‐dependent manner. This relaxant effect was not affected by the M3 antagonist J‐104129. Amara extract also inhibited M2, but not M3, receptor activity in CHO‐K1 cells (IC50 219 μg mL−1), and specifically bound the M2 receptor (IC50 294 μg mL−1). Of the nine herbal components of Amara extract, Juniperus communis, P. ostruthium, and Salvia officinalis inhibited M2 receptor activity (IC50 32.0, 20.8, and 20.1 μg mL−1, respectively), and P. ostruthium was sufficient to reverse carbachol‐induced ex vivo contraction of guinea pig fundic smooth muscles.

Conclusion and Inferences

Amara extract relaxes gastric smooth muscles by inhibiting the M2 muscarinic receptor. This study suggests the potential benefit of Amara extract for patients with impaired gastric accommodation.
Pathogenic Germline Variants in Uveal Melanoma Driver and BAP1‐Associated Genes in Finnish Patients with Uveal Melanoma
Authors: Repo Pauliina E. , Jakkula Eveliina , Hiltunen Juho , Putkuri Heidi , Staskiewicz‐Tuikkanen Aleksandra , Järvinen Reetta‐Stiina , Täll Martin , Raivio Virpi , Al‐Jamal Rana'a T. , Kivelä Tero T. , Turunen Joni A.
Published: September 2024

Uveal melanoma (UM) is a rare yet aggressive eye cancer causing over 50% mortality from metastasis. Familial UM, amounting to 1%–6% of patients in Finland and the United States, mostly lack identified genetic cause, while 8% show associations with other cancer syndromes. We searched novel genetic associations for predisposition to UM, additional to already studied BAP1 and MBD4, by using targeted amplicon sequencing of 19 genes associated with UM, BAP1, or renal cell carcinoma in 270 consecutively enrolled Finnish patients with UM. Key UM drivers GNAQ, GNA11, CYSLTR2, PLCB4, EIF1AX, and SF3B1 lacked pathogenic germline variants. One patient carried the pathogenic BRCA1 variant c.3626del p.(Leu1209*), and one harbored a novel truncating MET variant c.252C > G p.(Tyr84*), classified as likely pathogenic. FLCN and BRCA2, previously identified with pathogenic variants in patients with UM, did not have such variants in our cohort. Two patients were heterozygous for a pathogenic recessive BLM variant c.2824‐2A > T. None of the carriers of identified variants had familial UM. We identified BRCA1 and MET as genes with pathogenic germline variants in Finnish UM patients, each with a frequency of 0.4% (95% confidence interval, 0–2).
Network analysis of metabolomics, transcriptome and hormones reveals propionic acid‐mediated novel survival strategy against drought in wheat
Authors: Li Zongzhen , Lian Yanhao , Guo Hui , Li Chenxi , Ren Yongzhe , Xin Zeyu , Lin Tongbao , Wang Zhiqiang
Published: September 2024

Propionic acid (PA), a low‐molecular‐weight organic acid, is crucial to plant life metabolism. However, the regulatory mechanism of PA‐mediated drought resistance in wheat remains largely unknown. Herein, we reported on a regulatory network of PA‐mediated drought resistance in wheat using integrated transcriptome and metabolomics analysis and verified genes associated with drought resistance. Compared to the water‐treated group, the application of PA alleviated the damage of drought by increasing plant water content, antioxidant enzyme activities and decreasing the malondialdehyde level (MDA). Transcriptome and metabolomics analysis revealed that PA triggered upregulation of key genes and metabolites, including TaBCAT, TaALDH6A1, TaALDH7A1, TaCHI, TaFLS, chrysin, and galangin, which were involved in valine, leucine and isoleucine degradation or flavonoid biosynthesis, respectively. In addition, the expression of genes encoding auxin‐related transcription factors (TFs) strikingly increased, such as auxin/indoleacetic acid (AUX/IAA) and auxin response factor (ARF). Moreover, PA activated abscisic acid (ABA) and indole‐3‐acetic acid (IAA) signalling pathways. Taken together, our findings suggest that PA promotes energy metabolism and antioxidant activities to confer wheat drought resistance by introducing comprehensive and systemic effects of valine, leucine and isoleucine degradation flavonoid biosynthesis. Furthermore, activated AUX/IAA and ARF TFs might serve vital roles in drought resistance via modulating IAA signalling. This study provides novel insights into PA‐mediated crop resistance and the improvement of the agroecological environment.
The module consisting of transcription factor WRKY14 and thaumatin‐like protein TLP25 is involved in winter adaptation in Ammopiptanthus mongolicus
Authors: Liu Qi , Zeng Weiying , Qi Lanting , Li Xuting , Zhou Yijun , Gao Fei
Published: September 2024

Thaumatin‐like proteins (TLPs) are conserved proteins involved in the defense and stress responses of plants. Previous studies showed that several TLPs were accumulated in leaf apoplast in Ammopiptanthus mongolicus in winter, indicating that TLPs might be related to the adaptation to winter climate in A. mongolicus. To investigate the roles of TLPs in winter adaptation, we first analyzed the expression pattern of TLP genes in A. mongolicus and then focused on the biological function and regulation pathway of AmTLP25 gene. Several TLP genes, including AmTLP25, were upregulated during winter and in response to both cold and osmotic stress. Overexpression of the AmTLP25 gene led to an increased tolerance of transgenic Arabidopsis to freezing and osmotic stress. Furthermore, the elevated AmWRKY14 transcription factor during winter activated AmTLP25 gene expression by specifically binding to its promoter. It is speculated that the AmWRKY14 – AmTLP25 module contributes to the adaptation to temperate winter climate in A. mongolicus. Our research advances the current understanding of the biological function and regulatory pathway of TLP genes and provides valuable information for understanding the molecular mechanism of temperate evergreen broad‐leaved plants adapting to winter climate.
Response of submarine braided channels to varying inflow hydrographs: Geomorphic experiments and stratigraphic implications
Authors: Lai Steven Y. J. , Liu Hsin‐Yun , Foreman Brady Z. , Limaye Ajay B.
Published: September 2024

Submarine channels on the seafloor experience a range of turbidity current‐flood hydrographs. The characteristics of the flood hydrograph influence channel dimensions, the number of channel threads (i.e. braiding intensity) and the depositional properties of sandbars within the channels. However, the morphodynamic response of submarine braided channels to different hydrograph patterns is poorly understood. In this study, six geomorphic experiments are used to test how varied flood hydrographs affect the braiding intensity and sandbar geometry within submarine channels. Three experiments represent the control group with constant density‐current inflow, and three experiments use different time‐varying hydrograph patterns. The experiments show that, as the inflow‐to‐sediment discharge ratio increases, multiple small channels coalesce into a few main channels, causing a decrease in active braiding intensity defined by the channel threads with flow. When the flow returns to the initial low flow rate, active braiding intensity increases again. These observations show that the inflow‐to‐sediment discharge ratio determines the value of active braiding intensity. Additionally, active braiding intensity is directly proportional to dimensionless sediment‐stream power and dimensionless stream power, in agreement with previously established trends for both submarine and fluvial braided channels. In contrast to active braiding intensity changes, the measured sandbar aspect ratio and compactness ratio (i.e. ratio of planform area to perimeter) of submarine braided channels is insensitive to changes in the hydrograph. However, when inflows reach peak discharge, the higher transport capacity erodes pre‐existing deposits, forming noticeable erosional surfaces, and subsequently depositing thicker sandbars during that stage. These observations imply that sandbar planform morphology is largely insensitive to hydrograph, but hydrograph variability induces a greater variability in the resultant stratigraphic packages. The experimental results predict that field‐scale stratigraphy should be dominated by strata deposited during intervals of high flow, but that these strata will also exhibit reduced lateral continuity compared to formation scenarios with constant discharge.
Comparative Religious Studies: A Pedagogy for Troubled Times?
Authors: Jensen Christopher , Vargas‐O'Bryan Ivette
Published: September 2024

In this article, the authors explore their motivations for conceiving of and assembling the current issue on comparative religious studies as a viable pedagogical orientation for our troubled times. Situated in both the history of comparison as a method and scholarship on effective pedagogy, it argues that disciplined, scholarly, sound comparative thinking (whether at the level of textbook authorship, course design, or selection of classroom activities) can help us to respond to our students dynamically, reflexively, and, most importantly, humanely.
Becoming cultural and disability activists who challenge dominant narratives: The parallax effect of survivors of chemical warfare in Iran
Authors: Bajoghli Narges
Published: September 2024

This article discusses how Faye Ginsburg's work on ethnographic filmmaking, cultural activism, disability studies, and the parallax effect inspired me to collaborate over two decades with survivors of chemical warfare in Iran and Iraq. In order to continue to advocate for their needs for subsidized medical treatment, survivors of chemical weapons in Iran took up disability rights and carved out an important spaces as cultural activists to advocate for peace over war. Their creation of the Tehran Peace Museum and the many attendant media products it has produced, serve as an important parallax effect that has been instrumental in making critical dents into the extremely well‐funded state produced media about the war in Iran.
Novel non‐involutive solutions of the Yang–Baxter equation from (skew) braces
Authors: Doikou Anastasia , Rybołowicz Bernard
Published: September 2024

We produce novel non‐involutive solutions of the Yang–Baxter equation coming from (skew) braces. These solutions are generalisations of the known ones coming from braces and skew braces, and surprisingly in the case of braces, they are not necessarily involutive. In the case of two‐sided (skew) braces, one can assign such solutions to every element of the set. Novel bijective maps associated to the inverse solutions are also introduced. Moreover, we show that the recently derived Drinfeld twists of the involutive case are still admissible in the non‐involutive frame, and we identify the twisted ‐matrices and twisted coproducts. We observe, as in the involutive case, that the underlying quantum algebra is not a quasi‐triangular bialgebra, as one would expect, but a quasi‐triangular quasi‐bialgebra. The same applies to the quantum algebra of the twisted ‐matrices, contrary to the involutive case.
Small‐scale distribution of linear patterns of primes
Authors: Pandey Mayank , Woo Katharine
Published: September 2024

Let be a system of linear forms with finite complexity. In their seminal paper, Green and Tao showed the following prime number theorem for values of the system :
where are the corresponding local densities. In this paper, we demonstrate limits to equidistribution of these primes on small scales; we show the analog to Maier's result on primes in short intervals. In particular, we show that for all , there exist such that for sufficiently large, there exist boxes of sidelengths at least such that
Online peer-to-peer health communities for individuals affected by chronic kidney disease: a scoping review protocol
Authors: Coulson Neil , Beach Sarah , Buchanan Heather
Published: September 2024

Objective:

The objective of this scoping review is to identify and describe research exploring online peer-to-peer health communities for individuals affected by chronic kidney disease.

Introduction:

The proliferation of online peer-to-peer health communities has created new opportunities for individuals affected by chronic kidney disease to come together for mutual social, emotional, and informational support.

Inclusion criteria:

This scoping review will include qualitative, quantitative, mixed methods, and evidence synthesis studies, as well as gray literature relating to online peer-to-peer health communities for individuals affected by chronic kidney disease. The search will not be limited by language, time frame, geographic location, or publication date.

Methods:

This review will be undertaken in accordance with the JBI methodology for scoping reviews and reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist. The following databases will be searched: Cochrane Register of Controlled Trials (CENTRAL), CINAHL (EBSCOhost), Embase (Ovid), MEDLINE (Ovid), PsycINFO (Ovid), and Web of Science. Gray literature will be searched via MedNar, Google Scholar, and ProQuest Dissertations and Theses. After duplicates have been removed, 2 reviewers will independently screen the titles, abstracts, and full text of the eligible sources. Data will be extracted using a modified data extraction tool as per JBI guidance, and presented in tabular format, accompanied by a narrative summary describing how the findings relate to the scoping review questions.

Review registration:

Open Science Framework https://osf.io/kfj9v
Uncertainty Quantification in the Prediction of Remaining Useful Life Considering Multiple Failure Modes
Authors: Gandur Nazir Laureano , Ekwaro-Osire Stephen
Published: September 2024

Despite the substantive literature on remaining useful life (RUL) prediction, less attention is paid to the influence of epistemic uncertainty and aleatory uncertainty in multiple failure behaviors in the accuracy of RUL. The research question in this study was: can uncertainties be quantified in predicting the RUL of systems with multiple failure modes? The first objective was to quantify the uncertainties in the prediction of RUL, considering known multiple failure modes. This objective used vibration data from accelerated degradation experiments of rolling element bearings. The second objective was to calculate the uncertainties in the prediction of RUL, considering the multiple failure modes as unknown. The experimental data used in this objective were from run-to-failure tests of Li-ion batteries. An analysis was performed on how the uncertainties affect the RUL prediction in systems with known multiple failure modes and systems where the multiple failure modes were unknown. A Bayesian neural network (BNN) was used to quantify epistemic and aleatory uncertainty while predicting RUL. The results of the qualitative uncertainties on RUL in systems with multiple failure modes were presented and discussed. Also, the study yielded an RUL uncertainty quantification model for multiple failure modes. The proposed framework's performance in the RUL prediction was demonstrated. Finally, the epistemic and aleatory uncertainties were quantified in the system's RUL. It was shown that systems that fail due to the same failure mode tend to have similar uncertainty values over time. The results in this paper may lead to the design of more reliable systems that exhibit multiple failure modes.
Characterization of Three-Mode Combination Internal Resonances in Electrostatically Actuated Flexible–Flexible Microbeams
Authors: Kumar Praveen
Published: September 2024

Nonlinear intermodal coupling based on internal resonances in MEMS resonators has advanced significantly over the past two decades for various real-world applications. In this study, we demonstrate the existence of various three-mode combination internal resonances between the first five flexural modes of electrostatically actuated flexible–flexible beams and dynamic modal interaction between three modes via internal resonance. We first calculate the natural frequencies of the beam as a function of the stiffnesses of the transverse and rotational springs of the flexible supports, utilizing both analytical formulation and finite element analysis (FEA). Following this, we identify six combination internal resonances among the first five modes and use applied DC voltage to validate the exactness of one commensurable internal resonance condition (ω2=ω5−ω4). Subsequently, we studied a detailed forced vibration analysis corresponding to this resonance condition by solving the five-mode coupled governing equations through numerical time integration and the method of multiple scales. The results compellingly exhibit three-mode intermodal coupling among the second, fourth, and fifth modes as a function of excitation amplitude and frequency. Alongside this, intriguing nonlinear phenomena such as threshold behavior, saturation phenomena, and autoparametric instability are observed. Finally, this paper provides a systematic methodology for investigating three-mode combination internal resonances and related nonlinear dynamics, offering significant insights that could be used in observing phonon or mechanical lasing phenomena in MEMS resonators.
Three-Dimensional Space Chaotic Scrolls Generated by Memristive Hopfield Neural Network and Its Application in Robot Path Planning
Authors: Guo Linyang , Yang Runxian , Tang Mingjun , Wang Lixia , Xu Chunlin
Published: September 2024

In this paper, a novel three-dimensional space-scroll chaotic attractor is constructed by introducing piece-wise linear memristors into a three-neurons-based Hopfield neural network to simulate the electromagnetic influence on neural dynamics. The dynamical behaviors of the novel memristive Hopfield neural network are discussed by means of numerical methods including the Lyapunov exponent spectrum, bifurcation diagrams, phase plots and dynamic maps. Furthermore, we also investigated different neurons subject to the memristive electromagnetic influence, where the two-dimensional grid-scroll chaotic attractors can be generated by one neuron subjects to the electromagnetic influence and three-dimensional space-scroll chaotic attractors can be generated by all of the neurons subject to the memristive electromagnetic influence. Moreover, we present a three-dimensional space-scroll scroll attractor-based chaotic mobile robot system. Superiority of the proposed space-scroll-based chaotic mobile robot system compared to existing methods has been demonstrated through numerical simulations.
Experimental Design Validation of a Swirl-Stabilized Burner With Fluidically Variable Swirl Number
Authors: Eck Mattias E. G. , Nedden Philipp zur , von Saldern Jakob G. R. , Peisdersky Christoph , Orchini Alessandro , Paschereit Christian Oliver
Published: September 2024

Swirling flows are commonly used for flame stabilization in gas turbine combustors, which are hence equipped with suitable swirler units. In these units the air rotation, quantified by the swirl number, is fixed through the geometry and represents a parameter significantly affecting flame stability and dynamics. The possibility of a continuous swirl variation, on the other hand, would be advantageous for the assessment and control of thermoacoustic instabilities. This is especially true for fuel-flexible applications, for which different swirl numbers are needed to stabilize flames arising from the combustion of different fuels. Most swirl-varying systems rely on mechanical adjustments. In this work, instead, a novel swirl-stabilized burner is investigated experimentally, which is based exclusively on fluidic actuation. For the experimental assessment of the resulting flow field, the axial and azimuthal velocity components are determined through laser Doppler anemometry (LDA) measurements. The measurements are performed in a volume downstream of the burner's mixing tube. The data are processed and computed into swirl-numbers in order to quantify the degree of swirl as a function of the fluidic actuation. The characteristics of two different burner geometries are investigated, with and without a central cone within the swirler, respectively. The configuration with the cone is found to generate higher swirl over the investigated operational range. For this configuration, the technically relevant operating range is determined in which the swirl number can be continuously set from zero to around 0.9. Our experimental results show that fluidic actuation is a viable way to continuously change the swirl number, and that the achievable swirl range is quantitatively comparable to that of state-of-the-art swirl-stabilized burners.
Importance-Induced Customer Segmentation Using Explainable Machine Learning
Authors: Park Seyoung , Jiang Yilan , Kim Harrison
Published: September 2024

Customer segmentation plays a critical role in enhancing a company’s product penetration rate in the market. It enables numerous downstream applications such as customer-oriented product development and trend analysis. Previous approaches to customer segmentation have relied either on survey-based methods or data-driven approaches. However, these methods face challenges such as high human labor requirements or the generation of noisy segments. To address these challenges, this paper proposes a new methodology based on data-driven network construction and an importance-enhanced framework. The framework incorporates two techniques: (1) the utilization of a neural network model to compute feature importance values and (2) the proposal of a novel network connection rule. This framework addresses the limitation of the previous approach, sentiment-polarity-based networking, by connecting customers based on feature importance. We further validated the effectiveness of the framework using three real-world datasets and demonstrated that the proposed method outperformed the previous approach.
Error Sensitivity Analysis of a 1T2R Kinematically Redundant Parallel Mechanism With Closed-Loop Chain
Authors: Zhou Zhizhen , Qu Haibo , Li Xiao , Hu Buqin , Guo Sheng
Published: September 2024

In this paper, a generalized method for error modeling of the spatial 1T2R three degrees-of-freedom kinematically redundant parallel mechanism with a closed-loop chain is proposed, which is based on the matrix differential method. First, the detailed process of generalized error modeling and error analysis are described. Based on the proposed method, the error model of the spatial 3PRR(RR)S-P (P—prismatic joint, R—revolute joint, S—spherical joint, and the underline indicates that the joint is the actuator) kinematically redundant parallel mechanism is established as an example, and the correctness of the error model is verified by combining forward with inverse kinematics. Then, the patterns affecting the output error of the moving platform are discussed for the case where the mechanism contains only static error or dynamic error, respectively. In addition, the error sensitivity indices are defined to evaluate the error sensitivity of the moving platform to different redundant parameters L4 under a certain pose. Finally, in order to identify the key error terms, the sensitivity of the output error of the mechanism to a single error term is analyzed. The results show that the error sensitivity of the spatial kinematically redundant parallel mechanism can be effectively reduced by adjusting the kinematically redundant parameters, so that the mechanism can maintain a low error sensitivity in a certain pose.
Computational Aeroacoustics of Low-Pressure Axial Fans Installed in Parallel
Authors: Ghosh Debarshee , Vourakis Michail , Andersson Niklas , Etemad Sassan
Published: September 2024

Ducted rotor-only low-pressure axial (LPA) fans play an integral role in automotive thermal management of electric vehicles and are the primary source of noise from the underhood region. Multiple LPA fans are often placed in parallel in cooling packages of electric vehicles. There is little scientific work concerning aeroacoustics of ducted LPA fans operating in parallel. This work aims to address this gap through hybrid computational aeroacoustic simulations. Three-dimensional, full-annulus, transient simulations are done using the delayed detached eddy simulation (DDES) turbulence model. First, a numerical validation study is presented, where aerodynamic and aeroacoustic results from this work are compared to experimental results for a LPA fan issued by the European Acoustics Association (EAA). In the second part, aeroacoustic performance of two-fans placed in parallel is presented. A local diffusion zone is observed in the region where the two-fans are closest to one another. A previously unidentified vortex which envelopes the local diffusion zone is observed. For two-fans in parallel, the amplification of the acoustic spectrum scales in accordance to having two identical equally strong sound sources, i.e., by 6 dB. The scaling of the acoustic spectrum for two-fans in parallel in comparison to a single-fan suggests limited interaction between the acoustic field of the two-fans.
Ultrasound of the spleen – an update on measurements, reference values, and influencing factors. A systematic review.
Authors: Lucius Claudia , Meier Jennifer , Gschmack Anna , Zervides Constantinos , Jenssen Christian , Dong Yi , Graumann Ole , Petry Marieke , Dietrich Christoph F
Published: September 2024

Reliable and reproducible measurement methods have been established, and reference values are used in almost all scientific disciplines. The knowledge of reference values is crucial to distinguish physiological from pathological processes and, therefore, subsequently, for the clinical management of patients. The image storage and documentation of measurements and normal findings should be part of quality assurance in imaging. This paper aims to review published literature and provide current knowledge of sonographic measurements of the spleen, examination techniques, and knowledge of normal values with their possible clinical implications. Moreover, the role of clinical influencing factors such as age, gender, or ethnicity is also analyzed.
Endoscopy and endoscopic ultrasound for embedded or migratory digestive foreign body
Authors: Xie Jia , Qin Yan , Wang Mojin , Wang Rui
Published: September 2024

Embedded or migratory ingested foreign bodies (FBs) may be a disaster when not found intraluminally and can be seriously life-threatening. Endoscopic ultrasound (EUS) has advantages of transmural, close range and real-time imaging. Under its guidance, minimally invasive endoscopic removal of FBs and abscess drainage become available and safe to avoid unnecessary surgery. However, relatively few diagnostic applications of EUS have been reported. Endoscopic removal and abscess drainage with or without EUS-guidance were even scarce. We found 21 cases of migratory FBs reported in which EUS was used to diagnose and/or treat including our case. We further summarized clinical characteristics and EUS manifestations of embedded or migratory FBs for future differentiation, and treatment strategies by endoscopy and EUS. EUS is a valuable tool in recognizing and differentiating embedded or migratory FBs. EUS-guided endoscopic removal is a minimally invasive, safe and innovative solution. EUS with novel device also assists in sufficient and secure drainage for FBs related abscess collections. A multidisciplinary team consult is sometimes mandatory for complicated cases. This would break a conceptual barrier in therapeutic endoscopy.
Promoting subsurface Sn incorporation at Nb(100) oxide surface sites leading to homogeneous Nb3Sn film growth for superconducting radiofrequency applications
Authors: Willson Sarah A. , Farber Rachael G. , Sibener S. J.
Published: September 2024

For next-generation superconducting radiofrequency (SRF) cavities, the interior walls of existing Nb SRF cavities are coated with a thin Nb3Sn film to improve the superconducting properties for more efficient, powerful accelerators. The superconducting properties of these Nb3Sn coatings are limited due to inhomogeneous growth resulting from poor nucleation during the Sn vapor diffusion procedure. To develop a predictive growth model for Nb3Sn grown via Sn vapor diffusion, we aim to understand the interplay between the underlying Nb oxide morphology, Sn coverage, and Nb substrate heating conditions on Sn wettability, intermediate surface phases, and eventual Nb3Sn nucleation. In this work, Nb-Sn intermetallic species are grown on a single crystal Nb(100) in an ultrahigh vacuum chamber equipped with in situ surface characterization techniques including scanning tunneling microscopy, Auger electron spectroscopy, and x-ray photoelectron spectroscopy. Sn adsorbate behavior on oxidized Nb was examined by depositing Sn with submonolayer precision on a Nb substrate held at varying deposition temperatures (Tdep). Experimental data of annealed intermetallic adlayers provide evidence of how Nb substrate oxidization and Tdep impact Nb-Sn intermetallic coordination. The presented experimental data contextualize how vapor and substrate conditions, such as the Sn flux and Nb surface oxidation, drive homogeneous Nb3Sn film growth during the Sn vapor diffusion procedure on Nb SRF cavity surfaces. This work, as well as concurrent growth studies of Nb3Sn formation that focus on the initial Sn nucleation events on Nb surfaces, will contribute to the future experimental realization of optimal, homogeneous Nb3Sn SRF films.
Influence of hydrogen-bonded 3-mercaptopropionic acid bilayers on binary self-assembled monolayer formation
Authors: Penland Lindsey N. , Hirushan H. H. , Dissanayake N. , Farber Rachael G.
Published: September 2024

The influence of the monolayer order, defect density, and bilayer formation on the formation of binary self-assembled monolayers (SAMs) was investigated via the solution-phase displacement of 3-mercaptopropionic acid (MPA) by 1-decanethiol (DT). The ultrahigh vacuum scanning tunneling microscopy results confirm that well-ordered, pristine MPA SAMs are displaced at slower rates than MPA SAMs with less long-range order and greater defect density. Furthermore, MPA samples containing regions of an MPA bilayer displayed the slowest rates of displacement with DT. For pristine MPA samples and MPA samples with regions of an MPA bilayer, displacement with DT resulted in the formation of the low-density, lying down phase of DT. Our results suggest that the presence of an MPA bilayer, the result of hydrogen bonding between carboxylic acid groups in MPA, significantly lowers the rate of total displacement of MPA by DT compared to moderately defected MPA SAMs. These results highlight the importance of the structure, composition, and intermolecular forces, such as hydrogen bonding, when considering binary SAM formation via solution-phase displacement methods.
Contribution of direct InhA inhibitors to novel drug regimens in a mouse model of tuberculosis
Authors: Encinas Lourdes , Li Si-Yang , Rullas-Trincado Joaquin , Tasneen Rokeya , Tyagi Sandeep , Soni Heena , Garcia-Perez Adolfo , Lee Jin , González del Río Rubén , De Mercado Jaime , Sousa Verónica , Sosič Izidor , Gobec Stanislav , Mendoza-Losana Alfonso , Converse Paul J. , Mdluli Khisi , Fotouhi Nader , Barros-Aguirre David , Nuermberger Eric L.
Published: September 2024

Isoniazid is an important first-line medicine to treat tuberculosis (TB). Isoniazid resistance increases the risk of poor treatment outcomes and development of multidrug resistance, and is driven primarily by mutations involving
katG
, encoding the prodrug-activating enzyme, rather than its validated target, InhA. The chemical tractability of InhA has fostered efforts to discover direct inhibitors of InhA (DIIs). In this study, we bridge the gap in understanding the potential contribution of DIIs to novel combination regimens and demonstrate a clear distinction of DIIs, like GSK693 and the newly described GSK138, from isoniazid, based on activity against clinical isolates and contribution to novel drug regimens. The results suggest that DIIs, specifically GSK138 and GSK693, could be promising partners in novel drug regimens, including those used against isoniazid-resistant TB, potentially enhancing their efficacy and/or preventing the selection of resistant mutants and supporting the continued exploration of InhA as a promising target for TB drug development.
Tetracistronic minigenomes elucidate a functional promoter for Ghana virus and unveils Cedar virus replicase promiscuity for all henipaviruses
Authors: Haas Griffin D. , Kowdle Shreyas , Schmitz Katharina S. , Azarm Kristopher D. , Johnson Kendra N. , Klain William R. , Freiberg Alexander N. , Cox Robert M. , Plemper Richard K. , Lee Benhur
Published: September 2024

Batborne henipaviruses, such as Nipah and Hendra viruses, represent a major threat to global health due to their propensity for spillover, severe pathogenicity, and high mortality rate in human hosts. Coupled with the absence of approved vaccines or therapeutics, work with the prototypical species and uncharacterized, emergent species is restricted to high biocontainment facilities. There is a scarcity of such specialized spaces for research, and often, the scope and capacity of research, which can be conducted at BSL-4, is limited. Therefore, there is a pressing need for innovative life-cycle modeling systems to enable comprehensive research within lower biocontainment settings. This work showcases tetracistronic, transcription, and replication-competent minigenomes for the Nipah, Hendra, and Cedar viruses, which encode viral proteins facilitating budding, fusion, and receptor binding. We validate the functionality of all encoded viral proteins and demonstrate a variety of applications to interrogate the viral life cycle. Notably, we found that the Cedar virus replicase exhibits remarkable promiscuity, efficiently driving replication and transcription of minigenomes from all tested henipaviruses. We also apply this technology to Ghana virus (GhV), an emergent species that has so far not been isolated in culture. We demonstrate that the reported sequence of GhV is incomplete, but that this missing sequence can be substituted with analogous sequences from other henipaviruses. The use of our GhV system establishes the functionality of the GhV replicase and identifies two antivirals that are highly efficacious against the GhV polymerase.

IMPORTANCE

Henipaviruses are recognized as significant global health threats due to their high mortality rates and lack of effective vaccines or therapeutics. Due to the requirement for high biocontainment facilities, the scope of research which may be conducted on henipaviruses is limited. To address this challenge, we developed innovative tetracistronic, transcription, and replication-competent minigenomes. We demonstrate that these systems replicate key aspects of the viral life cycle, such as budding, fusion, and receptor binding, and are safe for use in lower biocontainment settings. Importantly, the application of this system to the Ghana virus revealed that its known sequence is incomplete; however, substituting the missing sequences with those from other henipaviruses allowed us to overcome this challenge. We demonstrate that the Ghana virus replicative machinery is functional and can identify two orally efficacious antivirals effective against it. Our research offers a versatile system for life-cycle modeling of highly pathogenic henipaviruses at low biocontainment.
Characterization and functional analysis of
Toxoplasma
Golgi-associated proteins identified by proximity labeling
Authors: Pasquarelli Rebecca R. , Quan Justin J. , Cheng Emily S. , Yang Vivian , Britton Timmie A. , Sha Jihui , Wohlschlegel James A. , Bradley Peter J.
Published: September 2024

Toxoplasma gondii
possesses a highly polarized secretory pathway that contains both broadly conserved eukaryotic organelles and unique apicomplexan organelles, which play essential roles in the parasite’s lytic cycle. As in other eukaryotes, the
T. gondii
Golgi apparatus sorts and modifies proteins prior to their distribution to downstream organelles. Many of the typical trafficking factors found involved in these processes are missing from apicomplexan genomes, suggesting that these parasites have evolved unique proteins to fill these roles. Here, we identify a Golgi-localizing protein (ULP1), which is structurally similar to the eukaryotic trafficking factor p115/Uso1. We demonstrate that depletion of ULP1 leads to a dramatic reduction in parasite fitness that is the result of defects in microneme secretion, invasion, replication, and egress. Using ULP1 as bait for TurboID proximity labeling and immunoprecipitation, we identify 11 more Golgi-associated proteins and demonstrate that ULP1 interacts with the
T. gondii
-conserved oligomeric Golgi (COG) complex. These proteins include both conserved trafficking factors and parasite-specific proteins. Using a conditional knockdown approach, we assess the effect of each of these 11 proteins on parasite fitness. Together, this work reveals a diverse set of
T. gondii
Golgi-associated proteins that play distinct roles in the secretory pathway. As several of these proteins are absent outside of the Apicomplexa, they represent potential targets for the development of novel therapeutics against these parasites.

IMPORTANCE

Apicomplexan parasites such as
Toxoplasma gondii
infect a large percentage of the world’s population and cause substantial human disease. These widespread pathogens use specialized secretory organelles to infect their host cells, modulate host cell functions, and cause disease. While the functions of the secretory organelles are now better understood, the Golgi apparatus of the parasite remains largely unexplored, particularly regarding parasite-specific innovations that may help direct traffic intracellularly. In this work, we characterize ULP1, a protein that is unique to parasites but shares structural similarity to the eukaryotic trafficking factor p115/Uso1. We show that ULP1 plays an important role in parasite fitness and demonstrate that it interacts with the conserved oligomeric Golgi (COG) complex. We then use ULP1 proximity labeling to identify 11 additional Golgi-associated proteins, which we functionally analyze via conditional knockdown. This work expands our knowledge of the
Toxoplasma
Golgi apparatus and identifies potential targets for therapeutic intervention.
Exploring the tolerable region for HiBiT tag insertion in the hepatitis B virus genome
Authors: Murayama Asako , Igarashi Hitomi , Yamada Norie , Aly Hussein Hassan , Toyama Masaaki , Isogawa Masanori , Shimakami Tetsuro , Kato Takanobu
Published: September 2024

A cell culture system that allows the reproduction of the hepatitis B virus (HBV) life cycle is indispensable to exploring novel anti-HBV agents. To establish the screening system for anti-HBV agents, we exploited the high affinity and bright luminescence (HiBiT) tag and comprehensively explored the regions in the HBV genome where the HiBiT tag could be inserted. The plasmids for the HiBiT-tagged HBV molecular clones with a 1.38-fold HBV genome length were prepared. The HiBiT tag was inserted into five regions: preS1, preS2, hepatitis B e (HBe), hepatitis B X (HBx), and hepatitis B polymerase (HB pol). HiBiT-tagged HBVs were obtained by transfecting the prepared plasmids into sodium taurocholate cotransporting polypeptide-transduced HepG2 (HepG2/NTCP) cells, and their infectivity was evaluated in human primary hepatocytes and HepG2/NTCP cells. Among the evaluated viruses, the infection of HiBiT-tagged HBVs in the preS1 or the HB pol regions exhibited a time-dependent increase of the hepatitis B surface antigen (HBsAg) level after infection to HepG2/NTCP cells as well as human primary hepatocytes. Immunostaining of the hepatitis B core (HBc) antigen in infected cells confirmed these viruses are infectious to those cells. However, the time-dependent increase of the HiBiT signal was only detected after infection with the HiBiT-tagged HBV in the preS1 region. The inhibition of this HiBiT-tagged HBV infection in human primary hepatocytes and HepG2/NTCP cells by the preS1 peptide could be detected by measuring the HiBiT signal. The infection system with the HiBiT-tagged HBV in HepG2/NTCP cells facilitates easy, sensitive, and high-throughput screening of anti-HBV agents and will be a useful tool for assessing the viral life cycle and exploring antiviral agents.

IMPORTANCE

Hepatitis B virus (HBV) is the principal causative agent of chronic hepatitis. Despite the availability of vaccines in many countries, HBV infection has spread worldwide and caused chronic infection. In chronic hepatitis B patients, liver inflammation leads to cirrhosis, and the accumulation of viral genome integration into host chromosomes leads to the development of hepatocellular carcinoma. The currently available treatment strategy cannot expect the eradication of HBV. To explore novel anti-HBV agents, a cell culture system that can detect HBV infection easily is indispensable. In this study, we examined the regions in the HBV genome where the high affinity and bright luminescence (HiBiT) tag could be inserted and established an HBV infection system to monitor infection by measuring the HiBiT signal by infecting the HiBiT-tagged HBV in sodium taurocholate cotransporting polypeptide-transduced HepG2 (HepG2/NTCP) cells. This system can contribute to screening for novel anti-HBV agents.
PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in
Escherichia coli
Authors: Choi Byoung Jun , Choi Umji , Ryu Dae-Beom , Lee Chang-Ro
Published: September 2024

Tetracyclines and glycylcycline are among the important antibiotics used to combat infections caused by multidrug-resistant Gram-negative pathogens. Despite the clinical importance of these antibiotics, their mechanisms of resistance remain unclear. In this study, we elucidated a novel mechanism of resistance to tetracycline and glycylcycline antibiotics via lipopolysaccharide (LPS) modification. Disruption of the
Escherichia coli
PhoPQ two-component system, which regulates the transcription of various genes involved in magnesium transport and LPS modification, leads to increased susceptibility to tetracycline, minocycline, doxycycline, and tigecycline. These phenotypes are caused by enhanced expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core sugar of LPS. PhoPQ-mediated regulation of EptB expression appears to affect the intracellular transportation of doxycycline. Disruption of EptB increases resistance to tetracycline and glycylcycline antibiotics, whereas the other two phosphoethanolamine transferases, EptA and EptC, that participate in the modification of other LPS residues, are not associated with resistance to tetracyclines and glycylcycline. Overall, our results demonstrated that PhoPQ-mediated modification of a specific residue of LPS by phosphoethanolamine transferase EptB governs intrinsic resistance to tetracycline and glycylcycline antibiotics.

IMPORTANCE

Elucidating the resistance mechanisms of clinically important antibiotics helps in maintaining the clinical efficacy of antibiotics and in the prescription of adequate antibiotic therapy. Although tetracycline and glycylcycline antibiotics are clinically important in combating multidrug-resistant Gram-negative bacterial infections, their mechanisms of resistance are not fully understood. Our research demonstrates that the
E. coli
PhoPQ two-component system affects resistance to tetracycline and glycylcycline antibiotics by controlling the expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core residue of lipopolysaccharide (LPS). Therefore, our findings highlight a novel resistance mechanism to tetracycline and glycylcycline antibiotics and the physiological significance of LPS core modification in
E. coli
.
Deep marine records of Deccan Trap volcanism before the Cretaceous–Paleogene (K–Pg) mass extinction
Authors: Sinnesael Matthias , Percival Lawrence M.E. , Schulz Toni , Vellekoop Johan , Goderis Steven , Daems Kato , Gao Yue , Leermakers Martine , Montanari Alessandro , Coccioni Rodolfo , Koeberl Christian , Claeys Philippe
Published: September 2024

The Cretaceous–Paleogene boundary is marked by a large impact and coeval mass extinction event that occurred 66 m.y. ago. Contemporaneous emplacement of the volcanic Deccan Traps also affected global climate before, during, and after the mass extinction. Many questions remain about the timing and eruption rates of Deccan volcanism, its precise forcing of climatic changes, and its signature in the marine geochemical sedimentary proxy record. Here, we compile new and existing mercury (Hg) concentration and osmium isotope (187Os/188Os) records for various stratigraphic sections worldwide. Both geochemical proxies have been suggested to reflect past variations in Deccan volcanic activity. New data from deep marine pelagic carbonate records are compared to contemporaneous records from shallower marine sites correlated through high-resolution cyclostratigraphic age models. The robustness of the proxy records is evaluated on a common timeline and compared to two different Deccan eruption history scenarios. Results show that the global 187Os/188Os signal is clearly reproducible, while the global Hg record does not form a consistent pattern. Moreover, the deep marine sections investigated do not record clear variations in the Hg cycle, particularly in the latest Cretaceous, prior to the extinction event. A detailed reevaluation of the precise depth of the redistribution of impactor-sourced platinum group elements does not exclude the possibility of a minor drop in 187Os/188Os corresponding with a pulse of Deccan volcanism ~50,000 years before the Cretaceous–Paleogene boundary. Simple Os isotope mass balance modeling indicates that the latest Cretaceous was marked by significant levels of basalt weathering. CO2 sequestration during this weathering likely overwhelmed the emission of Deccan volatiles, thereby contributing to the end of the late Maastrichtian warming.