bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of periplasmic solute binding proteins with specificity for ketone bodies: β‐hydroxybutyrate binding proteins
Authors: Kane Bryant J. , Okuda‐Shimazaki Junko , Andrews Madelyn M. , Kerrigan Joseph A. , Murphy Kyle V. , Sode Koji 
Published: June 2024

AbstractPolyhydroxyalkanoates are a class of biodegradable, thermoplastic polymers which represent a major carbon source for various bacteria. Proteins which mediate the translocation of polyhydroxyalkanoate breakdown products, such as β‐hydroxybutyrate (BHB)—a ketone body which in humans serves as an important biomarker, have not been well characterized. In our investigation to screen a solute‐binding protein (SBP) which can act as a suitable recognition element for BHB, we uncovered insights at the intersection of bacterial metabolism and diagnostics. Herein, we identify SBPs associated with putative ATP‐binding cassette transporters that specifically recognize BHB, with the potential to serve as recognition elements for continuous quantification of this analyte. Through bioinformatic analysis, we identified candidate SBPs from known metabolizers of polyhydroxybutyrate—including proteins from Cupriavidus necator, Ensifer meliloti, Paucimonas lemoignei, and Thermus thermophilus. After recombinant expression in Escherichia coli, we demonstrated with intrinsic tryptophan fluorescence spectroscopy that four candidate proteins interacted with BHB, ranging from nanomolar to micromolar affinity. Tt.2, an intrinsically thermostable protein from Thermus thermophilus, was observed to have the tightest binding and specificity for BHB, which was confirmed by isothermal calorimetry. Structural analyses facilitated by AlphaFold2, along with molecular docking and dynamics simulations, were used to hypothesize key residues in the binding pocket and to model the conformational dynamics of substrate unbinding. Overall, this study provides strong evidence identifying the cognate ligands of SBPs which we hypothesize to be involved in prokaryotic cellular translocation of polyhydroxyalkanoate breakdown products, while highlighting these proteins' promising biotechnological application.
Molecular basis for different substrate‐binding sites and chaperone functions of the BRICHOS domain
Authors: Chen Gefei , Wang Yu , Zheng Zihan , Jiang Wangshu , Leppert Axel , Zhong Xueying , Belorusova Anna , Siegal Gregg , Jegerschöld Caroline , Koeck Philip J. B. , Abelein Axel , Hebert Hans , Knight Stefan D. , Johansson Jan 
Published: June 2024

AbstractProteins can misfold into fibrillar or amorphous aggregates and molecular chaperones act as crucial guardians against these undesirable processes. The BRICHOS chaperone domain, found in several otherwise unrelated proproteins that contain amyloidogenic regions, effectively inhibits amyloid formation and toxicity but can in some cases also prevent non‐fibrillar, amorphous protein aggregation. Here, we elucidate the molecular basis behind the multifaceted chaperone activities of the BRICHOS domain from the Bri2 proprotein. High‐confidence AlphaFold2 and RoseTTAFold predictions suggest that the intramolecular amyloidogenic region (Bri23) is part of the hydrophobic core of the proprotein, where it occupies the proposed amyloid binding site, explaining the markedly reduced ability of the proprotein to prevent an exogenous amyloidogenic peptide from aggregating. However, the BRICHOS‐Bri23 complex maintains its ability to form large polydisperse oligomers that prevent amorphous protein aggregation. A cryo‐EM‐derived model of the Bri2 BRICHOS oligomer is compatible with surface‐exposed hydrophobic motifs that get exposed and come together during oligomerization, explaining its effects against amorphous aggregation. These findings provide a molecular basis for the BRICHOS chaperone domain function, where distinct surfaces are employed against different forms of protein aggregation.
Structural study for substrate recognition of human N‐terminal glutamine amidohydrolase 1 in the arginine N‐degron pathway
Authors: Kang Jin Mo , Park Joon Sung , Lee Jae Seok , Jang Jun Young , Han Byung Woo 
Published: June 2024

AbstractThe N‐degron pathway determines the half‐life of proteins by selectively destabilizing the proteins bearing N‐degrons. N‐terminal glutamine amidohydrolase 1 (NTAQ1) plays an essential role in the arginine N‐degron (Arg/N‐degron) pathway as an initializing enzyme via the deamidation of the N‐terminal (Nt) glutamine (Gln). However, the Nt‐serine‐bound conformation of hNTAQ1 according to the previously identified crystal structure suggests the possibility of other factors influencing the recognition of Nt residues by hNTAQ1. Hence, in the current study, we aimed to further elucidate the substrate recognition of hNTAQ1; specifically, we explored 12 different substrate‐binding conformations of hNTAQ1 depending on the subsequent residue of Nt‐Gln. Results revealed that hNTAQ1 primarily interacts with the protein Nt backbone, instead of the side chain, for substrate recognition. Here, we report that the Nt backbone of proteins appears to be a key component of hNTAQ1 function and is the main determinant of substrate recognition. Moreover, not all second residues from Nt‐Gln, but rather distinctive and charged residues, appeared to aid in detecting substrate recognition. These new findings define the substrate‐recognition process of hNTAQ1 and emphasize the importance of the subsequent Gln residue in the Nt‐Gln degradation system. Our extensive structural and biochemical analyses provide insights into the substrate specificity of the N‐degron pathway and shed light on the mechanism underlying hNTAQ1 substrate recognition. An improved understanding of the protein degradation machinery could aid in developing therapies to promote overall health through enhanced protein regulation, such as targeted protein therapies.
The oligomeric states of dye‐decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation
Authors: Lučić Marina , Allport Thomas , Clarke Thomas A. , Williams Lewis J. , Wilson Michael T. , Chaplin Amanda K. , Worrall Jonathan A. R. 
Published: June 2024

AbstractA common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye‐decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A‐type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo‐EM on preparations of the B‐type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo‐EM data detected sub‐populations of higher‐order oligomers, with one of these formed by an arrangement of two B‐type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long‐range electron transfer for substrate oxidation and in the “storage” of oxidizable equivalents on the heme until a two‐electron donor is available.
Phenotypic and genotypic characterization of fifty strains of Beauveria spp. (Ascomycota, Cordycipitaceae) fungal entomopathogens from diverse geographic origins against the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae)
Authors: Reyes‐Haro Laura , Prince Gillian , Granja‐Travez Rommel Santiago , Chandler David 
Published: June 2024

AbstractBACKGROUNDThe diamondback moth (DBM) (Plutella xylostella) causes large losses to global crop production. Conventional insecticides are losing effectiveness due to resistance. Consequently, there is a growing interest in sustainable control methods like entomopathogenic fungi (EPF) in Integrated Pest Management. However, the field efficacy of fungi varies due to environmental influences. In this study, a group of 50 Beauveria strains sourced from different locations were characterized by genotype and phenotype with respect to their conidial production, temperature and UV‐B radiation tolerance, and virulence against DBM.RESULTSPhylogenetic analysis revealed two distinct species: Beauveria bassiana (84%) and B. pseudobassiana (16%). Most strains showed optimal growth between 25 °C and 28 °C, with germination severely affected at 10 °C and 33 °C. Notably, 44% displayed high resistance to UV‐B radiation (5.94 kJ  m−2), with germination rates between 60.9% and 88.1%. Geographical origin showed no correlation with temperature or UV radiation tolerance. In virulence experiments, 52% of strains caused mortality rates exceeding 80% in DBM second instars at 7 days after exposure to a 4 mL conidial suspension (107 conidia/mL).CONCLUSIONSurvival under environmental conditions is crucial for EPF‐based commercial products against DBM. Results suggest strain tolerance to environmental stressors is more tied to specific micro‐climatic factors than geographical origin. Each strain exhibited unique characteristics; for example, the most virulent strain (#29) was highly UV‐sensitive. Therefore, characterizing diverse strains provides essential genotypic and phenotypic insights, which are fundamental for understanding their role as biocontrol agents while facilitating efficient biopesticide product development and uptake. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
The therapeutic potential of typical plant‐derived compounds for the management of metabolic disorders
Authors: Roy Debajyoti , Kaur Prabhjot , Ghosh Maitrayee , Choudhary Deepika , Rangra Naresh Kumar 
Published: June 2024

AbstractObesity and Type 2 diabetes are prevalent metabolic dysfunctions that present significant health challenges worldwide. Available cures for these ailments have constraints with accompanying unwanted effects that persistently exist. Compounds originated from plants have recently been introduced as hopeful remedies to treat metabolic disorders because of their diverse pharmacological activities. This detailed observation gives an introduction into the treatment capacity of plant‐derived compounds regarding metabolic syndromes while analyzing various groups alongside their performance in this field despite unique mechanisms designed by nature itself. Interestingly, this study provides some examples including curcumin, resveratrol, quercetin, berberine, epigallocatechin gallate (EGCG), and capsaicin, which highlights potential therapeutic impacts for future testing. However, current clinical trials inspecting human studies investigating efficacies concerning metabolism challenge present limitations. Finally, the review weighs up bad reactions possibly inflicted after administering plant‐originated materials though suggestive insights will be provided later. Above all, it outlines the chance to identify novel therapies encapsulated within natural substances based upon recent developments could hold significant promise toward managing misplaced metabolisms globally.
Two prospective, multicenter studies for the identification of biomarker signatures for early detection of pulmonary hypertension (PH): The CIPHER and CIPHER‐MRI studies
Authors: Lawrie Allan , Chin Kelly , Fong Yiu‐Lian , Gargano Cynthia , Gitton Xavier , He Cheng , Kiely David G. , Zhou Li , Zhou Lihan , Maron Bradley A. , Quinn Debbie , Rosenkranz Stephan , Stamatiadis Dimitri , Toshner Mark , Wilkins Martin R. , Howard Luke , Preston Ioana R. 
Published: June 2024

AbstractA blood test identifying patients at increased risk of pulmonary hypertension (PH) could streamline the investigative pathway. The prospective, multicenter CIPHER study aimed to develop a microRNA‐based signature for detecting PH in breathless patients and enrolled adults with a high suspicion of PH who had undergone right heart catheterization (RHC). The CIPHER‐MRI study was added to assess the performance of this CIPHER signature in a population with low probability of having PH who underwent cardiac magnetic resonance imaging (cMRI) instead of RHC. The microRNA signature was developed using a penalized linear regression (LASSO) model. Data were modeled both with and without N‐terminal pro‐brain natriuretic peptide (NT‐proBNP). Signature performance was assessed against predefined thresholds (lower 98.7% CI bound of ≥0.73 for sensitivity and ≥0.53 for specificity, based on a meta‐analysis of echocardiographic data), using RHC as the true diagnosis. Overall, 926 CIPHER participants were screened and 888 were included in the analysis. Of 688 RHC‐confirmed PH cases, approximately 40% were already receiving PH treatment. Fifty microRNA (from 311 investigated) were algorithmically selected to be included in the signature. Sensitivity [97.5% CI] of the signature was 0.85 [0.80–0.89] for microRNA‐alone and 0.90 [0.86–0.93] for microRNA+NT‐proBNP, and the corresponding specificities were 0.33 [0.24–0.44] and 0.28 [0.20–0.39]. Of 80 CIPHER‐MRI participants with evaluable data, 7 were considered PH‐positive by cMRI whereas 52 were considered PH‐positive by the microRNA signature. Due to low specificity, the CIPHER miRNA‐based signature for PH (either with or without NT‐proBNP in model) did not meet the prespecified diagnostic threshold for the primary analysis.
Robust stabilization of uncertain switched nonlinear systems via saturated impulsive control
Authors: Pan Shiyao , Xie Xiangpeng , Gao Lixin 
Published: June 2024

AbstractThis article investigates the stabilization problem of uncertain switched nonlinear systems. Uncertainty and saturated impulses are first considered together in switched nonlinear systems. It appears that the considered systems are robustly locally exponentially stable under the fast average dwell time method and the designed saturated impulsive controller even though subsystems are unstable. At the same time, our conclusions cover some previous results. A step‐by‐step strategy for optimizing multiple objectives is designed to estimate the basin of attraction of the systems as large as possible. At last, the efficacy of our conclusions is illustrated by two given examples.
An enhanced coupling nonlinear control for quadrotor with suspended double‐pendulum payload
Authors: Yan Bing , Lin Hong , Cai Chenxiao , Shi Peng 
Published: June 2024

AbstractIn the field of logistics transportation, unmanned aerial vehicles are commonly utilized for cargo transport in a suspended manner, and the suspended payloads will exhibit the double‐pendulum dynamic characteristics (dPDC). However, due to the underactuation and load‐swing problems caused by the dPDC, it is challenging to design controllers for a quadrotor with a suspended double‐pendulum type payload. Existing related studies simplify the dPDC to a single‐pendulum dynamic characteristic, which results in degraded transient performance. To overcome the issue, this article presents a novel controller approach that considers the real dynamic characteristics, that is, dPDC. The proposed approach tackles the quadrotor position control and anti‐swing problem in two steps. First, a composite signal incorporating both the quadrotor position and the payload swing angles is introduced to restrain the payload swing. Second, a nonlinear controller based on the energy analysis method is proposed to overcome the coupling between rotation and translation, which addresses the underactuation problem. Theoretical analysis confirms the asymptotic stability of the system under this control strategy. Numerical and experimental results are provided to demonstrate the effectiveness of the proposed controller.
Anti‐modal‐asynchrony sliding mode control for semi‐Markov jump systems
Authors: Shen Feiyue , Qi Wenhai , Cao Jinde , Yan Huaicheng , Abdel‐Aty Mahmoud , Cheng Jun 
Published: June 2024

AbstractThis article investigates the issue of anti‐modal‐asynchrony sliding mode control (SMC) for discrete semi‐Markov jump systems with bi‐boundary sojourn time. Asynchronous mechanism refers to the mismatch phenomenon between the system mode and the controller mode, in which the modal lag is mode‐dependent to reduce some conservatism compared with traditional mode‐independent lag. In contrast to traditional semi‐Markov jump systems, the sojourn time of each mode in this article is considered to have upper‐and‐lower bounds, representing better characteristics than the upper bound. Based on the semi‐Markov kernel and the Lyapunov function related to the elapsed time of current mode, a sufficient condition is proposed to ensure that the mean‐square stability of the underlying system is achieved under an equivalent SMC mechanism. The conditions for the existence of the designed controller are obtained, which shows that the constructed SMC mechanism is effective against asynchronous mode jumps. An anti‐modal‐asynchrony SMC mechanism is constructed to achieve the reachability of discrete quasi‐sliding mode. Finally, the F‐404 aircraft engine model is given to validate the effectiveness of the control strategy.
Distributed finite‐time attitude coordination control of spacecraft formations with multiple constraints
Authors: Tang Yanling , Lai Bixia , Li Xiaoting , Zou An‐Min , Yang Xuerong 
Published: June 2024

SummaryThis paper addresses the issue of distributed finite‐time attitude coordination control of spacecraft formations with multiple constraints on angular velocities and control torques. First, the multiple constrained problem is transformed into a bounded issue by virtue of the nonlinear transformation technique and an input saturation model. Next, the nearest neighbor rule is applied to deal with the problem of the unavailability of the leader's information to all followers. Then, a distributed attitude coordination control algorithm is derived to enforce that all attitude tracking errors can converge to a neighborhood around the origin in finite time even when there exist multiple constraints and external disturbances imposed on spacecraft systems. Finally, several numerical simulation examples are presented to illustrate the efficiency of the derived method.
On the rank, Kernel, and core of sparse random graphs
Authors: DeMichele Patrick , Glasgow Margalit , Moreira Alexander 
Published: June 2024

AbstractWe study the rank of the adjacency matrix of a random Erdős‐Rényi graph . It is well known that when , with high probability, is singular. We prove that when , with high probability, the corank of is equal to the number of isolated vertices remaining in after the Karp‐Sipser leaf‐removal process, which removes vertices of degree one and their unique neighbor. We prove a similar result for the random matrix , where all entries are independent Bernoulli random variables with parameter . Namely, we show that if is the bipartite graph with bi‐adjacency matrix , then the corank of is with high probability equal to the max of the number of left isolated vertices and the number of right isolated vertices remaining after the Karp‐Sipser leaf‐removal process on . Additionally, we show that with high probability, the ‐core of is full rank for any and . This partially resolves a conjecture of Van Vu for . Finally, we give an application of the techniques in this paper to gradient coding, a problem in distributed computing.
Dynamics of founding team diversity and venture outcomes: A simulation approach
Authors: Sundriyal Vivek Kumar , Lévesque Moren , Wennberg Karl , Norgren Axel 
Published: June 2024

AbstractResearch summaryEntrepreneurship research overlooks the dynamics of changing diversity in founding teams. Our simulations calibrated from existing studies suggest that founding teams that change diversity exhibit greater discounted performance for their ventures due to being less diverse and thus their ventures surviving longer, compared to teams that maintain their diversity. Moreover, discounted performance is higher for teams changing diversity due to other teams' performance than due to their own poor performance. Simulating without membership changes the interdependence between team diversity, venture performance, and team disruption, we find that while team diversity is overall performance‐enhancing, this association differs across contexts and its impact varies as ventures mature. Founding team diversity should thus be seen as a continuum where moderate diversity can best serve teams in turbulent environments.Managerial summaryWe simulated the behavior of founding teams over time to show that compared to teams that do not change their diversity, those who do experience greater discounted performance for their business ventures. This improvement stems from the increased longevity, and thus greater accumulated performance, for teams that switch since they are more rather than less homogeneous. Our investigation also indicates that ventures led by teams that change diversity because they aspire to outperform other teams, tend to exhibit greater discounted performance than those that change diversity to outperform themselves. When we investigate the interconnectedness of teams' diversity, ventures' performance, and disruption, albeit without allowing for any changes in team diversity, we find that while diversity usually helps, teams moderately diversified tend to perform best in turbulent times.
MXene/Nitrogen‐Doped Carbon Nanosheet Scaffold Electrode toward High‐Performance Solid‐State Zinc Ion Supercapacitor
Authors: Chen Anli , Wei Huige , Peng Zhuojian , Wang Yuanzhe , Akinlabi Stephen , Guo Zhanhu , Gao Faming , Duan Sidi , He Ximin , Jia Chunjiang , Xu Ben Bin 
Published: June 2024

AbstractWhile MXene is widely used as an electrode material for supercapacitor, the intrinsic limitation of stacking caused by the interlayer van der Waals forces has yet to be overcome. In this work, a strategy is proposed to fabricate a composite scaffold electrode (MCN) by intercalating MXene with highly nitrogen‐doped carbon nanosheets (CN). The 2D structured CN, thermally converted and pickling from Zn‐hexamine (Zn‐HMT), serves as a spacer that effectively prevents the stacking of MXene and contributes to a hierarchically scaffolded structure, which is conducive to ion movement; meanwhile, the high nitrogen‐doping of CN tunes the electronic structure of MCN to facilitate charge transfer and providing additional pseudocapacitance. As a result, the MCN50 composite electrode achieves a high specific capacitance of 418.4 F g−1 at 1 A g−1. The assembled symmetric supercapacitor delivers a corresponding power density of 1658.9 W kg−1 and an energy density of 30.8 Wh kg−1. The all‐solid‐state zinc ion supercapacitor demonstrates a superior energy density of 68.4 Wh kg−1 and a power density of 403.5 W kg−1 and shows a high capacitance retention of 93% after 8000 charge‐discharge cycles. This study sheds a new light on the design and development of novel MXene‐based composite electrodes for high performance all‐solid‐state zinc ion supercapacitor.