bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hierarchical spatio‐temporal object knowledge graph model for dynamic scene representation
Authors: Zhao Xinke , Cao Yibing , Wang Jiahe , Fan Xinhua , Chen Minjie 
Published: October 2023

AbstractSpatio‐temporal knowledge is essential in understanding the dynamic aspects of complex scenes. However, existing knowledge graphs have limitations, such as inadequate time description, inflexible expression of semantic relationships, and difficulties in accessing GIS platforms. The article proposes the spatio‐temporal object knowledge graph (STOKG), consisting of the object concept layer, spatio‐temporal object layer, and dynamic version layer. To demonstrate the practical usefulness of the STOKG model, the Henan epidemic knowledge graph is created using epidemiological data from early 2020, which shows the dynamic evolution of the spatio‐temporal objects of cases from the geography and semantic perspectives. Finally, the STOKG model is compared with the existing models in terms of accuracy, completeness and repetitiveness. The experimental results show that the STOKG model provides a more flexible and comprehensive approach to representing spatio‐temporal knowledge, which is useful for applications in fields such as geography, epidemiology, and environmental science.
Hybrid Optimal Control of a Flying+Sailing Drone
Authors: Yasini Taha , Pakniyat Ali 
Published: October 2023

Abstract
This paper studies the combined maneuver of flying and sailing for a robotic system which is referred to as a flying+sailing drone. Due to the emergence of hybrid systems behavior in tasks which involve both the flying and sailing modes, a hybrid systems formulation of the robotic system is presented. Key characteristics of the system are (i) changes in the dimension of the state space as the system switches from flying to sailing and vice versa and (ii) the presence of autonomous switchings triggered only upon the landing of the drone on the water surface. For the scenario in which the drone’s initial state is given in the flying mode and a fixed terminal state is specified in the sailing mode, the associated optimal control problems are studied within the vertical plane passing through the given points, hence the dynamics of the drone in the flying mode are represented in a five-dimensional state space (associated with three degrees-of-freedom) and in a three-dimensional state space in the sailing mode (associated with two degrees-of-freedom). In particular, the optimal control problems for the minimization of time and the minimization of the control effort are formulated, the associated necessary optimality conditions are obtained from the hybrid minimum principle (HMP), and the associated numerical simulations are presented.
Koopman Operator Based Predictive Control With a Data Archive of Observables
Authors: Loya Kartik , Buzhardt Jake , Tallapragada Phanindra 
Published: October 2023

Abstract
The control of complex systems is often challenging due to high-dimensional nonlinear models, unmodeled phenomena, and parameter uncertainty. The increasing ubiquity of sensors measuring such systems and increased computational resources has led to an interest in purely data-driven control methods, particularly using the Koopman operator. In this paper, we elucidate the construction of a linear predictor based on a sequence of time realizations of observables drawn from a data archive of different trajectories combined with subspace identification methods for linear systems. This approach is free of any predefined set of basis functions but instead depends on the time realization of these basis functions. The prediction and control are demonstrated with examples. The basis functions can be constructed using time-delayed coordinates of the outputs, enabling the application to purely data-driven systems. The paper thus shows the link between Koopman operator-based control methods and classical subspace identification methods. The approach in this paper can be extended to adaptive online learning and control.
Data-Based Stiffness Estimation for Control of Robot–Workpiece Elastic Interactions
Authors: McCann Lance , Gombo Yoshua , Tiwari Anuj , Garbini Joseph , Devasia Santosh 
Published: October 2023

Abstract
In manufacturing operations such as clamping and drilling of elastic structures, tool–workpiece normality must be maintained, and shear forces minimized to avoid tool or workpiece damage. The challenge is that the combined stiffness of a robot and workpiece, needed to control the robot–workpiece elastic interactions, are often difficult to model and can vary due to geometry changes of the workpiece caused by large deformations and associated pose variations of the robot. The main contribution of this article is an algorithm (i) to learn the robot–workpiece stiffness relationship using a model-free data-based approach and (ii) to use it for applying desired forces and torques on the elastic structure. Moreover, comparative experiments with and without the data-based stiffness estimation show that clamping operating speed is increased by four times when using the stiffness estimation method while interaction forces and torques are kept within acceptable bounds.
Analyzing the Sensitivity of Wave Frequency Responses of Floating Vessels to Uncertain System Variables Utilizing Polynomial Chaos Expansion
Authors: Radhakrishnan Gowtham , Leira Bernt J. , Gao Zhen , Sævik Svein , Han Xu 
Published: October 2023

Abstract
From a mathematical viewpoint, the frequency domain analysis of vessel motion responses due to wave actions is based on integration of system dynamics idealized in terms of response amplitude operators for six degrees-of-freedom (DOFs) rigid body motions and an input wave spectrum in order to obtain the response spectrum. Various quantities of interest can be deduced from the response spectrum, which are then used for deriving response-based operational limits for marine operations, also including extreme value and fatigue analysis. The variation of such quantities, owing to the uncertainties associated with the vessel system parameters, can be quantified by performing uncertainty propagation and consequent sensitivity analysis. This study emphasizes and proposes a computational-efficient way of assessing the sensitivity of the system model output with respect to the uncertainties residing in the input parameters by operating on a surrogate model representation. In this respect, the global sensitivity analysis was effectively carried out by deploying an efficient nonintrusive polynomial chaos expansion surrogate model built using a point collocation strategy. Successively, Sobol’ indices were obtained from the analytical decomposition of the polynomial coefficients. The indices, eventually, are employed to quantitatively measure the effects of input uncertainties on the output 6DOF vessel root-mean-square responses.
Are envelope stress responses essential for persistence to β-lactams in
Escherichia coli
?
Authors: Rousseau Clothilde J. , Fraikin Nathan , Zedek Safia , Van Melderen Laurence 
Published: October 2023

ABSTRACT

Bacterial persistence to antibiotics defines the ability of small sub-populations of sensitive cells within an isogenic population to survive high doses of bactericidal antibiotics. Here, we investigated the importance of the five main envelope stress responses (ESRs) of
Escherichia coli
in persistence to five bactericidal β-lactam antibiotics by combining classical time-kill curve experiments and single-cell analysis using time-lapse microscopy. We showed that the survival frequency of mutants for the Bae, Cpx, Psp, and Rcs systems treated with different β-lactams is comparable to that of the wild-type strain, indicating that these ESRs do not play a direct role in persistence to β-lactams. Since the σ
E
-encoding gene is essential, we could not directly test its role. Using fluorescent reporters to monitor the activation of ESRs, we observed that σ
E
is induced by high doses of meropenem. However, the dynamics of σ
E
activation during meropenem treatment did not reveal any difference in persister cells compared to the bulk of the population, indicating that σ
E
activation is not a hallmark of persistence. The Bae, Cpx, Psp, and Rcs responses were neither induced by ampicillin nor by meropenem. However, pre-induction of the Rcs system by polymyxin B increased survival to meropenem in an Rcs-dependent manner, suggesting that this ESR might confer some yet uncharacterized advantages during meropenem treatment or at the post-antibiotic recovery step. Altogether, our data suggest that ESRs are not key actors in
E. coli
persistence to β-lactams in the conditions we tested.
Locations of membrane protein production in a cyanobacterium
Authors: Mahbub Moontaha , Mullineaux Conrad W. 
Published: October 2023

ABSTRACT

Cyanobacteria show an unusually complex prokaryotic cell structure including a distinct intracytoplasmic membrane system, the thylakoid membranes that are the site of the photosynthetic light reactions. The thylakoid and plasma membranes have sharply distinct proteomes, but the mechanisms that target proteins to a specific membrane remain poorly understood. Here, we investigate the locations of translation of thylakoid and plasma membrane proteins in the model unicellular cyanobacterium
Synechococcus elongatus
PCC 7942. We use fluorescent
in situ
hybridization to probe the locations of mRNAs encoding membrane-integral proteins, plus Green Fluorescent Protein tagging of the RplL subunit to reveal the location of ribosomes under different conditions. We show that membrane-integral thylakoid and plasma membrane proteins are translated in different locations. Thylakoid membrane proteins are translated in patches at the innermost thylakoid membrane surface facing the nucleoid. However, different proteins are translated in different patches, even when they are subunits of the same multiprotein complex. This implies that translation is distributed over the proximal thylakoid surface, with newly inserted proteins migrating within the membrane prior to incorporation into complexes. mRNAs encoding plasma membrane proteins form patches at the plasma membrane. Ribosomes can be observed at similar locations near the thylakoid and plasma membranes, with more ribosomes near the plasma membrane when conditions force rapid production of plasma membrane proteins. There must be routes for ribosomes and mRNAs past the thylakoids to the plasma membrane. We infer a system to chaperone plasma membrane mRNAs to prevent their translation prior to arrival at the correct membrane.

IMPORTANCE
Cyanobacteria have a complex and distinct membrane system within the cytoplasm, the thylakoid membranes that house the photosynthetic light reactions. The thylakoid and plasma membranes contain distinct sets of proteins, but the steps that target proteins to the two membranes remain unclear. Knowledge of the protein sorting rules will be crucial for the biotechnological re-engineering of cyanobacterial cells, and for understanding the evolutionary development of the thylakoids. Here, we probe the subcellular locations of the mRNAs that encode cyanobacterial membrane proteins and the ribosomes that translate them. We show that thylakoid and plasma membrane proteins are produced at different locations, providing the first direct evidence for a sorting mechanism that operates prior to protein translation.
Corrected and republished from: “VP4 Is a Determinant of Alpha-Defensin Modulation of Rotaviral Infection”
Authors: Hu Ciara T. , Diaz Karina , Yang Linda C. , Sharma Anjali , Greenberg Harry B. , Smith Jason G. 
Published: October 2023

ABSTRACT
Fecal-oral pathogens encounter constitutively expressed enteric alpha-defensins in the intestine during replication and transmission. Alpha-defensins can be potently antiviral and antibacterial; however, their primary sequences, the number of isoforms, and their activity against specific microorganisms often vary greatly between species, reflecting adaptation to species-specific pathogens. Therefore, alpha-defensins might influence not only microbial evolution and tissue tropism within a host but also species tropism and zoonotic potential. To investigate these concepts, we generated a panel of enteric and myeloid alpha-defensins from humans, rhesus macaques, and mice and tested their activity against group A rotaviruses, an important enteric viral pathogen of humans and animals. Rotaviral adaptation to the rhesus macaque correlated with resistance to rhesus enteric but not myeloid alpha-defensins and sensitivity to human alpha-defensins. Infection by mouse and human rotaviruses was either resistant to or increased by host enteric alpha-defensins, although the effects of cross-species alpha-defensins did not follow an obvious pattern. Because infection by all rotaviruses tested was resistant to or enhanced by enteric alpha-defensins from their hosts, exposure to alpha-defensins may have shaped their evolution. We then used a genetic approach to identify the viral attachment and penetration protein, VP4, as a determinant of alpha-defensin sensitivity. Our results provide a foundation for future studies of the VP4-dependent mechanism of defensin neutralization, highlight the species-specific activities of alpha-defensins, and focus future efforts on a broader range of rotaviruses that differ in VP4 to uncover the potential for enteric alpha-defensins to influence species tropism.

Importance
Rotavirus is a leading cause of severe diarrhea in young children. Like other fecal-oral pathogens, rotaviruses encounter abundant, constitutively expressed defensins in the small intestine. These peptides are a vital part of the vertebrate innate immune system. By investigating the impact that defensins from multiple species have on the infectivity of different strains of rotavirus, we show that some rotaviral infections can be inhibited by defensins. We also found that rotaviruses may have evolved resistance to defensins in the intestine of their host species, and some even appropriate defensins to increase their infectivity. Because rotaviruses infect a broad range of animals and rotaviral infections are highly prevalent in children, identifying immune defenses against infection and how they vary across species and among viral genotypes is important for our understanding of the evolution, transmission, and zoonotic potential of these viruses as well as the improvement of vaccines.
Activation of AIM2 by hepatitis B virus results in antiviral immunity that suppresses hepatitis C virus during coinfection
Authors: Li Yongqi , Yang Yang , Li Tianyang , Wang Zhengmin , Gao Chunfeng , Deng Rilin , Ma Faxiang , Li Xinyang , Ma Licong , Tian Renyun , Li Huiyi , Zhu Haizhen , Zeng Lei , Gao Yanhang , Lv Guoyue , Niu Junqi , Crispe Ian Nicholas , Tu Zhengkun 
Published: October 2023

ABSTRACT
Hepatitis B virus (HBV) infection in immunocompetent adults is mostly self-limiting, whereas Hepatitis C virus (HCV) infection more often becomes chronic, suggesting that HBV is more susceptible to the host immune response. It is unclear how HBV induces effective antiviral immunity, but HBV also causes anti-HCV immunity leading to lower HCV viral loads in co-infected patients. Here, we found that a pathway in which HBV dsDNA is sensed by the inflammasome protein absent in melanoma-2, leading to caspase-1 activation in monocytes, cleavage of pro-IL-18 and secretion of IL-18 protein, activation of NK cells, and their synthesis of interferon-γ. Such activation could suppress not only HBV but also HCV replication, suggesting a mechanism through which the two viruses could engage in cross-talk during coinfection.

IMPORTANCE
Clinical data suggest that Hepatitis C virus (HCV) levels are generally lower in Hepatitis B virus (HBV) co-infected patients, but the mechanism is unknown. Here, we show that HBV, but not HCV, activated absent in melanoma-2. This in turn results in inflammasome-mediated cleavage of pro-IL-18, leading to an innate immune activation cascade that results in increased interferon-γ, suppressing both viruses.
The L-DBF vaccine cross protects mice against different
Shigella
serotypes after prior exposure to the pathogen
Authors: Lu Ti , Howlader Debaki R. , Das Sayan , Dietz Zackary K. , Nagel Aaron C. , Whittier Sean K. , Picking William D. , Picking Wendy L. 
Published: October 2023

ABSTRACT

Shigellosis (bacillary dysentery) is a severe diarrheal disease caused by members of the genus
Shigella
, which results in 90 million cases annually around the world. The
Shigella
type III secretion system (T3SS) is a specialized secretion system that is the primary virulence factor it uses to infect the colonic mucosa. The type III secretion apparatus (T3SA) proteins IpaB and IpaD, as well as the genetic fusion, DBF, have been demonstrated to protect mice from
Shigella
spp. infection in a lethal pulmonary model. In a previous study, we fused LTA1, the active moiety of lethal toxin from enterotoxigenic
Escherichia coli
to DBF to produce a self-adjuvanting vaccine candidate L-DBF, which cross-protected mice against four serotypes of
Shigella flexneri
and
Shigella sonnei
. Here, we exposed mice with one or two sublethal doses of
S. flexneri
2a to identify whether the immune response induced by L-DBF in the host would be affected by prior infection by homologous or heterologous
Shigella
serotypes. We demonstrate that pre-infection with two sublethal doses of
S. flexneri
2a did not elicit cross-protection against
S. sonnei
, while vaccination with L-DBF did. Our results indicate that L-DBF is a feasible vaccine candidate that offers cross-protection against
Shigella
’s different serotypes even after prior exposure to the pathogen. This work provides a proof of concept that a novel subunit vaccine can not only protect a naïve host from
Shigella
challenge, but also can protect against challenge after prior infection by the same or different
Shigella
serotypes.

IMPORTANCE

Shigellosis is endemic to low- and middle-income regions of the world where children are especially vulnerable. In many cases, there are pre-existing antibodies in the local population and the effect of prior exposure should be considered in the development and testing of vaccines against
Shigella
infection. Our study shows that L-DBF-induced immune responses are not adversely affected by prior exposure to this pathogen. Moreover, somewhat different cytokine profiles were observed in the lungs of vaccinated mice not having been exposed to
Shigella
, suggesting that the immune responses elicited by
Shigella
infection and L-DBF vaccination follow different pathways.
Discovery of a new highly pathogenic toxin involved in insect sepsis
Authors: Zhang Yuan , Li Hao , Wang Fang , Liu Chang , Reddy Gadi V. P. , Li Hu , Li Zhihong , Sun Yucheng , Zhao Zihua 
Published: October 2023

ABSTRACT

Insect sepsis is a severe consequence that arises from the invasion of the hemocoel by symbionts of entomopathogenic nematodes and bacteria. In the present study, we unveiled the heightened virulence of the entomopathogenic nematode
Steinernema feltiae
and the entomopathogenic bacteria
Xenorhabdus bovienii
, which operate symbiotically, against the wax moth
Galleria mellonella
. Maximum mortality was observed at 25°C while the optimal infestation efficiency was 20 nematodes per host. After infestation,
G. mellonella
displayed rapid darkening and softening, accompanied by an escalated esterase activity at 9 h. The
X. bovienii
, released by
S. feltiae
, underwent substantial proliferation and discharged toxins that attacked hemocytes, thus triggering extensive hemolysis and sepsis. The host
G. mellonella
was usually killed within 24 h due to disseminated septicemia. Additionally,
X. bovienii
infestation led to the upregulation of metabolites like 3-hydroxyanthranilic acid. Strikingly, we identified the perilous actinomycin D, generated through kynurenine metabolites, representing a novel biomarker of insect sepsis. Furthermore, a comprehensive transcriptomic analysis unveiled a noteworthy upregulation of gene expression associated with actinomycin D. Overall,
X. bovienii
induced apoptosis and sepsis through actinomycin D production, indicating its pivotal role in infestation activity. These findings open up new avenues for studying the mechanism of sepsis and developing innovative biotic pesticides.

IMPORTANCE

As a current biocontrol resource, entomopathogenic nematodes and their symbiotic bacterium can produce many toxin factors to trigger insect sepsis, having the potential to promote sustainable pest management. In this study, we found
Steinernema feltiae
and
Xenorhabdus bovienii
were highly virulent against the insects. After infective juvenile injection,
Galleria mellonella
quickly turned black and softened with increasing esterase activity. Simultaneously,
X. bovienii
attacked hemocytes and released toxic components, resulting in extensive hemolysis and sepsis. Then, we applied high-resolution mass spectrometry-based metabolomics and found multiple substances were upregulated in the host hemolymph. We found extremely hazardous actinomycin D produced via 3-hydroxyanthranilic acid metabolites. Moreover, a combined transcriptomic analysis revealed that gene expression of proteins associated with actinomycin D was upregulated. Our research revealed actinomycin D might be responsible for the infestation activity of
X. bovienii
, indicating a new direction for exploring the sepsis mechanism and developing novel biotic pesticides.
Phosphorus starvation response and PhoB-independent utilization of organic phosphate sources by
Salmonella enterica
Authors: Bruna Roberto E. , Kendra Christopher G. , Pontes Mauricio H. 
Published: October 2023

ABSTRACT

Inorganic orthophosphate (Pi, PO
4
3−
) is the preferred phosphorus (P) source of most living cells. In enteric bacterial species such as
Salmonella enterica
serovar Typhimurium (
Salmonella
), removal of Pi from the growth medium activates a dedicated two-component signal transduction system which is composed of the membrane-bound sensor kinase PhoR and its cognate transcriptional regulator PhoB. Activated PhoB promotes transcription of genes that are involved in adaptations to low Pi conditions, such as high-affinity Pi transporters and genes required for the assimilation of alternative P sources, allowing bacteria to adapt to low Pi environments. Here, we characterize the PhoB-dependent and independent transcriptional changes elicited by
Salmonella
in response to P starvation. We identify a set of organic molecules that can serve as the sole P source and pinpoint genes that are involved in their assimilation. Intriguingly, a number of these genes are not under PhoB/PhoR control, indicating that in the absence of environmental Pi,
Salmonella
may fulfill its biosynthetic demands for P without activating a transcriptional response to Pi starvation.

IMPORTANCE

Phosphorus (P) is the fifth most abundant element in living cells. This element is acquired mainly as inorganic phosphate (Pi, PO
4
3−
). In enteric bacteria, P starvation activates a two-component signal transduction system which is composed of the membrane sensor protein PhoR and its cognate transcription regulator PhoB. PhoB, in turn, promotes the transcription of genes that help maintain Pi homeostasis. Here, we characterize the P starvation response of the bacterium
Salmonella enterica
. We determine the PhoB-dependent and independent transcriptional changes promoted by P starvation and identify proteins enabling the utilization of a range of organic substrates as sole P sources. We show that transcription and activity of a subset of these proteins are independent of PhoB and Pi availability. These results establish that
Salmonella enterica
can maintain Pi homeostasis and repress PhoB/PhoR activation even when cells are grown in medium lacking Pi.