bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of Self-Organizing Systems Using Multi-Agent Reinforcement Learning and the Compromise Decision Support Problem Construct
Authors: Jiang Mingfei , Ming Zhenjun , Li Chuanhao , Allen Janet K. , Mistree Farrokh 
Published: February 2024

Abstract
In this paper, we address the following question: How can multi-robot self-organizing systems be designed so that they show the desired behavior and are able to perform tasks specified by the designers? Multi-robot self-organizing systems, e.g., swarm robots, have great potential for adapting when performing complex tasks in a changing environment. However, such systems are difficult to design due to the stochasticity of system performance and the non-linearity between the local actions/interaction and the desired global behavior. In order to address this, in this paper, we propose a framework for designing self-organizing systems using Multi-Agent Reinforcement Learning (MARL) and the compromise Decision-Support Problem (cDSP) construct. The proposed framework consists of two stages, namely, preliminary design followed by design improvement. In the preliminary design stage, MARL is used to help designers train the robots so that they show stable group behavior for performing the task. In the design improvement stage, the cDSP construct is used to explore the design space and identify satisfactory solutions considering several performance indicators. Surrogate models are used to map the relationship between local parameters and global performance indicators utilizing the data generated in the preliminary design. These surrogate models represent the goals of the cDSP. Our focus in this paper is to describe the framework. A multi-robot box-pushing problem is used as an example to test the framework’s efficacy. This framework is general and can be extended to design other multi-robot self-organizing systems.
Tracking Flying Targets and Measurements of Their Surface Temperature using High Speed Infrared Imaging.
Authors: Tombet Stephane Boubanga , Marcotte Frederick , Morton Vince 
Published: February 2024

Abstract
Measurements of the flying target’s dynamic parameters is of growing interest for space scientists and army researchers. As flying target velocities increase, the study of heat exchange dynamics between the projectile and its environment is one of the indexes for assessing the performances of materials for the fabrication of bombs and cannons, as well as thermal protection systems used by planetary-entry and Earth-return missions. One of the challenges in ballistic heat transfer studies is the measurements of projectile surface temperature. Temperature is one of the critical parameters used in the design of projectile materials and shapes. While there are a significant number of numerical codes which predict projectile surface temperatures for a variety of conditions, relatively little experimental data has been produced for the purpose of verifying these numerical predictions. In this work, a Telops infrared camera mounted to a trajectory tracker was used to track a space re-entry probe at supersonic velocities and measure its in-flight heat transfer with the surrounding atmosphere. Physical phenomena such as shock waves were successfully captured by the IR camera and the interaction between the probe and the shock waves was studied. The unique features of Telops IR cameras make them well-suited investigation tools to bring ballistic tracking and research to the next level.
Articulating Hypervelocity Linear Accelerator Structure (Atlas) for Planetary Impact Science
Authors: Morton Joseph , Barnouin Olivier , Cooper Scott , Lamberson Leslie , Daly R. Terik 
Published: February 2024

Abstract
Hypervelocity impact cratering by asteroids and comets is one of the most common geological processes in the solar system. Investigations of the cratering process can be used to characterize the physical attributes of planetary surfaces and interiors, and to understand solar system evolution. Fundamental parameters including density, mass, and macro-porosity can dramatically affect a surface’s response to impact, consequently affecting the understanding of its evolution and history. Further, most natural impact events are oblique and can occur at a wide range of velocities, ranging from m/s for re-impacting crater ejecta, to 10s of km/s for asteroids and comets on terrestrial planets. As a result, laboratory experiments are a critical tool for investigating planetary impact cratering. Impact experiments can readily use rubble-pile and granular-media targets, which are difficult to model numerically, span a range of impact angles, and access hypervelocities. A new alternative design has been developed for conducting hypervelocity impact experiments for planetary impact science, using an Articulating hypervelociTy Linear Accelerator Structure (ATLAS). This design provides a concise solution for the investigation of a broader range of parameters on planetary bodies in hypervelocity impact research. Impact experiments require a relatively environment-free target chamber with little to no interference from combustion contaminants or sub-system gases associated with the accelerator. To address these needs, we present a combustionfree, two-stage light-gas-gun facility and articulating substructure that will be retrofitted to an existing linear singlestage accelerator housed at the Planetary Impact Laboratory at the Johns Hopkins University Applied Physics Laboratory [1].
Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing
Authors: Grinevich Dmitry , Harden Lyndy , Thakur Siddhartha , Callahan Benjamin 
Published: February 2024

ABSTRACT

The resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens
Salmonella
and
Escherichia coli
, the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping
Salmonella enterica
and
E. coli
. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting
Salmonella
serotypes on
in silico
test data and identified key pathogenic serovars of
Salmonella
and
E. coli
in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable.

IMPORTANCE

In order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens
Escherichia coli
and
Salmonella enterica
to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.
Increased antibody titers but induced T cell AICD and apoptosis response in COVID-19 convalescents by inactivated vaccine booster
Authors: Zhao Jingmin , Zhang Han , Jiang Lina , Cheng Fang , Li Wei , Wang Zihao , Liu Hongyang , Li Shaohua , Jiang Yiyun , Li Meiling , Li Yan , Liu Shuhong , Fang Min , Zhou Xuyu , Ye Xin , Zhao Shousong , Zheng Yuxuan , Meng Songdong 
Published: February 2024

ABSTRACT

It is urgently needed to evaluate the necessity and benefits of booster vaccination against the coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2) Omicron to facilitate clinical decision-making for 2019 coronavirus disease (COVID-19) convalescents. We conducted a multicenter, prospective clinical trial (registration number: ChiCTR2100045810) in the first patients with COVID-19 from 28 January 2020 to 20 February 2020 to assess the long-term durability of neutralizing antibodies against live Omicron BA.5 and further assess the efficiency and safety of CoronaVac in the convalescent group. A total of 96 COVID-19 convalescents were enrolled in this study. Neutralizing antibody titers in convalescents were significantly reduced in 9–10 months. A dose-refreshing vaccination in 28 convalescents with an antibody titer below 96 significantly induced neutralizing antibodies against live Omicron by 4.84-fold. Meanwhile, the abundance of naive T cells increased dramatically, and T
EMRA
and T
EM
cells gradually decreased after vaccination. Activation-induced cell death and apoptosis-related genes were significantly elevated after vaccination in all T-cell subtypes. One-dose booster vaccination was effective in inducing a robust antibody response against SARS-CoV-2 Omicron in COVID-19 convalescents with low antibody titers. However, vaccine-mediated T-cell consumption and regeneration patterns may be detrimental to the antiviral response.

IMPORTANCE
The globally dominant coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2) Omicron variant raises the possibility of repeat infections among 2019 coronavirus disease (COVID-19) convalescents with low neutralizing antibody titers. The importance of this multicenter study lies in its evaluation of the long-term durability of neutralizing antibodies in COVID-19 convalescents and the efficacy of a booster vaccination against the live Omicron. The findings suggest that a one-dose booster vaccination is effective in inducing a robust antibody response against SARS-CoV-2 Omicron in convalescents with low antibody titers. However, the study also highlights the potential detrimental effects on the antiviral response due to vaccine-mediated T-cell consumption and regeneration patterns. These results are crucial for facilitating clinical decision-making for COVID-19 convalescents and informing public health policies regarding booster vaccinations.
The potential of
Rhodobacter sphaeroides
extract as an alternative supplement for cell culture systems
Authors: Lee Subin , Kim Yang-Hoon , Min Jiho 
Published: February 2024

ABSTRACT

It is essential to identify suitable supplements that enhance cell growth, viability, and functional development in cell culture systems. The use of fetal bovine serum (FBS) has been common, but it has limitations, such as batch-to-batch variability, ethical concerns, and risks of environmental contamination. In this study, we explore the potential of
Rhodobacter sphaeroides
extract, derived from a probiotic photosynthetic bacterium, as an alternative supplement. Our results demonstrate that the extract from
R. sphaeroides
significantly improves various aspects of cell behavior compared to serum-free conditions. It enhances cell growth and viability to a greater extent than FBS supplementation. Additionally, the extract alleviates oxidative stress by reducing intracellular levels of reactive oxygen species and stimulates lysosomal activity, contributing to cellular processes. The presence of abundant amino acids, glycine and arginine, in the extract may play a role in promoting cell growth. These findings emphasize the potential of
R. sphaeroides
extract as a valuable supplement for cell culture, offering advantages over the use of FBS.

IMPORTANCE

The choice of supplements for cell culture is crucial in biomedical research, but the widely used fetal bovine serum (FBS) has limitations in terms of variability, ethics, and environmental risks. This study explores the potential of an extract from
Rhodobacter sphaeroides
, a probiotic bacterium, as an alternative supplement. The findings reveal that the
R. sphaeroides
extract surpasses FBS in enhancing cell growth, viability, and functionality. It also mitigates oxidative stress and stimulates lysosomal activity, critical for cellular health. The extract’s abundance of glycine and arginine, amino acids with known growth-promoting effects, further highlights its potential. By providing a viable substitute for FBS, the
R. sphaeroides
extract addresses the need for consistent, ethical, and environmentally friendly cell culture supplements. This research paves the way for sustainable and reliable cell culture systems, revolutionizing biomedical research and applications in drug development and regenerative medicine.
Coordination of prophage and global regulator leads to high enterotoxin production in staphylococcal food poisoning-associated lineage
Authors: Sato'o Yusuke , Hisatsune Junzo , Aziz Fatkhanuddin , Tatsukawa Nobuyuki , Shibata-Nakagawa Mari , Ono Hisaya K. , Naito Ikunori , Omoe Katsuhiko , Sugai Motoyuki 
Published: February 2024

ABSTRACT

Staphylococcus
species in food produce Staphylococcal enterotoxins (SEs) that cause Staphylococcal food poisoning (SFP). More than 20 SE types have been reported, among which Staphylococcal enterotoxin A (SEA) has been recognized as one of the most important SEs associated with SFP. However, the regulatory mechanisms underlying its production remain unclear. Previously, we identified a major SFP clone in Japan, CC81 subtype-1, which exhibits high SEA production. In this study, we attempted to identify the factors contributing to this phenomenon. Thus, we demonstrated that the attenuation of the activity of endogenous regulator, Staphylococcal accessory regulator S (SarS), and the lysogenization of a high SEA-producing phage contributed to this phenomenon in CC81 subtype-1. Furthermore, our results indicated that SarS could directly bind to the promoter upstream of the
sea
gene and suppress SEA expression; this low SarS repression activity was identified as one of the reasons for the high SEA production observed. Therefore, we revealed that both exogenous and endogenous factors may probably contribute to the high SEA production. Our results confirmed that SE production is a fundamental and critical factor in SFP and clarified the associated production mechanism while enhancing our understanding as to why a specific clone frequently causes SFP.

IMPORTANCE

The importance of this study lies in its unveiling of a molecular regulatory mechanism associated with the most important food poisoning toxin and the evolution of Staphylococcal food poisoning (SFP)-associated clone. SFP is primarily caused by
Staphylococcus aureus
, with Staphylococcal enterotoxin A (SEA) being commonly involved in many cases. Thus, SEA has been recognized as a major toxin type. However, despite almost a century since its discovery, the complete mechanism of SEA production is as yet unknown. In this study, we analyzed an SEA-producing SFP clone isolated in East Asia and discovered that this strain, besides acquiring the high SEA-producing phage, exhibits remarkably high SEA production due to the low activity of SarS, an intrinsic regulatory factor. This is the first report documenting the evolution of the SFP clone through the coordinated action of exogenous mobile genetic factors and endogenous regulators on this notorious toxin.
Regulation of Onecut2 by miR-9-5p in Japanese encephalitis virus infected neural stem/progenitor cells
Authors: Sharma Shivangi , Majumdar Atreye , Basu Anirban 
Published: February 2024

ABSTRACT

Japanese encephalitis virus (JEV) is one of the major neurotropic viral infections that is known to dysregulate the homeostasis of neural stem/progenitor cells (NSPCs) and depletes the stem cell pool. NSPCs are multipotent stem cell population of the central nervous system (CNS) which are known to play an important role in the repair of the CNS during insults/injury caused by several factors such as ischemia, neurological disorders, CNS infections, and so on. Viruses have evolved to utilize host factors for their own benefit and during JEV infection, host factors, including the non-coding RNAs such as miRNAs, are reported to be affected, thereby cellular processes regulated by the miRNAs exhibit perturbed functionality. Previous studies from our laboratory have demonstrated the role of JEV infection in dysregulating the function of neural stem cells (NSCs) by altering the cell fate and depleting the stem cell pool leading to a decline in stem cell function in CNS repair mechanism post-infection. JEV-induced alteration in miRNA expression in the NSCs is one of the major interest to us. In prior studies, we have observed an altered expression pattern of certain miRNAs following JEV infection. In this study, we have validated the role of JEV infection in NSCs in altering the expression of miR-9-5p, which is a known regulator of neurogenesis in NSCs. Furthermore, we have validated the interaction of this miRNA with its target, Onecut2 (OC2), in primary NSCs utilizing miRNA mimic and inhibitor transfection experiments. Our findings indicate a possible role of JEV mediated dysregulated interaction between miR-9-5p and its putative target OC2 in NSPCs.

IMPORTANCE
MicroRNAs have emerged as key disease pathogenic markers and potential therapeutic targets. In this study, we solidify this concept by studying a key miRNA, miR-9-5p, in Japanese encephalitis virus infection of neural stem/progenitor cells. miRNA target Onecut2 has a possible role in stem cell pool biology. Here, we show a possible mechanistic axis worth investing in neurotropic viral biology.
A photocontrolled one-pot isothermal amplification and CRISPR-Cas12a assay for rapid detection of SARS-CoV-2 Omicron variants
Authors: Sun Qian , Lin Hongqing , Li Yuan , Yuan Liping , Li Baisheng , Ma Yunan , Wang Haiying , Deng Xiaoling , Chen Hongliang , Tang Shixing 
Published: February 2024

ABSTRACT

CRISPR-Cas technology has widely been applied to detect single-nucleotide mutation and is considered as the next generation of molecular diagnostics. We previously reported the combination of nucleic acid amplification (NAA) and CRISPR-Cas12a system to distinguish major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the mixture of NAA and CRISPR-Cas12a reagents in one tube could interfere with the efficiency of NAA and CRISPR-Cas12a cleavage, which in turn affects the detection sensitivity. In the current study, we employed a novel photoactivated CRISPR-Cas12a strategy integrated with recombinase polymerase amplification (RPA) to develop one-pot RPA/CRISPR-Cas12a genotyping assay for detecting SARS-CoV-2 Omicron sub-lineages. The new system overcomes the potential inhibition of RPA due to early CRISPR-Cas12a activation and cleavage of the target template in traditional one-pot assay using photocleavable p-RNA, a complementary single-stranded RNA to specifically bind crRNA and precisely block Cas12a activation. The detection can be finished in one tube at 39℃ within 1 h and exhibits a low limit of detection of 30 copies per reaction. Our results demonstrated that the photocontrolled one-pot RPA/CRISPR-Cas12a assay could effectively identify three signature mutations in the spike gene of SARS-CoV-2 Omicron variant, namely, R346T, F486V, and 49X, and distinguish Omicron BA.1, BA.5.2, and BF.7 sub-lineages. Furthermore, the assay achieved a sensitivity of 97.3% and a specificity of 100.0% and showed a concordance of 98.3% with Sanger sequencing results.

IMPORTANCE
We successfully developed one-pot recombinase polymerase amplification/CRISPR-Cas12a genotyping assay by adapting photocontrolled CRISPR-Cas technology to optimize the conditions of nucleic acid amplification and CRISPR-Cas12a-mediated detection. This innovative approach was able to quickly distinguish severe acute respiratory syndrome coronavirus 2 Omicron variants and can be readily modified for detecting any nucleic acid mutations. The assay system demonstrates excellent clinical performance, including rapid detection, user-friendly operations, and minimized risk of contamination, which highlights its promising potential as a point-of-care testing for wide applications in resource-limiting settings.
The Brans–Dicke field in non-metricity gravity: cosmological solutions and conformal transformations
Authors: Paliathanasis Andronikos 
Published: February 2024

AbstractWe consider the Brans–Dicke theory in non-metricity gravity, which belongs to the family of symmetric teleparallel scalar–tensor theories. Our focus lies in exploring the implications of the conformal transformation, as we derive the conformal equivalent theory in the Einstein frame, distinct from the minimally coupled scalar field theory. The fundamental principle of the conformal transformation suggests the mathematical equivalence of the related theories. However, to thoroughly analyze the impact on physical variables, we investigate the spatially flat Friedmann–Lemaître–Robertson–Walker geometry, defining the connection in the non-coincidence gauge. We construct exact solutions for the cosmological model in one frame and compare the physical properties in the conformal related frame. Surprisingly, we find that the general physical properties of the exact solutions remain invariant under the conformal transformation. Finally, we construct, for the first time, an analytic solution for the symmetric teleparallel scalar–tensor cosmology.