bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of CSF‐filled cavities on scalp EEG and its implications
Authors: Piai Vitória , Oostenveld Robert , Schoffelen Jan Mathijs , Piastra Maria Carla 
Published: June 2024

AbstractPrevious studies have found electroencephalogram (EEG) amplitude and scalp topography differences between neurotypical and neurological/neurosurgical groups, being interpreted at the cognitive level. However, these comparisons are invariably accompanied by anatomical changes. Critical to EEG are the so‐called volume currents, which are affected by the spatial distribution of the different tissues in the head. We investigated the effect of cerebrospinal fluid (CSF)‐filled cavities on simulated EEG scalp data. We simulated EEG scalp potentials for known sources using different volume conduction models: a reference model (i.e., unlesioned brain) and models with realistic CSF‐filled cavities gradually increasing in size. We used this approach for a single source close or far from the CSF‐lesion cavity, and for a scenario with a distributed configuration of sources (i.e., a “cognitive event‐related potential effect”). The magnitude and topography errors between the reference and lesion models were quantified. For the single‐source simulation close to the lesion, the CSF‐filled lesion modulated signal amplitude with more than 17% magnitude error and topography with more than 9% topographical error. Negligible modulation was found for the single source far from the lesion. For the multisource simulations of the cognitive effect, the CSF‐filled lesion modulated signal amplitude with more than 6% magnitude error and topography with more than 16% topography error in a nonmonotonic fashion. In conclusion, the impact of a CSF‐filled cavity cannot be neglected for scalp‐level EEG data. Especially when group‐level comparisons are made, any scalp‐level attenuated, aberrant, or absent effects are difficult to interpret without considering the confounding effect of CSF.
Phylogenomic reconstruction influenced by assembly and annotation parameters: Using whole genome data to unravel the relationships of Spionidae (Annelida)
Authors: Bogantes Viktoria E. , Meiβner Karin , Waits Damien S. , Kocot Kevin M. , Halanych Kenneth M. 
Published: June 2024

AbstractMost efforts at improving accuracy in phylogenomic reconstructions have focused on improving tree‐building methods or orthology determination. Even though the use of whole genome sequence or transcriptome data is increasing, the degree to which accurate genome assembly and annotation influence phylogenetic inference has not been well explored. Here, we use low‐coverage whole genome sequencing of spionid annelids to explore the impact of different assemblers and annotation strategies on tree reconstruction. We also produce a phylogenetic hypothesis that spans the breadth of Spionidae, examining the current systematics of the group, which is based on morphological parsimony analyses and classical taxonomy. Our results show that both assembly and annotation can have important consequences for the pool of loci that may be available for tree reconstruction. When an identical phylogenomic pipeline is used, differences in assembly and annotation can account for variation in reconstructed topologies. Interestingly, the completeness and depth of the data used for training annotation software (i.e. data from model systems) appear to be more important, by some measures, than the degree of phylogenetic relatedness of the organism from which training data are drawn. Despite variation in recovered topologies, the recognised subfamily Spioninae is nested within Nerininae, suggesting that diagnostic characters of Nerininae (e.g. thick egg membrane, short‐headed sperm) are symplesiomorphies of Spionidae rather than apomorphies of a particular subclade. With the increased use of genomic data, our results advocate for a broader consideration of how assembly and annotation may impact data matrices used in phylogenomic analyses.
Acute neuromuscular, cardiovascular, and muscle oxygenation responses to low‐intensity aerobic interval exercises with blood flow restriction
Authors: Lavigne Colin , Mons Valentin , Grange Maxime , Blain Grégory M. 
Published: June 2024

AbstractWe investigated the influence of short‐ and long‐interval cycling exercise with blood flow restriction (BFR) on neuromuscular fatigue, shear stress and muscle oxygenation, potent stimuli to BFR‐training adaptations. During separate sessions, eight individuals performed short‐ (24 × 60 s/30 s; SI) or long‐interval (12 × 120 s/60 s; LI) trials on a cycle ergometer, matched for total work. One leg exercised with (BFR‐leg) and the other without (CTRL‐leg) BFR. Quadriceps fatigue was quantified using pre‐ to post‐interval changes in maximal voluntary contraction (MVC), potentiated twitch force (QT) and voluntary activation (VA). Shear rate was measured by Doppler ultrasound at cuff release post‐intervals. Vastus lateralis tissue oxygenation was measured by near‐infrared spectroscopy during exercise. Following the initial interval, significant (P < 0.05) declines in MVC and QT were found in both SI and LI, which were more pronounced in the BFR‐leg, and accounted for approximately two‐thirds of the total reduction at exercise termination. In the BFR‐leg, reductions in MVC (–28 ± 15%), QT (–42 ± 17%), and VA (–15 ± 17%) were maximal at exercise termination and persisted up to 8 min post‐exercise. Exercise‐induced muscle deoxygenation was greater (P < 0.001) in the BFR‐leg than CTRL‐leg and perceived pain was more in LI than SI (P < 0.014). Cuff release triggered a significant (P < 0.001) shear rate increase which was consistent across trials. Exercise‐induced neuromuscular fatigue in the BFR‐leg exceeded that in the CTRL‐leg and was predominantly of peripheral origin. BFR also resulted in diminished muscle oxygenation and elevated shear stress. Finally, short‐interval trials resulted in comparable neuromuscular and haemodynamic responses with reduced perceived pain compared to long‐intervals.
Self-Oscillation of a Liquid Crystal Elastomer String-Mass System Under Constant Gradient Temperature
Authors: Ge Dali , Liang Haiyi , Li Kai 
Published: June 2024

Abstract
Recent experiments have found that a fiber-mass system can self-oscillate along the vertical direction under a non-uniform temperature field, which necessitates significant vertical space. To address the challenge in adapting to situations with limited vertical space, the current work introduces a self-oscillating string-mass system, comprising of a mass ball and a thermally responsive liquid crystal elastomer string exposed to a constant gradient temperature. By employing theoretical modeling and numerical simulation, we have identified two motion regimes of the system, namely, the static regime and the self-oscillation regime, and elucidated the mechanism of self-oscillation. Utilizing the analytical method, we derived the expressions for bifurcation point, amplitude, and frequency of the self-oscillation, and investigated the impact of system parameters on these aspects, which were verified by numerical solutions. Compared to a fiber-mass system, the string-mass system has superior stability to deal with small horizontal disturbances, can amplify its amplitude and frequency limited by small thermal deformation of material, and saves a significant amount of vertical space. Given these attributes, such self-oscillating string-mass system presents novel possibilities for designing energy harvesters, active machinery, and soft robots.
What to Consider at the Development of Educational Programs and Courses About Next-Generation Cyber-Physical Systems?
Authors: Horváth Imre , Erden Zühal 
Published: June 2024

Abstract
We live in an age in which new things are emerging faster than their deep understanding. This statement, in particular, applies to doing research and educating university students concerning next-generation cyber-physical systems (NG-CPSs). The fast evolution of this system paradigm would have expected a rapid and comprehensive paradigmatic change in research and education concerning this family of systems. However, this has not happened yet. Seeking a sufficient explanation, this paper reviews the current literature and attempts to cast light on the most significant recent developments in the field of NG-CPSs. The main assumptions of the authors are that research and education should appear in harmony in academic knowledge acquisition and distribution processes and that the academic education of NG-CPSs should be organized and conducted according to a defendable future vision. Combining the results of a broadly based study of the literature with prognostic critical thinking and personal experiences, this review-based position paper first discusses the current socio-techno-scientific environment, the involved stakeholders, and the demands and two approaches of truly systems-oriented education. Then, it concentrates on (i) the recognized limitations of mono- and interdisciplinary research, (ii) supradisciplinary organization of research, and (iii) transdisciplinary knowledge generation for NG-CPSs. As main contributions, the paper (i) identifies and analyzes the latest theoretical, engineering, and technological developments, (ii) reveals the major trends and their presumably significant implications, and (iii) presents several thought-provoking findings and makes propositions about the desirable actions.
Development of Rail Anchor Testing Through Literature Review of CWR Buckling Resistance Evaluation
Authors: Rodriguez Juan , Zhou Siang , Tarawneh Constantine M. , Sanchez Alberto , Salazar-Flores Teresa , Rahmaninezhad Mustapha , Gorabi Hameem 
Published: June 2024

Abstract
Continuously welded rail (CWR) is among the most used railroad systems worldwide with great improvements compared to jointed tracks, including refined ride quality, increased fatigue life of track and rolling stock, and reduced maintenance costs. Rail buckling is one of the key remaining issues for CWRs to further reduce safety hazards and infrastructure deterioration, and save required track retrofit material and efforts. CWR buckling is induced by combined longitudinal, lateral, and torsional forces on the track that are caused by the synergy of rail components, the loading from moving trains, the interaction between track and substructure, and the effect of thermal variations. A systematic evaluation of factors that contribute to rail longitudinal, lateral, and torsional stiffnesses and a thorough investigation of their interactions are critical to understand rail buckling and enhance buckling resistance on CWR. This paper compiles, summarizes, and interprets existing research related to rail buckling resistance, considering parameters such as time-dependent neutral temperature of the tracks, the type of trains, various track resistors (rails, sleepers, and ballasts), and other accessories (anchors and fasteners). A discussion of previous experiments that studied resistors and rail buckling resistances is presented, which guides development of an experimental arrangements as part of an on-going large-scale rail resistance testing project in Edinburg, Tx. The information summarized in this article greatly points out additional needs for experimental and numerical studies, enlightens future research, and provides structured background for prospective improvements on rail buckling and stiffnesses of CWR.
AI-Based Hazard Detection for Railway Crossings
Authors: Espinoza Darren , Ali Gasser , Tarawneh Constantine 
Published: June 2024

Abstract
Grade crossings are critical elements of the railway infrastructure due to the potential risk of vehicle collisions with trains. According to the National Highway Traffic Safety Administration, there were more than 1,600 vehicle-train, and 500 human-train collisions in 2020. Researchers, transportation organizations, and government bodies are constantly exploring practices and technologies to improve safety at crossings. Examples of safety standards include sensors, motion detectors, depth cameras, and many other innovative technologies. The goal of this paper is to investigate the applications of computer vision using Artificial Intelligence (AI) deep learning models to enhance railway safety. Deep learning models can provide a robust and cost-effective solution to detect multiple hazards at crossings under different conditions such as lightning and weather. To achieve that goal, a model is developed and trained using a dataset of images at crossings collected and labeled by the authors. The trained model can use footage from cameras installed at grade crossings to detect multiple hazards such as vehicles, pedestrians, and animals. The model can be a robust solution to provide uninterrupted monitoring of crossings.
Counteracting Freeze-Thaw Deterioration Using Fiber Reinforced Concrete for Railroad Ties
Authors: Albahttiti Mohammed , Fernandez Janet , Zarate Yesenia , Naso Colin 
Published: June 2024

Abstract
Prestressed concrete railroad ties are crucial components of the railway system. These ties carry heavy loads and endure constant exposure to the elements. As water infiltrates the concrete, it can freeze and expand, exerting substantial pressure on the material. Subsequently, when the temperature rises, the ice within the concrete melts, causing the material to contract. This continuous expansion and contraction can lead to the formation of cracks, weakening the structural integrity of the concrete. In railway applications, this poses a significant problem, as damaged ties can compromise the safety and reliability of train tracks.
The focus of this study is to determine the impact of fiber reinforcement on the performance of concrete under freeze-thaw conditions. Notably, fiber reinforcement has been used as a means to reduce and control cracking in various concrete applications. The entire concrete construction is reinforced by a network made of steel fibers. The fibers act as a bonding agent when a fracture develops, allowing for the delayed propagation of cracks and the absorption of tensile loads at any point.
Concrete with steel fiber reinforcement has a greater potential to absorb energy during fracture. Demonstrating greater support structure, homogeneity and easier application logistics are just two advantages of fiber-reinforced concrete. This observation raises questions about the role that fiber reinforcement can have in increasing freeze-thaw durability and resistance to cracking. The random distribution of fibers in concrete railroad ties, often used to enhance tensile strength and crack resistance, might be the missing link needed for better durability of these ties. The aim of this research is to find a middle ground between improving concrete strength and longevity through fiber reinforcement and reducing the chances of localized damage from freeze-thaw cycles.
ι-Carrageenan catabolism is initiated by key sulfatases in the marine bacterium
Pseudoalteromonas haloplanktis
LL1
Authors: Liu Guang-Lei , Wu Sheng-Lei , Sun Zhe , Xing Meng-Dan , Chi Zhen-Ming , Liu Ya-Jun 
Published: June 2024

ABSTRACT

Marine bacteria contribute substantially to cycle macroalgae polysaccharides in marine environments. Carrageenans are the primary cell wall polysaccharides of red macroalgae. The carrageenan catabolism mechanism and pathways are still largely unclear.
Pseudoalteromonas
is a representative bacterial genus that can utilize carrageenan. We previously isolated the strain
Pseudoalteromonas haloplanktis
LL1 that could grow on ι-carrageenan but produce no ι-carrageenase. Here, through a combination of bioinformatic, biochemical, and genetic analyses, we determined that
P. haloplanktis
LL1 processed a desulfurization-depolymerization sequential pathway for ι-carrageenan utilization, which was initiated by key sulfatases PhSulf1 and PhSulf2. PhSulf2 acted as an endo/exo-G4S (4-O-sulfation-β-D-galactopyranose) sulfatase, while PhSulf1 was identified as a novel endo-DA2S sulfatase that could function extracellularly. Because of the unique activity of PhSulf1 toward ι-carrageenan rather than oligosaccharides,
P. haloplanktis
LL1 was considered to have a distinct ι-carrageenan catabolic pathway compared to other known ι-carrageenan-degrading bacteria, which mainly employ multifunctional G4S sulfatases and exo-DA2S (2-O-sulfation-3,6-anhydro-α-D-galactopyranose) sulfatase for sulfate removal. Furthermore, we detected widespread occurrence of PhSulf1-encoding gene homologs in the global ocean, indicating the prevalence of such endo-acting DA2S sulfatases as well as the related ι-carrageenan catabolism pathway. This research provides valuable insights into the enzymatic processes involved in carrageenan catabolism within marine ecological systems.

IMPORTANCE

Carrageenan is a type of linear sulfated polysaccharide that plays a significant role in forming cell walls of marine algae and is found extensively distributed throughout the world’s oceans. To the best of our current knowledge, the ι-carrageenan catabolism in marine bacteria either follows the depolymerization-desulfurization sequential process initiated by ι-carrageenase or starts from the desulfurization step catalyzed by exo-acting sulfatases. In this study, we found that the marine bacterium
Pseudoalteromonas haloplanktis
LL1 processes a distinct pathway for ι-carrageenan catabolism employing a specific endo-acting DA2S-sulfatase PhSulf1 and a multifunctional G4S sulfatase PhSulf2. The unique PhSulf1 homologs appear to be widely present on a global scale, indicating the indispensable contribution of the marine bacteria containing the distinct ι-carrageenan catabolism pathway. Therefore, this study would significantly enrich our understanding of the molecular mechanisms underlying carrageenan utilization, providing valuable insights into the intricate roles of marine bacteria in polysaccharide cycling in marine environments.
Osmotic stress response of the coral and oyster pathogen
Vibrio coralliilyticus
: acquisition of catabolism gene clusters for the compatible solute and signaling molecule
myo
-inositol
Authors: Boas Lichty Katherine E. , Loughran Rachel M. , Ushijima Blake , Richards Gary P. , Boyd E. Fidelma 
Published: June 2024

ABSTRACT

Marine bacteria experience fluctuations in osmolarity that they must adapt to, and most bacteria respond to high osmolarity by accumulating compatible solutes also known as osmolytes. The osmotic stress response and compatible solutes used by the coral and oyster pathogen
Vibrio coralliilyticus
were unknown. In this study, we showed that to alleviate osmotic stress
V. coralliilyticus
biosynthesized glycine betaine (GB) and transported into the cell choline, GB, ectoine, dimethylglycine, and dimethylsulfoniopropionate, but not
myo
-inositol.
Myo
-inositol is a stress protectant and a signaling molecule that is biosynthesized and used by algae. Bioinformatics identified
myo
-inositol (
iol
) catabolism clusters in
V. coralliilyticus
and other
Vibrio
,
Photobacterium
,
Grimontia
, and
Enterovibrio
species. Growth pattern analysis demonstrated that
V. coralliilyticus
utilized
myo
-inositol as a sole carbon source, with a short lag time of 3 h. An
iolG
deletion mutant, which encodes an inositol dehydrogenase, was unable to grow on
myo
-inositol. Within the
iol
clusters were an MFS-type (
iolT1
) and an ABC-type (
iolXYZ
) transporter and analyses showed that both transported
myo
-inositol. IolG and IolA phylogeny among
Vibrionaceae
species showed different evolutionary histories indicating multiple acquisition events. Outside of
Vibrionaceae
, IolG was most closely related to IolG from a small group of
Aeromonas
fish and human pathogens and
Providencia
species. However, IolG from hypervirulent
A. hydrophila
strains clustered with IolG from
Enterobacter,
and divergently from
Pectobacterium
,
Brenneria
, and
Dickeya
plant pathogens. The
iol
cluster was also present within
Aliiroseovarius
,
Burkholderia
,
Endozoicomonas
,
Halomonas
,
Labrenzia
,
Marinomonas
,
Marinobacterium
,
Cobetia
,
Pantoea
, and
Pseudomonas
, of which many species were associated with marine flora and fauna.

IMPORTANCE

Host associated bacteria such as
Vibrio coralliilyticus
encounter competition for nutrients and have evolved metabolic strategies to better compete for food. Emerging studies show that
myo
-inositol is exchanged in the coral-algae symbiosis, is likely involved in signaling, but is also an osmolyte in algae. The bacterial consumption of
myo
-inositol could contribute to a breakdown of the coral-algae symbiosis during thermal stress or disrupt the coral microbiome. Phylogenetic analyses showed that the evolutionary history of
myo
-inositol metabolism is complex, acquired multiple times in
Vibrio
, but acquired once in many bacterial plant pathogens. Further analysis also showed that a conserved
iol
cluster is prevalent among many marine species (commensals, mutualists, and pathogens) associated with marine flora and fauna, algae, sponges, corals, molluscs, crustaceans, and fish.
Generation of recombinant viruses directly from clinical specimens of COVID-19 patients
Authors: Yamamoto Hirotaka , Tamura Tomokazu , Ichikawa Takaya , Taguchi Yudai , Mori Kento , Oguri Satoshi , Suzuki Rigel , Suzuki Saori , Teshima Takanori , Fukuhara Takasuke 
Published: June 2024

ABSTRACT

Rapid characterization of the causative agent(s) during a disease outbreak can aid in the implementation of effective control measures. However, isolation of the agent(s) from crude clinical samples can be challenging and time-consuming, hindering the establishment of countermeasures. In the present study, we used saliva specimens collected for the diagnosis of SARS-CoV-2—a good example of a practical target—and attempted to characterize the virus within the specimens without virus isolation. Thirty-four saliva samples from coronavirus disease 2019 patients were used to extract RNA and synthesize DNA amplicons by PCR. New primer sets were designed to generate DNA amplicons of the full-length spike (S) gene for subsequent use in a circular polymerase extension reaction (CPER), a simple method for deriving recombinant viral genomes. According to the S sequence, four clinical specimens were classified as BA. 1, BA.2, BA.5, and XBB.1 and were used for the
de novo
generation of recombinant viruses carrying the entire S gene. Additionally, chimeric viruses carrying the gene encoding GFP were generated to evaluate viral propagation using a plate reader. We successfully used the RNA purified directly from clinical saliva samples to generate chimeric viruses carrying the entire S gene by our updated CPER method. The chimeric viruses exhibited robust replication in cell cultures with similar properties. Using the recombinant GFP viruses, we also successfully characterized the efficacy of the licensed antiviral AZD7442. Our proof-of-concept demonstrates the novel utility of CPER to allow rapid characterization of viruses from clinical specimens.

IMPORTANCE

Characterization of the causative agent(s) for infectious diseases helps in implementing effective control measurements, especially in outbreaks. However, the isolation of the agent(s) from clinical specimens is often challenging and time-consuming. In this study, saliva samples from coronavirus disease 2019 patients were directly subjected to purifying viral RNA, synthesizing DNA amplicons for sequencing, and generating recombinant viruses. Utilizing an updated circular polymerase extension reaction method, we successfully generated chimeric SARS-CoV-2 viruses with sufficient
in vitro
replication capacity and antigenicity. Thus, the recombinant viruses generated in this study were applicable for evaluating the antivirals. Collectively, our developed method facilitates rapid characterization of specimens circulating in hosts, aiding in the establishment of control measurements. Additionally, this approach offers an advanced strategy for controlling other (re-)emerging viral infectious diseases.