bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean
Authors: Howe Kathryn L. , Zaugg Julian , Mason Olivia U. 
Published: August 2024

ABSTRACT

Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all
Cycloclasticus
. Furthermore, all
Bermanella
encoded and expressed genes for non-gaseous
n
-alkane degradation; however, DWH
Bermanella
encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast,
Colwellia
were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.

IMPORTANCE
Microbial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based ‘omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.
Deciphering the adsorption machinery of Deep-Blue and Vp4, two myophages targeting members of the
Bacillus cereus
group
Authors: Nuytten Manon , Leprince Audrey , Goulet Adeline , Mahillon Jacques 
Published: August 2024

ABSTRACT

In tailed phages, the baseplate is the macromolecular structure located at the tail distal part, which is directly implicated in host recognition and cell wall penetration. In myophages (i.e., with contractile tails), the baseplate is complex and comprises a central puncturing device and baseplate wedges connecting the hub to the receptor-binding proteins (RBPs). In this work, we investigated the structures and functions of adsorption-associated tail proteins of Deep-Blue and Vp4, two
Herelleviridae
phages infecting members of the
Bacillus cereus
group. Their interest resides in their different host spectrum despite a high degree of similarity. Analysis of their tail module revealed that the gene order is similar to that of the
Listeria
phage A511. Among their tail proteins, Gp185 (Deep-Blue) and Gp112 (Vp4) had no structural homolog, but the C-terminal variable parts of these proteins were able to bind
B. cereus
strains, confirming their implication in the phage adsorption. Interestingly, Vp4 and Deep-Blue adsorption to their hosts was also shown to require polysaccharides, which are likely to be bound by the arsenal of carbohydrate-binding modules (CBMs) of these phages’ baseplates, suggesting that the adsorption does not rely solely on the RBPs. In particular, the BW Gp119 (Vp4), harboring a CBM fold, was shown to effectively bind to bacterial cells. Finally, we also showed that the putative baseplate hub proteins (i.e., Deep-Blue Gp189 and Vp4 Gp110) have a bacteriolytic activity against
B. cereus
strains, which supports their role as ectolysins locally degrading the peptidoglycan to facilitate genome injection.

IMPORTANCE

The
Bacillus cereus
group comprises closely related species, including some with pathogenic potential (e.g.,
Bacillus anthracis
and
Bacillus cytotoxicus
). Their toxins represent the most frequently reported cause of food poisoning outbreaks at the European level. Bacteriophage research is undergoing a remarkable renaissance for its potential in the biocontrol and detection of such pathogens. As the primary site of phage-bacteria interactions and a prerequisite for successful phage infection, adsorption is a crucial process that needs further investigation. The current knowledge about
B. cereus
phage adsorption is currently limited to siphoviruses and tectiviruses. Here, we present the first insights into the adsorption process of
Herelleviridae
Vp4 and Deep-Blue myophages preying on
B. cereus
hosts, highlighting the importance of polysaccharide moieties in this process and confirming the binding to the host surface of Deep-Blue Gp185 and Vp4 Gp112 receptor-binding proteins and Gp119 baseplate wedge.
Small hydrophobic (SH) proteins of
Pneumoviridae
and
Paramyxoviridae
: small but mighty
Authors: Brynes Adam , Williams John V. 
Published: August 2024

ABSTRACT

Small hydrophobic (SH) proteins are a class of viral accessory proteins expressed by many members of the negative-stranded RNA viral families
Paramyxoviridae and Pneumoviridae
. Identified SH proteins are type I or II transmembrane (TM) proteins with a single-pass TM domain. Little is known about the functions of SH proteins; however, several possess viroporin activity, enhancing membrane permeability of infected cells or those expressing SH protein. Moreover, several SH proteins inhibit apoptosis and immune signaling pathways within infected cells, including TNF and interferon signaling, or activate inflammasomes. SH proteins are generally nonessential for viral replication
in vitro
, but loss of SH is often associated with reduced replication
in vivo
, suggesting a role in enhancing viral replication or evading host immunity. Analogous proteins are expressed by a variety of pathogens of public health importance; thus, understanding the functional importance and mechanisms of SH proteins provides insight into the pathogenesis and replication of negative-sense RNA viruses.
Draft genome sequence of a methicillin-resistant
Staphylococcus aureus
strain isolated from a chronic wound
Authors: Allison Kira N. , Mejlaoui Rayhane , DeZeeuw Katrina G. , Marek Jonah E. , Cassol Edana , Overhage Joerg 
Published: August 2024

ABSTRACT

We report the draft genome sequence and antimicrobial resistance gene profile of a methicillin-resistant
Staphylococcus aureus
(MRSA) clinical isolate recovered from a chronic pressure injury wound infection of an adult female patient. The draft genome sequence included a 2.86-Mb chromosome, which was accompanied by a 27-kb plasmid containing
blaZ
.
Arc magma heterogeneity induced by subslab mantle upwelling
Authors: Li Xiaohui , Guo Kun , Li Sanzhong , Yang Huixin , Pi Ju-lien , Zhong Yuan , Chen Long , Suo Yanhui , Stern Robert J. , Wang Xiaoyuan , Li Dongyong , Yu Shengyao 
Published: August 2024

Abstract
Tomographic images of the Ryukyu subduction zone suggest upwelling of asthenospheric mantle through slab tears; this can affect the genesis of arc magma. However, geochemical evidence testing this hypothesis is lacking. Here, we analyzed magnesium (Mg) isotopes of volcanic rocks from various regions in the Ryukyu subduction zone and combined these with trace element and Sr-Nd isotopes to understand how heterogeneous mantle contributed to arc magmas. The δ26Mg values of Okinawa Trough samples (−0.30‰ to −0.09‰) are sometimes slightly higher than those of typical mantle; we think this reflects the role of slab-derived ﬂuids. Kueishantao lavas exhibit radiogenic Sr-Nd isotopes and mantle-like δ26Mg values (−0.27‰ to −0.19‰), which are primarily contaminated by the continental crust. Notably, samples from the northern Taiwan volcanic zone display lower δ26Mg values in basalts (−0.45‰ to −0.28‰) and higher values in andesitic rocks (−0.18‰ to −0.14‰). We postulate that elevated δ26Mg values stem from the contribution of slab-derived fluids. Conversely, the heat and material transported by upwelling of subslab asthenosphere around the slab edge or tear may induce melting of carbonate sediment at subarc depths to yield low-δ26Mg melts, explaining the lower δ26Mg values in basalts. This study provides direct geochemical evidence underscoring the involvement of subslab asthenospheric material in the formation of arc magma and helps elucidate the causes of arc mantle heterogeneity.
The Dirichlet Problem for an Elliptic Functional Differential Equation with the Compressed, Expanded, and Rotated Argument
Authors: Rossovskii L. E. , Tovsultanov A. A. 
Published: August 2024

Abstract
The paper is devoted to the Dirichlet problem in a plain bounded domain for a linear divergent-form second-order functional differential equation with the compressed (expanded) and rotated argument of the highest derivatives of the unknown function. Necessary and sufficient conditions for the Gårding-type inequality are obtained in algebraic form. The result may depend not only on the absolute value of the coefficients but also on their signature. Under some restrictions on the structure of the operator and the geometry of the domain, the questions of existence, uniqueness, and smoothness of generalized solutions are studied for all possible values of the coefficients and parameters of transformations in the equation, even when the equation is not strongly elliptic.
Five years of discourse related to Indonesia tobacco control reform: a content analysis of online media coverage
Authors: Amalia Beladenta , Astuti Putu Ayu Swandewi , Cohen Joanna E 
Published: August 2024

BackgroundIn 2017, Indonesia initiated the amendment of its 11-year-old tobacco control regulation (PP 109/2012) to reduce smoking among youth, but the process was stalled. The proposed changes in the regulation include a full ban on tobacco advertising, promotion and sponsorship (TAPS), increasing health warning label (HWL) size and regulating electronic cigarettes (e-cigarettes). This study analysed the arguments and actors for and against the PP 109/2012 amendment in online media articles.MethodContent analysis of 326 online articles reporting on the PP 109/2012 amendment published from 2018 to 2023, retrieved from the Tobacco Watcher platform. We coded articles for statements supporting or opposing the amendment (position statement), content of the arguments used to support (supporting argument) and oppose (opposing argument) the amendment, actors presenting the arguments and tobacco control measures. We iteratively reviewed and coded data and presented the frequency of categories.ResultsOf 332 position statements, 53.3% were against the amendment. The main categories of supporting arguments (N=1448) included smoking trends (21.1%), health implications (16.6%), science-based evidence (9.6%) and protecting the population (9.2%). Opposing arguments (N=1413) emphasised the tobacco farmers’ welfare (16.6%), impact on the industry (16.4%) and current regulation is sufficient (11.0%). Supporting actors were predominantly health-related entities and government officials (89.3%), while 62.1% of opposing actors included trade and Islamic groups, the tobacco industry and front groups. HWLs, e-cigarette/heated tobacco product regulation and TAPS were the main (77.8%) tobacco control measures mentioned in the proamendment arguments, while HWLs, TAPS and cigarette sale restrictions were the dominant (79.3%) tobacco control measures in anti-amendment arguments.ConclusionIndonesia’s tobacco control reform faced opposition by false claims primarily from industry allies, resulting in a 5-year delay in enactment. Future tobacco control media advocacy must address these claims and emphasise the alignment of economic interests with public health goals.
Symmetry-resolved entanglement entropy for local and non-local QFTs
Authors: Pirmoradian Reza , Tanhayi M. Reza 
Published: August 2024

AbstractIn this paper, we investigate symmetry-resolved entanglement entropy (SREE) in free bosonic quantum many-body systems. Utilizing a lattice regularization scheme, we compute symmetry-resolved Rényi entropies for free complex scalar fields and a specific class of non-local field theories, where entanglement entropy (EE) exhibits volume-law scaling. We present effective and approximate eigenvalues for the correlation matrix used in computing SREE and demonstrate their consistency with numerical results. Furthermore, we explore the equipartition of EE, verifying its effective behavior in the massless limit. Finally, we comment on EE in non-local quantum field theories and provide an explicit expression for the symmetry-resolved Rényi entropies.
Meson scattering in a non-minimally Lorentz-violating scalar QED at finite temperature
Authors: Araújo M. C. , Maluf R. V. , Furtado J. 
Published: August 2024

AbstractIn this paper we study meson scattering in a non-minimally Lorentz-violating scalar QED at finite temperature. The meson scatterings were investigated in tree level and the finite temperature effects were addressed by using the thermofield dynamics formalism. We have considered three types of scattering, namely, meson-antimeson of a-type into meson-antimeson of b-type, meson-antimeson of a-type into meson-antimeson of a-type and meson-meson of a-type into meson-meson of a-type. For each scattering we have computed the cross section in order to investigate the influence of the finite temperature effects.
New norm and numerical radius bounds
Authors: Sababheh Mohammad , Moradi Hamid Reza 
Published: August 2024

Finding new bounds for norms and the numerical radius of certain matrix forms is a renowned topic that has attracted numerous researchers. In this paper, we show some new bounds for unitarily invariant norms and the numerical radius of certain matrix forms that involve products of matrices and sums of products. New arithmetic-geometric mean-type inequalities and a refinement of the celebrated Cauchy–Schwarz inequality are shown among the obtained results. Our results are compared with those in the literature through numerical examples and rigorous approaches.
COMPARING THE EFFECTS OF CYCLE TIME PROTOCOLS OF AUSSIE CURRENT NEUROMUSCULAR ELECTROSTIMULATION ON MULTIFIDUS MUSCLE ACTIVITY IN CHRONIC LOW BACK PAIN: A RANDOMIZED CLINICAL TRIAL
Authors: Kuhn Guilherme de Conto , Bloemer Aline , Alves Gabriel Galhardo , Franzen Júlio Augusto , Linzmeyer Alessandra , Fréz Andersom Ricardo , Aragão Fernando Amâncio , Carvalho Alberito Rodrigo de , Bertolini Gladson Ricardo Flor 
Published: August 2024

Introduction: Neuromuscular electrostimulation (NMES) represents a therapeutic approach for addressing chronic low back pain (CLBP); however, the influence of NMES dose on muscle activity remains subject to debate. Objective: To compare the impact of two distinct NMES protocols employing Aussie current, characterized by varying dosages emphasizing time cycle alterations, on electromyographic activity within the multifidus muscles in individuals afflicted with CLBP. Methods: A randomized clinical trial encompassed 18 volunteers diagnosed with mechanical CLBP. These volunteers were randomly assigned to two NMES intervention groups with dissimilar dosages: 15 repetitions ([Formula: see text][Formula: see text]) and 30 repetitions ([Formula: see text][Formula: see text] ). In both interventions, the current amplitude was tailored to individual perception and documented at the culmination of each session. Over the course of four weeks, two sessions took place per week. Electromyographic activity of the multifidus muscles was evaluated using surface electromyography before and after the intervention. The assessment focuses on both time-domain analysis using Root Mean Square (RMS) and frequency-domain analysis involving mean activation frequency (FREQ). Results: There are no interactions between the time and intervention, but there is the time effect on RMS, indicating that post-intervention muscle activity exceeded pre-intervention values in both groups. FREQ values did not exhibit statistically significant discrepancies. Conclusions: This study showed that NMES using the Aussie current is effective in increasing muscle activity in individuals with CLBP, and the results were not influenced by the different cycle times with equal volumes.
Discrete Element Modeling of Irregular-Shaped Particles Using an Automatic Generation Algorithm-Based Multi-Sphere Model
Authors: Chen Likuan , Ma Huaqing , Zhou Lianyong , Yuan Hui , Zhao Yongzhi 
Published: August 2024

Within the Discrete Element Method (DEM) framework, the multi-sphere model capable of creating irregular-shaped particles by several sub-spheres attracts increasing attention. Traditionally, the creation of irregular-shaped particles using the multi-sphere model requires manual determination of the position and diameter of each sub-sphere, which extremely increases the difficulty and workload of DEM modeling of irregular-shaped particles. To tackle this issue, a new automatic generation algorithm that helps to create arbitrary-shaped multi-sphere particles automatically was developed in this study. The quality of created multi-sphere particles can be easily controlled by adjusting the number of sub-spheres and size factor referred to as the size ratio of the smallest sub-sphere to the largest sub-sphere. To verify the effectiveness of the newly developed automatic generation algorithm, two verification tests were conducted in this study: (i) The packing behavior of irregular-shaped particles in a rectangular container and (ii) the mechanical behavior of irregular-shaped particles under the uniaxial compression. The fill heights of the simulations were in line with those of the experiments with an error of less than 8%. The mechanical behavior of irregular-shaped particles under the uniaxial compression can also be well reproduced. Besides, the influence of important parameters on simulation accuracy was also investigated. The results demonstrated that the newly developed automatic generation algorithm can accurately create complex-shaped particles with a small number of sub-spheres. Increasing the number of sub-spheres will improve the simulation accuracy but at the expense of computational efficiency. A larger size factor leads to higher computational efficiency in DEM simulation but is accompanied by a significant loss of accuracy.
Exposing Stealthy Wash Trading on Automated Market Maker Exchanges
Authors: Gan Rundong , Wang Le , Xue Liang , Lin Xiaodong 
Published: August 2024

Decentralized Finance (DeFi), a pivotal component of the emerging Web3 landscape, is gaining popularity but remains vulnerable to market manipulations, such as wash trading. Wash trading is an illegal practice, where traders buy and sell assets to themselves within cryptocurrency exchanges to artificially inflate trading volumes and distort market perceptions. However, current research primarily focuses on traditional exchanges based on the Order-book mechanism (similar to stock markets), while ignoring the Automated Market Maker (AMM) exchanges, which dominate over 75% of the market and represent a significant innovation within the DeFi.
This study utilizes entity recognition technology to detect wash trading on AMM exchanges within Ethereum-like systems, based on the understanding that colluding addresses (perceived as the same entity) must use ETH for transaction fees and exhibit direct or indirect ETH transfer links. We identify wash trading when addresses with transfer connections almost simultaneously buy and sell assets while their total asset holdings remain nearly constant. This comprehensive blockchain network analysis, compared to focusing solely on transactions within exchanges, unveils covert wash trading activities. Our detection method achieves a 95.9% recall and a 96.7% true negative rate in identifying pools affected by wash trading, demonstrating its superiority over existing methods. Furthermore, we apply our method to 98,945 pools from Uniswap V2 & V3 (the most popular AMM exchanges on Ethereum) and identify 1,070,626 abnormal transactions, totaling $27.51 billion in trading volume. Analysis of these transactions uncovers insights into wash traders’ behaviors, including the utilization of multiple addresses and the dual roles of certain addresses as wash traders and liquidity providers. These insights are crucial for developing more effective strategies to combat fraudulent activities in the DeFi ecosystem and enhance financial scrutiny.
Genetic Screen in a Preclinical Model of Sarcoma Development Defines Drivers and Therapeutic Vulnerabilities
Authors: Freeland Jack , Muñoz Maria , O’Donnell Edmond , Langerman Justin , Darrow Morgan , Bergonio Jessica , Suarez-Navarro Julissa , Thorpe Steven , Canter Robert , Randall Robert Lor , Plath Kathrin , Carraway Kermit L. , Witte Owen N. , Graeber Thomas G. , Carr-Ascher Janai R. 
Published: August 2024

Abstract

Purpose:
High-grade complex karyotype sarcomas are a heterogeneous group of tumors with a uniformly poor prognosis. Within complex karyotype sarcomas, there are innumerable genetic changes but identifying those that are clinically relevant has been challenging.

Experimental Design:
To address this, we utilized a pooled genetic screening approach, informed by The Cancer Genome Atlas (TCGA) data, to identify key drivers and modifiers of sarcoma development that were validated in vivo.

Results:
YAP1 and wild-type KRAS were validated as drivers and transformed human mesenchymal stem cells into two distinct sarcoma subtypes, undifferentiated pleomorphic sarcoma and myxofibrosarcoma, respectively. A subset of tumors driven by CDK4 and PIK3CA reflected leiomyosarcoma and osteosarcoma demonstrating the plasticity of this approach and the potential to investigate sarcoma subtype heterogeneity. All generated tumors histologically reflected human sarcomas and had increased aneuploidy as compared to simple karyotype sarcomas. Comparing differential gene expression of TCGA samples to model data identified increased oxidative phosphorylation signaling in YAP1 tumors. Treatment of a panel of soft tissue sarcomas with a combination of YAP1 and oxidative phosphorylation inhibitors led to significantly decreased viability.

Conclusions:
Transcriptional co-analysis of TCGA patient samples to YAP1 and KRAS model tumors supports that these sarcoma subtypes lie along a spectrum of disease and adds guidance for further transcriptome-based refinement of sarcoma subtyping. This approach can be used to begin to understand pathways and mechanisms driving human sarcoma development, the relationship between sarcoma subtypes, and to identify and validate new therapeutic vulnerabilities for this aggressive and heterogeneous disease.