bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-Sensor Towbody: A down looking and side looking platform for Detection, Classification, & Localization of inert munitions
Authors: Williams Kevin L. , Marston Timothy
Published: January 2025

MuST comprises a FOCUS-3 towbody manufactured by MacArtney Underwater Technology, two sonar systems manufactured by EdgeTech, a multi-beam system from RESON, a suite of towbody orientation and motion sensors, and a shipboard handling system. The baseline Multi-Sensor Towbody (MuST) hardware and operation are described. Next, shipboard data acquisition/visualization and post mission analysis are presented. This includes examples of the data products currently being used for detection and classification. Finally, the detection/localization/classification performance is quantified using data acquired over blind test beds placed in Sequim Bay, Washington, by the Pacific Northwest National Laboratory. The test beds had 20 to 50 objects on and in the sediment within a 100 m diameter region. Both the number of objects and their positions within the region were unknown to the MuST field team. Results indicate that the hardware implementation and current software processing chain allows classification of inert munitions, with diameters at or above 81mm, with a probability of correct classification of approximately 85%. Furthermore, the difference between ground truth and MuST geolocations were 2 meters or less for over 90% of the targets detected. [Work sponsored by ESTCP.]
Applying systems thinking in soundscape research and practice
Authors: Aletta Francesco , Zhou Koko , Oberman Tin , Mitchell Andrew , Pluchinotta Irene , Torresin Simone , Cerwén Gunnar , Kang Jian
Published: January 2025

This paper explores the future of soundscape research and practice in urban planning, emphasizing applied expertise and experience using the soundscape method. Soundscape studies recognize environmental sounds as a resource that can promote positive health effects, such as stress reduction and improved cognitive performance. However, enhancing soundscapes in urban areas may occasionally lead to unintended consequences, potentially exacerbating social inequalities. This study employs a systems thinking approach, involving participatory modelling workshops with experts to create a causal loop diagram (CLD) illustrating the complex interconnections between soundscape quality and public health. Key themes identified include noise pollution, socio-economic dimensions, environmental justice, and biodiversity. The CLD reveals feedback mechanisms and intervention points, suggesting research pathways, such as ecoacoustics, psychoacoustics, prediction models, and big data applications. These pathways aim to mitigate noise pollution, enhance biodiversity, and balance individual and community needs in soundscape design. This approach seeks to promote equitable and sustainable urban environments, advancing the discourse on soundscape research and its applications by integrating soundscape quality into urban planning and policy. Further interdisciplinary research and stakeholder engagement are essential to refine these insights and translate them into effective policies and practices.
The role of language proficiency on the perception of speech and song
Authors: Idris Reem , Czepiel Anna , Vanden Bosch der Nederlanden Christina
Published: January 2025

During everyday communication, background noise can affect our ability to comprehend speech accurately. Although many studies have investigated perception of speech in noisy environments, it is less clear how our perception in noisy environments could be enhanced by song, which could be beneficial due to melodic/rhythmic predictability. Language proficiency may also impact perception of song and speech. The current study aimed to clarify the unique struggles that people with low language proficiency face. We used the Test of Adolescent and Adult Language - Fourth Edition (TOAL-4) to divide 48 participants into low and high-English proficiency groups. Participants’ speech-in-noise performance was assessed across four blocks of sung and spoken sentences. As predicted, performance improved for both song and speech over the course of the experiment and was higher in high-proficiency participants than low-proficiency English speakers. However, contrary to our predictions, participants found it harder to comprehend song than speech. This did not interact with language proficiency (high versus low). Overall, our findings suggest that, regardless of language background, song does not benefit perception in noise, challenging previous research that highlight the benefit of melodies and rhythms in facilitating speech perception in noisy or difficult listening environments.
Acoustic characteristics of English intonation in Mandarin-English bilinguals
Authors: Yang Jie
Published: January 2025

In addition to segmental level contrast, Mandarin Chinese uses two levels of prosodic contrast, tone at word level and intonation at utterance level, to convey linguistic meaning. Mandarin speakers need to adjust fundamental frequency (f0) to maintain intelligibility at both word- and utterance-level. For English speakers, f0 changes at utterance level for intonation were not confined by word-level tonal requirements. The present study investigated the acoustic characteristics of English intonation produced by Mandarin-English bilinguals at different developmental stages. Six- and nine-year-old Mandarin-English bilingual children and adults (seven per group) completed the speech production tasks. Stimuli were three types of carrying sentences (statement, question with and without inversion) in English. Carrying sentences end with monosyllabic target words that are phonetically similar in Mandarin (e.g., [di], 帝 Dee). Average f0 and magnitude of f0 change were measured within word and over the entire utterance, and compared among age groups. Results indicated (1) average f0 was the highest in questions without inversion, followed by questions with inversion. Statements showed the lowest average f0. (2) Magnitude of f0 change was larger in speakers with more English exposure and in older children. Sentence type, language experience, and developmental age appear to influenced average f0 and magnitude of f0 change.
Phonetic segment switching based on differential-encoding of the vocal tract resonances
Authors: Story Brad H. , Bunton Kate
Published: January 2025

Previous work has shown that speech segments can be encoded by specifying relative acoustic events along a time axis that consist of directional changes of the vocal tract resonance frequencies called resonance deflection patterns (RDPs) [JASA, 146(4), 2522–2528]. These events are transformed via acoustic sensitivity functions, into time-varying modulations of the vocal tract shape. RDPs specifying /b, p/, /d, t/, and /g, k/, for example, would typically be coded as [−1 −1 −1], [−1 1 1], and [−1 1 −1], respectively, where the vectors indicate, from left to right, the targeted directional shift of the first, second, and third resonances of the vocal tract. The specific aim of this study was to determine if listeners' recognition of speech synthesized in the RDP paradigm aligns with the RDP settings. That is, if RDPs are conceived as a bank of switches, can word recognition be guided by changes in the pattern of switch settings. A synthesized version of “abracadabra” was used as the baseline word. Variations were generated by systematically changing the RDPs for consonants in the initial “abra” and in the final “dabra” to generate new targets such as “aglacabadra.” Listener responses to these variations will be reported.
Assessing individual speaker state and team based speech communication dynamics within the APOLLO lunar missions: Leveraging fearless steps APOLLO community resource
Authors: Omidi Zahra , Hansen John H.
Published: January 2025

In naturalistic speech communications, assessing individual speaker state and collaborative team dynamics is useful for problem solving in time sensitive tasks. The NASA Apollo program represents a massive longitudinal effort for team problem-solving. For the last decade, CRSS-UTDallas has worked to recover this data, creating the Fearless Steps Apollo (FS-APOLLO) community resource. This collection of 150000 h of digitized naturalistic audio and associated meta-data from advanced speech diarization/recognition is being released for speech science, technology, and historical preservation. This current effort focuses on comparing three Apollo missions to assess speaker stress/emotion/state and team communication dynamics. Apollo (A11, A7, and A13) missions were chosen, with 5 h of audio across five NASA team channels for each mission. A comprehensive speech and speaker analysis system was developed for independent measurement of stress, vocal intensity, Lombard effect, and emotion metrics. An integrated speech/speaker diarization pipeline was first applied to separate speech blocks. Next, this system was used to analyze Apollo team conversations, employing emotion recognition and task stress profiling to capture the social-linguistic-task based aspects of group interactions. Individual and team results will be presented from this study. Through this effort, we aim to create new opportunities for speech scientists and researchers to collaborate on developing effective metrics for speaker assessment.
Goal reasoning for intelligent parameter adaptation in active sonar
Authors: Nelson Jill K.
Published: January 2025

Active sonar systems include a variety of parameters that can be dynamically tuned to improve system performance. In practice, however, parameters are typically set and fixed over long periods based on expected environmental conditions, prior performance, etc. Dynamic tuning of system parameters by sonar operators is impractical due to both the short time frame between adaptations and the complex relationship among the parameters, goals, and system performance. In intelligent active sonar, the system tunes parameters based on a set of goals and evaluation of how well those goals are being met. This approach significantly reduces the cognitive load on the operator, who can set high-level goals that are interpreted by the system and translated into low-level parameter adjustments. Goal-driven autonomy (GDA), for example, detects discrepancies between predictions and observations and generates context-specific explanations when significant discrepancies are observed. These explanations may indicate that new goals need to be introduced or existing goals de-activated. The explanation generation and goal formation aspects of GDA provide insight into how the intelligent system is reasoning about its actions and allow an operator to have direct input to the intelligent system when desired.
Experts from multiple fields exchange perspectives on optimizing the acoustic environment in healthcare
Authors: Schnitta Bonnie , Solet Joanne , Pitts Francis M. , Harkin Sean , Roselli Nicholas , Hamza Omar , Acre Paul
Published: January 2025

This diverse panel of experts will discuss the impact and challenges associated with acoustics in healthcare from multiple perspectives: design, regulation, clinical care, research, and engineering, and will entertain questions from participants.
Ocean soundscapes reveal climatic and economic oscillations
Authors: ZoBell Vanessa M. , Posdaljian Natalie , Lenssen Kieren , Wiggins Sean , Hildebrand John , Baumann-Pickering Simone , Frasier Kait
Published: January 2025

An accumulation of 26 859 days of acoustic recordings (spanning over 74 years at six sites) was processed and analyzed to investigate the interannual, seasonal, and diel patterns within six ocean soundscapes. Biological sound levels (18-25 Hz and 40–45 Hz) quantified acoustic energy from fin and blue whales, ambient sound levels (63-Hz and 800-Hz one-third-octave) quantified energy from ships and wind, and broadband spectra (15 Hz to 1 kHz) identified changes across time and space. Biological sound levels varied seasonally and correlated with large-scale climatic patterns and long-term ocean fluctuations. During marine heatwaves, baleen whale associated sound levels decreased in southern sites and increased in sites adjacent to the California Current. Ship sound levels at high-traffic sites reflected economic events such as the financial crisis, labor shortages and negotiations, and changes to port flows. Wind speeds and associated sound levels reflected on-shore/off-shore relationships and decreased during the morning hours. Understanding marine soundscapes aids in understanding the ocean’s ecological health amidst the ever-changing impact of climate change.
Identifying narwhal vocalizations to assess marine conservation areas in the changing Arctic
Authors: Rodrigues Moron Juliana , Dosso Stan , Halliday William D.
Published: January 2025

Climate-change related increases in sea surface temperatures and associated declines in sea ice in the Arctic are driving phenological shifts in habitat use of several species of marine mammals, which are also facing higher noise levels from increasing human activities. While some protected areas have been established, their effectiveness for species of interest, such as narwhal, have not been assessed. Sound is important for communication and navigation in marine mammals, which makes passive acoustic monitoring an appropriate tool for studying these species, being particularly effective in remote and harsh Arctic environments. Recordings collected in the Disko Fan and Davis Strait Conservation Areas (southern Baffin Bay), known habitat for narwhals, are analyzed using a new method for identifying narwhal whistles in long-term passive acoustic datasets. We identify narwhal whistles by assuming that any whistles produced around the same time as narwhal echolocation clicks (manually identified on spectrograms) were produced by narwhal. These whistles are then used to train a new deep learning detector to process long-term passive acoustic datasets for narwhal presence. This is an important step toward understanding the impacts of climate change on the distribution of this species and the effectiveness of conservation areas.
Physical acoustics lab at the university of oxford
Authors: Kwan James , Roy Ronald A.
Published: January 2025

We want to welcome everyone to have a look at our lab's space where the academic magic happens. Our group boasts some unique bespoke acoustic equipment and experimental methods that cover topics including physical acoustics, ultrasound enhanced drug delivery, and sonochemistry. In the video, we will walk through the lab and showcase some of our brilliant students and the experimental techniques they are developing.
Shaping sound field through acoustic metasurfaces: An optimisation method for correcting loudspeaker emissions
Authors: Chisari Letizia , Philippides Andy , Memoli Gianluca
Published: January 2025

In a loudspeaker system, the acoustic wave front modulation can be achieved using active control systems that adopt algorithms to modulate the acoustic wave front emitted, adapting to the environmental conditions or to the specific requirements of the sound source. To be efficient, a large number of loudspeakers and the digital processing of the signal are required. Acoustic metasurfaces are sub-wavelength structures that can manipulate sound, allowing the control of, e.g., the shape or direction of the wave front. In this work, we aim to reduce the number of speakers by coupling acoustic metasurfaces at the outlet of a single transducer. To design the metasurface for this task direct methods, which rely on unit cells geometrical parameters retrieved by finite element simulations, are traditionally used. This approach has to be repeated iteratively and demands significant efforts to investigate the enormous number of possible metamaterial combinations. More recent methods include topology optimization, physics-informed neural networks, and machine learning. These methods frequently limit their focus on optimization for unit cell structures and do not provide a design or strategy for the whole metasurface. In this work, the metasurface phase profile is instead retrieved by combining a finite element method to generate the search space and a gradient-free optimization algorithm to retrieve the best metasurface configuration required to satisfy a desired pressure distribution pattern in a 2D listening area.
Low-cost low-power underwater acoustic data acquisition and processing system
Authors: Blanco Julian , Campbell Richard L. , Verlinden Christopher M.
Published: January 2025

There is a need for low-cost acoustic recording and processing instruments. Cheaply available and highly capable off-the-shelf microcontrollers and analog-to-digital converters (ADC's) allow rapid prototyping of novel systems to achieve minimum performance requirements without overhead. Combined with low-cost manufacturing capabilities for pre-assembled printed circuit boards (PCBs), acoustic recording hardware and processing have become more accessible. Prototypes can be designed and delivered for less than $100 USD per iteration. Using this methodology, we developed the Self Contained Acoustic Recording Instrument (SCARI). While consuming less than ∼40 mW, two channels of 48 ksps acoustic data can be recorded to .wav files on a microSD card with a SAMD51 microcontroller, an SGTL5000 ADC, and differential pre-amplifier on a compact PCB. Data can be saved to a microSD card or streamed via USB to be saved/processed by an embedded computer, with resources left over for simple real-time processing.
An update on horn-based vehicle signaling, and newer sound effects for convenience, nostalgia, and entertainment
Authors: Botta Jeanine , Fink Daniel
Published: January 2025

A presentation at the 2013 International Congress on Acoustics explored vehicle horn-based lock alert use and the conflicts it created among neighbors. From 2007 to 2012, more than 60% of vehicles manufactured for the North American market left factories with horn-based alerts to signal locking and unlocking. Most were set to honk at the second press of the key fob’s lock button, although settings could be changed to flashing lights or no audible or visual alert. Automakers addressed questions about legality in user manuals, stating that owners should observe local laws. By 2013, internal combustion engine vehicles had become quieter, and electric and hybrid vehicles seemed to offer a chance to reduce noise further. Instead, automakers adopted horn-based features in electric and hybrid vehicles, and added sounds for convenience, nostalgia, and entertainment, using external speakers. Reviewing auto industry data, noise ordinances, federal, state, and local regulations, and case law, we examine legal and regulatory aspects of non-emergency horn signals and vehicle sound effects.
Directivity patterns for road traffic auralization
Authors: Dreier Christian , Kamps Simon , Vorlaender Michael
Published: January 2025

Auralizations enable the simulation of sound fields in complex environments. For example, they can be used to investigate the perceptual aspects of sound emitted by vehicles. As input for the signal processing chain, sound source models must adequately represent the acoustic spatial and spectro-temporal characteristics of real vehicle emissions. An in-situ measurement method for determining the velocity-dependent directionality of moving sound sources is presented. The work presents results for different vehicle types. Finally, the implementation of the directional characteristics into an urban sound auralization model is discussed in order to simulate the sound transmission in anurban environment including complex propagation effects.
Lyric intelligibility of musical segments for older individuals with hearing loss
Authors: Whitmer William M. , McShefferty David , Akeroyd Michael A. , Bannister Scott , Barker Jon P. , Cox Trevor J. , Roa Gerardo , Fazenda Bruno , Firth Jennifer L. , Graetzer Simone , Greasley Alinka , Vos Rebecca
Published: January 2025

Understanding lyrics is a major barrier to enjoying music for people with hearing loss. To improve lyric understanding through machine-learning, metrics need to be informed by the experiences of the target population. Currently, there are no data on lyric-recall ability of older individuals with hearing loss. Twelve older participants with mostly mild-sloping hearing loss listened to and recalled 100 segments of popular music that varied in genre, duration and word count. In each trial, participants heard a randomly chosen segment twice with a 5-s interstimulus interval over headphones at an A-weighted level of 65 dB plus individualised frequency-dependent nonlinear gain. The proportion of words heard correctly varied greatly across samples, from 0 to 100%, and varied as a function of genre, similar to past studies with different populations. Individual intelligibility across samples was correlated with age; sample intelligibility across individuals, however, was not correlated with word count or rate. Improving sung-lyric intelligibility is a different challenge from spoken-speech enhancement for those with hearing loss. Not only does the enhancement need to be considered within the overall enjoyment of the music, but the variation in results—as seen in the current study—reflects variations in genre, orchestration and vocal quality in sung music.
Design of optimal discriminant using air-induced structural vibration for groundline health assessment of wooden utility poles
Authors: Lee Yishi
Published: January 2025

Wooden utility poles are the critical components of power distribution in the United States and many parts of the world. Due to its essential societal function, comprehensive structural health monitoring technology is lacking to reflect its importance. To address this concern, the study exploits the phenomenon of air-induced oscillation due to the vortex street developed in the wake of the pole. It extracts the features of this vibration and designs an optimal classifier that can infer the health condition around the groundline region based on oscillational acceleration data. The proposed methodology consists of the following steps: (1) Construct a transient and modal orthotropic finite element model with realistic soil conditions to analyze the vibrational properties of a class 2 55-foot wooden utility pole. (2) Produce temporal vibrational responses from periodic disturbance winds of different harmonic conditions from a given transmission cable configuration. (3) Explore feature extraction techniques and design an optimal discriminant function for structural health classification. This presentation will detail the techniques and examine the preliminary efficacy of the proposed discriminant function using empirical data. Its broader impact is to examine the technical feasibility of using structural vibration to determine the groundline health condition.
Use of Schwarz-ox direct-to-reverberant power ratio estimator for distance estimation near diffuse noise point in a complex plane
Authors: Wang Chuyang , Mung Wai Yin , Chu Karhang , Choy Tracy Y.
Published: January 2025

This study investigated the time- and frequency- dependent direct-to-reverberant power ratio (DRR) estimators from spatial coherence value of omnidirectional microphone array. We use a mathematical 2D geometry interpretation, complex plane, to analysis the deficiency of different DRR estimators bias and construct a better estimator near the diffuse noise point in the same plane. The diffuse noise point is a reflection of a certain distance in practical environment, where the received signals in microphone array are ideal diffuse. This estimator was then applied to distance estimation in a reverberant environment. DRR values are known to exhibit more effective performance in the case of distance estimation than other acoustic indicators in such environment; however, several proposed DRR estimators are not sufficiently robust near diffuse noise points in the complex plane. Therefore, this study proposes a method to accommodate the existing Schwarz DRR estimator to exhibit better performance around the point where the far-distance estimation is made. For validation, our results focused on different directions and inter-microphone distances in two reverberant classrooms. In addition, through an in-depth investigation of the proposed method, we found that it could be expanded into a more freedom-based method, which researchers can manipulate to draw the DRR estimator pattern in the complex plane as required.
Framework for multiclass vocal pathology classification using convolution neural network, continuous wavelet transform, and signal-to-noise ratio analysis
Authors: Rathi Bhawna , Hsu Timothy
Published: January 2025

Vocal disorders are potentially an underreported condition due to invasive diagnostic methods and a lack of general awareness. Traditionally, vocal damage is diagnosed through laryngoscopies, but recent research supports using audio processing and machine learning to distinguish between not only healthy and unhealthy voices but also between different vocal pathologies. This study introduces a framework for classifying multiple vocal pathologies—dysphonia, polyps, nodules, and paralysis, based on previous research focused on two-class classification. The current approach employs continuous wavelet transforms (CWT) and spectrograms from pathological voices, /AH/ and /EE/ audio files from the Indiana University (IU) Health Voice Center, as inputs for a convolutional neural network (CNN) classifier. The images from the wavelet transform achieve higher accuracy than spectrograms for both two-class and multiclass classification. Various wavelet shapes and sizes are compared for accuracy rates and processing time. Different signal-to-noise ratios and augmentation techniques are tested for classification robustness and accuracy. The study also compares male and female voices on classification accuracy and how parameters, like learning rates and filter layers, affect CNN performance. Results indicate that accuracy improves with a 0.0001 learning rate and optimal image sizes, demonstrating the potential for enhancing classification models through precise parameter tuning.
Interpreting user-generated recordings from the Trump assassination attempt on July 13, 2024
Authors: Maher Robert C.
Published: January 2025

Handheld smartphones are common at public events, and this increases the likelihood that user-generated recordings (UGRs) may capture sounds of interest to audio forensic investigations. The assassination attempt against presidential candidate Donald Trump that took place in Bulter, PA, on Saturday, July 13, 2024, is a prominent example, with a dozen or more official and user-generated videos of the incident. Audio forensic expertise is called upon to determine the physical meaning of the recorded material and to ascertain its authenticity. In the Trump rally shooting incident, multiple concurrent recordings were made from different positions around the scene, capturing the sounds of several audible gunshots. The set of multiple UGR recordings provides information useful to the forensic investigation, such as spatial information about the number, type, position, and orientation of firearms. Examination of the multiple recordings from the Trump rally incident requires interpretation of unsynchronized audio from locations that are not precisely known. Nevertheless, acoustical information obtained from user-generated material at the Trump incident provides essential corroborative information. Examples are presented showing the audio forensic analysis principles applied to the UGR evidence.
Nonclinical and clinical characterization of the absorption, metabolism, and excretion of islatravir
Authors: Fillgrove Kerry L. , Matthews Randolph P. , Lu Bing , Liang Yuexia , Patel Munjal , Liu Wen , Matthews Catherine Z. , Liu Yang , Stoch S. Aubrey , Sanchez Rosa I. , Iwamoto Marian
Published: January 2025

The development of new and improved antiretroviral therapies that allow for alternative dosing schedules is needed for people living with HIV-1. Islatravir is a deoxyadenosine analog in development for the treatment of HIV-1 that suppresses HIV-1 replication via multiple mechanisms of action, including reverse transcriptase translocation inhibition and delayed chain termination. Islatravir is differentiated from other HIV-1 antiretrovirals by its high potency, long
t
½
, broad tissue distribution, and favorable drug resistance profile. A comprehensive evaluation was performed to provide data on the mass balance, absorption, metabolism, and excretion of islatravir through studies in nonclinical species, and in adults without HIV-1 infection, using radiolabeled islatravir. Islatravir was well absorbed in both nonclinical species and humans following oral administration. The elimination of islatravir occurs primarily by a combination of oxidative deamination to 4′-ethynyl-2-fluoro-2′-deoxyinosine and renal excretion of unchanged islatravir. Islatravir and 4′-ethynyl-2-fluoro-2′-deoxyinosine are the major circulating drug components in all species assessed. Islatravir is readily taken up into cells with efficient phosphorylation to the mono-, di-, and triphosphate forms. The pharmacologically active islatravir triphosphate is the most abundant intracellular phosphorylated species, as shown by the results of
ex vivo
studies. This characterization of the absorption, metabolism, and elimination of islatravir in humans and nonclinical species supports its further development for the treatment of HIV-1.
Grass carp reovirus VP4 manipulates TOLLIP to degrade STING for inhibition of IFN production
Authors: Wang Yang-Yang , Wang Xue-Li , Li Zhuo-Cong , Zhang Can , Xu Xiao , Cui Bao-Jie , Tian Meng-Ze , Zhou Chu-Jing , Xu Na , Wu Yue , Yang Xiao-Li , Chen Dan-Dan , Lu Long-Feng , Li Shun
Published: January 2025

Although fish possess an effective interferon (IFN) system to defend against viral infection, grass carp reovirus (GCRV) still causes epidemic hemorrhagic disease and tremendous economic loss in grass carp. Therefore, it is necessary to investigate the immune escape strategies employed by GCRV. In this study, we show that the structural protein VP4 of GCRV (encoded by the S6 segment) significantly restricts IFN expression by degrading stimulator of IFN genes (STING) through the autophagy-lysosome-dependent pathway. First, overexpression of VP4 inhibited the expression of IFN induced by GCRV and polyinosinic-polycytidylic acid (poly I:C) at both the promoter and mRNA levels. Second, VP4 was found to associate with STING, and the N-terminal transmembrane domain is essential for this interaction. Additionally, VP4 dramatically blocked STING-induced IFN expression and weakened its antiviral capacity. Further mechanistic studies revealed that VP4 degrades STING via the autophagy-lysosome pathway in a dose-dependent manner. Interestingly, toll-interacting protein (TOLLIP), a selective autophagy receptor, was found to interact with VP4 and reduce VP4-mediated STING degradation after
tollip
knockdown. Finally, overexpression of VP4 facilitated GCRV proliferation, while its depletion had the opposite effect. These findings indicate that GCRV VP4 recruits TOLLIP to degrade STING and achieve immune escape. This enhances our comprehension of aquatic virus pathogenesis.

IMPORTANCE

Upon virus invasion, fish cells employ a multitude of strategies to defend against infection. Consequently, viruses have evolved a plethora of tactics to evade host antiviral mechanisms. To date, fewer studies have been conducted on the immune evasion mechanism of grass carp reovirus (GCRV). In this study, we demonstrate that VP4 of GCRV-873 inhibits interferon expression by interacting with stimulator of IFN gene and degrading it in an autophagy-lysosome-dependent manner through the manipulation of the selective autophagy receptor toll-interacting protein. The findings of this study contribute to our understanding of the novel evasion mechanisms of GCRV and widen our knowledge of the virus-host interactions in lower vertebrates.
phylotypr: an R package for classifying DNA sequences
Authors: Schloss Patrick D.
Published: January 2025

The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.
A genome-annotated bacterial collection of the plant food system microbiota
Authors: Pietrantonio Laura , Devers-Lamrani Marion , Thorpe Peter , Arnton Catherine , Robertson-Albertyn Senga , Savojardo Castrense , Hartmann Alain , Martin-Laurent Fabrice , Abbott James , Bulgarelli Davide
Published: January 2025

This study reports draft genomes of 30 bacteria representative of the plant food system microbiota and isolated from different sources in Italy and France. Individual genomes were reconstructed using PacBIO DNA sequencing: taxonomic classification and distribution of genes involved in microbe-environment interactions are reported to facilitate strains' characterization and utilization.
Antiviral defense systems in the rumen microbiome
Authors: Sáenz Johan S. , Rios-Galicia Bibiana , Seifert Jana
Published: January 2025

The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage–host interaction.

IMPORTANCE

Phages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the “pan-immune system” model, which appears to be common across different environments.
Wildlife policy, the food system and One Health: a complex systems analysis of unintended consequences for the prevention of emerging zoonoses in China, the Democratic Republic of the Congo and the Philippines
Authors: Clifford Astbury Chloe , Demeshko Anastassia , Aguilar Russel , Mapatano Mala Ali , Li Angran , Togño Kathleen Chelsea , Shi Zhilei , Wang Zhuoyu , Wu Cary , Yambayamba Marc K , Carabin Hélène , Clarke Janielle , De Leon Valentina , Desai Shital , Gallo-Cajiao Eduardo , Lee Kirsten Melissa , Sivapragasam Krishihan , Wiktorowicz Mary , Penney Tarra L
Published: January 2025

Introduction

Evolving human–wildlife interactions have contributed to emerging zoonoses outbreaks, and pandemic prevention policy for wildlife management and conservation requires enhanced consideration from this perspective. However, the risk of unintended consequences is high. In this study, we aimed to assess how unrecognised complexity and system adaptation can lead to policy failure, and how these dynamics may impact zoonotic spillover risk and food system outcomes.

Methodology

This study focused on three countries: China, the Democratic Republic of the Congo (DRC) and the Philippines. We combined evidence from a rapid literature review with key informant interviews to develop causal loop diagrams (CLDs), a form of systems map representing causal theory about system factors and interconnections. We analysed these CLDs using the ‘fixes that fail’ (FTF) systems archetype, a conceptual tool used to understand and communicate how system adaptation can lead to policy failure. In each country, we situated the FTF in the wider system of disease ecology and food system factors to highlight how zoonotic risk and food system outcomes may be impacted.

Results

We interviewed 104 participants and reviewed 303 documents. In each country, we identified a case of a policy with the potential to become an FTF: wildlife farming in China, the establishment of a new national park in the DRC, and international conservation agenda-setting in the Philippines. In each country, we highlighted context-specific impacts of the FTF on zoonotic spillover risk and key food system outcomes.

Conclusion

Our use of systems thinking highlights how system adaptation may undermine prevention policy aims, with a range of unintended consequences for food systems and human, animal and environmental health. A broader application of systems-informed policy design and evaluation could help identify instruments approporiate for the disruption of system traps and improve policy success. A One Health approach may also increase success by supporting collaboration, communication and trust among actors to imporove collective policy action.
Effectiveness of tobacco advertising, promotion and sponsorship bans on smoking prevalence, initiation and cessation: a systematic review and meta-analysis
Authors: Saad Christina , Cheng Brandon (Hsu-Chen) , Takamizawa Ryo , Thakur Arya , Lee Chae-Weon , Leung Lachlan , Veerman J Lennert , Aminde Leopold Ndemnge
Published: January 2025

Background

Bans on tobacco advertising, promotion and sponsorship (TAPS) have the potential to influence smoking behaviour. However, many countries are yet to implement such strategies.

Objective

This study aimed to synthesise contemporary evidence on the effectiveness of TAPS bans on smoking prevalence, initiation and cessation.

Data sources

Medline, EMBASE, Scopus, Cochrane Library and Web of Science databases were searched up to 11 April 2024. Sixteen eligible studies were included.

Data selection and extraction

Two reviewers independently screened each study and extracted relevant data. Quality assessment was performed in duplicate using the ROBINS-I tool. Discrepancies were resolved via consensus or a third reviewer. Random effects meta-analyses were conducted for reasonably comparable studies.

Data synthesis

The meta-analyses showed that TAPS bans were associated with a lower prevalence of current smoking (pooled OR= 0.80, 95% CI 0.68 to 0.95,I2=98.7%) and a reduced risk of smoking initiation (pooled HR=0.63, 95% CI 0.48 to 0.82,I2=95%). There was no association between TAPS bans and smoking cessation (pooled OR=1.10, 95% CI 0.86 to 1.40,I2=58.5%). Subgroup analyses revealed the effects of TAPS bans on smoking prevalence differed by duration of evaluation (p<0.01).

Conclusions

This review showed that TAPS bans were associated with a 20% lower odds of current smoking and a 37% reduced risk of smoking initiation. The available evidence suggests that TAPS bans influence smoking behaviour, which strengthens calls for the implementation and enforcement of these policies.
Static behavior of CFRP-strengthened RC beams subjected to freeze–thaw cycles
Authors: Ahmed Mohamed , Metiche Slimane , Masmoudi Radhouane , Gagne Richard , Charron Jean-Philippe
Published: January 2025

Highway bridge durability, particularly in northern climates, presents a significant challenge for civil engineers. With numerous bridges exhibiting structural deficiencies, the importance of bridge rehabilitation cannot be overstated. This study aimed at determining the structural performance of 25 RC beams that were strengthened with carbon fiber-reinforced polymers (CFRP) sheets. These beams were exposed to different freeze–thaw cycles (FTCs) (100, 200, and 300 cycles) then were tested monotonically up to failure under four-point load test setup. The findings indicate that unanchored strengthened beams experienced a significant decrease of 12.5% in flexural capacity after 300 FTCs. Additionally, there is a notable shift in debonding characteristics, transitioning to adhesive failure at the fiber-reinforced polymers/concrete interface or a mixed mode, deviating from the cohesive failure in the concrete cover. The study concludes that FTC negatively impact the flexural performance of CFRP-strengthened beams, resulting in a reduced load-carrying capacity over time.
Freshwater life-cycle timing of Pacific salmon and steelhead (Oncorhynchus spp.) in Canada
Authors: Wilson Samantha M. , Peacock Stephanie J.
Published: January 2025

Information on species’ phenology and distribution is essential for assessing and mitigating exposure to pressures that vary over space and time, such as development projects or climate changes. Pacific salmon ( Oncorhynchus spp.) have complex life cycles that span freshwater and marine environments and unfold over several years and many thousands of kilometers. Currently, there is no central repository of life-cycle timing for salmon and steelhead populations throughout their Canadian range, hindering conservation and recovery efforts. To fill this gap, we have compiled timing data for fry migration from incubation to rearing grounds, juvenile migration from rearing grounds to the ocean, adult entry into rivers, and spawning for salmon and steelhead from British Columbia and the Yukon, Canada. For each species, we analysed the compiled data using linear models to describe patterns in population-specific timing across latitude, distance from the ocean, river gradient, and life-history types. Although we found significant data gaps in remote regions, our compiled dataset represents the best-available information on life-history timing that can inform environmental planning and salmon conservation actions
UNDERSTANDING THE ROLE OF MOVABLE OIL IN THE COMPLEXITY OF SHALE PORE STRUCTURES BASED ON FRACTAL THEORY
Authors: LIU KOUQI , ZHANG HONG , WANG ZHENLIN , WANG YAMIN , ZHANG ZHENGCHEN , OSTADHASSAN MEHDI
Published: January 2025

Gaining a comprehensive insight into how shale’s pore structure changes due to the extraction of oil from smaller pores is pivotal for understanding the impact of movable oil in shale plays, particularly when estimating reserves. The fractal dimension, a parameter reflecting pore complexity, can be quantitatively employed to explore this aspect. In this research endeavor, we focused on assessing variations in pore structure resulting from oil removal in four samples from the Fengcheng shale Formation in Mahu Sag, China. To achieve this, we utilized two diverse probing techniques: Gas adsorption and small-angle X-ray scattering (SAXS). These methodologies allowed us to analyze pore structure alterations both before and after oil extraction. By comparing data gathered through these approaches, we calculated and compared fractal dimensions across pre- and post-extraction conditions. The outcomes revealed notable differences in fractal dimensions obtained from the two methods. Before extraction, the disparity in fractal dimensions calculated from these techniques ranged from 9.6% to 18.3% across the samples. Post-extraction, this variation decreased to a range of 1.6% to 25.1%. These differences originate from the inherent physics governing each method’s operational mode. Furthermore, both techniques indicated an increase in fractal dimension post-extraction, implying heightened pore complexity. In terms of the gas adsorption method, the increase in fractal dimensions across studied samples ranged from 6.385 to 13.435. Comparatively, for the SAXS method, this increase varied between 2.22% and 18.61%. These findings suggest that the movable oil, whether fully or partially occupying pore spaces or being adsorbed onto mineral/organic matter surfaces, could potentially reduce pore complexity. This study pioneers the role of adsorbed or freely moving oil within both connected and isolated pores of shale plays which is crucial for accurate reserve estimation and economic evaluation of shale plays. By elucidating the intricate interactions between oil and pore structures, our research lays the groundwork for more precise assessments in this critical domain.
The entropy-based modeling of chain hex-derived networks
Authors: Ahmed Wakeel , Saeed Zunaira , Zaman Shahid , Belay Melaku Berhe
Published: January 2025

Entropy is a statistical measure of unpredictability in a specific distribution that gives information about the complexity and organization of systems. In chemistry, entropy quantifies disorder and randomness among molecules in a system or process. The goal of this research is to determine the entropy-based topological indices. A wide range of alternative configurations indicates how erratic and unpredictable a system is. It quantifies uncertainty and facilitates effective data processing in information theory and computer science. Entropy is used in biology to comprehend complicated biological systems and in chemistry to analyze molecular disorders and reactions. In network analysis, topological indicators provide information on the connectivity and structure of a graph. The degree distribution, centrality metrics, and network modularity are few examples. These indicators aid in the discovery of patterns, the identification of significant nodes, and the characterization of complex system organization in several fields. The novelty of the work lies in the combination of entropy measures and degree-based indices to explore the complexity, organization, and connectivity of these networks. The graph structure is a crucial chemical network modeling, where chemical species are represented by nodes and reactions indicated by edges. In our work, we have calculated the entropy of a chain hex-derived network. We compute precise results for the recently introduced entropies by utilizing their topological indices, which are derived from the degrees of end vertices.