bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProkBERT PhaStyle: Accurate Phage Lifestyle Prediction with Pretrained Genomic Language Models
Authors: Juhász Judit , Babett Bodnár , Juhász János , Ligeti-Nagy Noémi , Pongor Sándor , Ligeti Balázs 
Published: December 2024

AbstractBackgroundPhage lifestyle prediction, i.e. classifying phage sequences as virulent or temperate, is crucial in biomedical and ecological applications. Phage sequences from metagenome or metavirome assemblies are often fragmented, and the diversity of environmental phages is not well known. Current computational approaches often rely on database comparisons and machine learning algorithms that require significant effort and expertise to update. We propose using genomic language models for phage lifestyle classification, allowing efficient direct analysis from nucleotide sequences without the need for sophisticated preprocessing pipelines or manually curated databases.MethodsWe trained three genomic language models (DNABERT-2, Nucleotide Transformer, and ProkBERT) on datasets of short, fragmented sequences. These models were then compared with dedicated phage lifestyle prediction methods (PhaTYP, DeePhage, BACPHLIP) in terms of accuracy, prediction speed, and generalization capability.ResultsProkBERT PhaStyle consistently outperforms existing models in various scenarios. It generalizes well for out-of-sample data, accurately classifies phages from extreme environments, and also demonstrates high inference speed. Despite having up to 20 times fewer parameters, it proved to be better performing than much larger genomic language models.ConclusionsGenomic language models offer a simple and computationally efficient alternative for solving complex classification tasks, such as phage lifestyle prediction. ProkBERT PhaStyle’s simplicity, speed, and performance suggest its utility in various ecological and clinical applications.
Meta-prediction extends human cortical and subcortical reward learning
Authors: Shin Jaehoon , Lee Jee Hang , Lee Sang Wan 
Published: December 2024

SummaryHuman reward learning is constrained by environmental structure. Stable environments facilitate reward prediction but limit learning experiences1–8, while uncertain environments hinder predictability and learnability9–12. We propose a novel framework extending these boundaries through “meta-prediction” – predicting human prediction. The meta-prediction entwines two Bellman equations: one for human prediction and the other for predicting the prediction error of the former. The framework pretrains computational models imitating individuals’ reward prediction (specification), then generates new tasks to extremize the models’ prediction errors (generalization). Simulations with 82 subjects’ data generated subject-independent task design across four scenarios without compromising learnability. In an independent fMRI experiment with 49 participants, meta-prediction guides behavior and neural activities in the ventral striatum, lateral prefrontal, and insular cortex, the areas encoding prediction errors. We also demonstrated that meta-prediction can generate complex tasks compositionally to discern human reward learning bias. Our framework redefines the role of tasks in cognitive science and AI.
Beyond dichotomy: diversity of rat’s ultrasonic vocalizations
Authors: Wada Reo , Hakataya Shiomi , Tachibana Ryosuke O. , Shiramatsu Tomoyo Isoguchi , Ito Tetsufumi , Kanno Kouta , Koshiishi Riseru , Matsumoto Jumpei , Saito Yumi , Toya Genta , Okabe Shota , Okanoya Kazuo 
Published: December 2024

SummaryUnderstanding animal emotions is of great interest to researchers in various fields, from neuroscience to animal welfare. Ultrasonic vocalizations (USVs) in rats (Rattus norvegicus) have been established as an ideal model for studying emotional expression because they reflect internal emotional states. Since the discovery of USVs in rats, it has gradually been revealed that two types of adult rats’ USVs with distinct acoustic features (high-short and low-long) are closely linked to positive and negative affect, respectively. Thus, for many years, most studies have grouped USVs into dichotomous categories: 50-kHz (positive) USVs and 22-kHz (negative) USVs, using these numbers as labels rather than measured values. However, the diversity of rats’ USVs may have been overlooked due to this 50- / 22-kHz dichotomous framework, as several recent studies claim to have found new categories in USVs outside the framework. Here, through a systematic survey of descriptions of rats’ USVs in the past literature, we confirmed a non-negligible number of reports on USVs that are outside the dichotomous framework. Our results support the abundance of diverse USVs beyond the dichotomy. This extends the traditional association between acoustic features and emotional states, highlighting the importance of research on diverse vocalizations that might reflect complex affective states beyond the simple distinction between positive and negative.
Behavior-relevant periodized neural representation of acoustic but not tactile rhythm in humans
Authors: Lenoir C , Lenc T , Polak R , Nozaradan S 
Published: December 2024

AbstractMusic makes people move. This human propensity to coordinate movement with the rhythm of music requires multiscale temporal integration, allowing fast sensory events composing rhythmic input to be mapped onto slower internal templates such as periodic beats. Relatedly, beat perception has been shown to involve a selective enhancement of the beat periodicities in the neural response to rhythm. However, the extent to which this ability to move to the beat, and the relatedperiodizedneural representation, are shared across the senses beyond audition remains unknown. Here we addressed this question using acoustic and tactile rhythms, while recording separately the electroencephalography (EEG) responses and finger tapping to these rhythms in healthy volunteers. Consistent with previous studies, EEG responses to the acoustic rhythm featured significant enhancement of the beat, and this periodized neural representation was specifically concentrated within a low-frequency range below 15 Hz. In contrast, the same rhythm conveyed with tactile inputs elicited responses over a broader frequency range, up to 25Hz, with no significant periodization, and resulted in less stable tapping. Together, these findings indicate that low-frequency neural activity preferentially supports behavior-relevant internal representation of rhythmic input. However, this neural representation is not necessarily shared across the senses, as well as the ability to move to the beat, corroborating multimodal differences in beat perception. This low-frequency neural representation may thus reflect a process of multiscale temporal integration allowing the auditory system to go beyond mere tracking of onset timing and support higher-level internal representation and motor entrainment to rhythm.Significance statementIntegrating the fast sensory events composing music into slower temporal units is a cornerstone of beat perception and social interaction through music. The current study shows that this ability critically relies on brain activity concentrated in a lower frequency range – below the recurrence of sensory events – in response to acoustic rhythm. In contrast, when the rhythm is conveyed through touch, brain responses comparatively exhibit higher frequency activity corresponding to the faithful tracking of each individual events of the tactile rhythm. Most importantly, these auditory-specific slow fluctuations feature a periodization of rhythmic inputs, compatible with behavior. This higher-level neural processing of rhythmic input could thus reflect internal representations of the beat that are not necessarily shared across sensory modalities, in line with the concept of auditory dominance in temporal event perception and motor entrainment to rhythm. The current study thus opens a promising avenue to gain fundamental knowledge on high-level multimodal perception and motor entrainment processes specific to humans.
How Do Particles with Complex Interactions Self-Assemble?
Authors: Koehler Lara , Ronceray Pierre , Lenz Martin 
Published: December 2024

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Because of this complexity, protein self-assembly results from a competition between a large number of distinct interaction energies, of the order of one per pair of patches. However, current self-assembly models typically ignore this aspect, and the principles by which it determines the large-scale structure of protein assemblies are largely unknown. Here, we use Monte Carlo simulations and machine learning to start to unravel these principles. We observe that despite widespread geometrical frustration, aggregates of particles with complex interactions fall within only a few categories that often display high degrees of spatial order, including crystals, fibers, and oligomers. We then successfully identify the most relevant aspect of the interaction complexity in predicting these outcomes, namely, the particles’ ability to form periodic structures. Our results provide a first extensive characterization of the rich design space associated with identical particles with complex interactions and could inspire engineered self-assembling nano-objects as well as help us to understand the emergence of robust functional protein structures.

Published by the American Physical Society
2024
A multivariable adaptive formation control for multiple UAVs with external uncertain disturbances
Authors: Ding Jian , Jiang Xiaotong , Zou Yuchun , Tang Zhen , Zhen Ziyang 
Published: December 2024

Purpose
A multivariable model reference adaptive control method is proposed to solve a distributed leader–follower formation control problem of unmanned aerial vehicles (UAVs) with uncertain parameters and unknown external disturbances for both leader and followers.

Design/methodology/approach
A case of uncertain stochastic external disturbances for UAVs is considered, and based on the distributed communication network of UAVs, a state-feedback adaptive controller is proposed to maintain the formation of UAVs consistently. Then, the stability and asymptotic tracking performance of the UAV formation control system are analyzed by the Lyapunov function.

Findings
The simulation results demonstrate that this formation control scheme can effectively solve the stochastic external disturbance problem of UAVs and ensure the stability of their formation.

Originality/value
The proposed multivariable model reference adaptive control method reduces the error of formation control system and improves the stability and control performance of UAV compared with fixed control.
Empowerment or ornament? Gender diversity’s impact on cash holdings amid quota enforcement in an emerging market
Authors: El-Dyasty Mohamed M. , Elamer Ahmed 
Published: December 2024

Purpose
This study examines the impact of female directors on cash holdings in Egyptian listed firms, particularly in light of Decree 123/2019, which mandates female board representation. This study aims to determine if female directors mitigate agency conflicts related to cash holdings and how these dynamics shift post-quota implementation.

Design/methodology/approach
Using a panel fixed-effects model, the research analyzes 1,563 firm-year observations from 223 non-financial Egyptian firms listed on the EGX between 2014 and 2022. The robustness of the findings is tested through additional analyses using alternative proxies for cash holdings, different sample periods and a two-stage least squares approach to address endogeneity concerns.

Findings
This study finds a significant negative association between female directors and cash holdings, suggesting that female board members may promote more conservative cash management practices. However, this relationship weakens post-quota implementation, becoming statistically insignificant. This implies that while quotas increase female representation, they do not necessarily enhance corporate governance effectiveness regarding cash management. The pre-quota positive link between female directors and excess cash holdings also becomes insignificant post-quota.

Research limitations/implications
The study focuses on female directors’ impact on cash holdings, excluding potential effects on other board subcommittees or functions. It does not capture long-term benefits of increased female representation, which may emerge as the pool of qualified female directors grows. Future research should explore broader implications of gender diversity guidelines and other diversity dimensions across various corporate governance aspects and institutional contexts.

Originality/value
This research provides empirical evidence from an emerging market context on the understudied impact of gender diversity on cash holdings. It critically evaluates the unintended consequences of mandatory gender quotas, highlighting the complexity of regulatory interventions in corporate governance. The study stresses the need for policymakers to address factors limiting the effectiveness of such quotas and to consider potential suboptimal outcomes when increasing female board representation without a corresponding increase in the supply of qualified female directors.
The relational model of sense of coherence: explaining refugees’ mental health and well-being in Austria
Authors: Rosenlechner-Urbanek Doris 
Published: December 2024

Purpose
This paper aims to construct a model explaining migrant health and well-being from a salutogenic perspective. Accounting for the relational, interactional factors impacting on the health of forced migrants, the “Relational Model of Sense of Coherence” combines elements from Antonovsky’s theory of salutogenesis with elements from Honneth’s theory of recognition.

Design/methodology/approach
The model has been developed from the empirical findings of a two-year qualitative study with 28 forced migrants in Austria. Besides initial and final surveys on the participants’ perception of health, health literacy and participation, data were gathered in a qualitative, participatory action research setting and analysed by the method of interpretative case reconstruction. The model is applied to the case reconstruction of a female refugee from Iraq explaining the dimensions impacting on her self-perceived status of health and well-being.

Findings
Next to consistency/comprehensibility and load balance/manageability persons need to experience participation/controllability as well as relatedness/self-confidence, recognition of rights/self-respect and social recognition/self-esteem to develop and/or maintain a strong, relational sense of coherence. All six dimensions contribute to feelings of meaningfulness; all components are necessary for a move towards the healthy end of the health-ease/dis-ease continuum.

Originality/value
The paper contributes to theory building in the fields of salutogenesis and recognition by developing a model based on an in-depth, participatory qualitative study with a vulnerable target group.
Governance of ESG implementations: governance dimensions and their structural implementation
Authors: Müller Ralf , Caron Marie-Andrée , Drouin Nathalie , Lereim Jon , Alonderienė Raimonda , Chmieliauskas Alfredas , Šimkonis Saulius , Šuminskienė Raminta 
Published: December 2024

PurposeThis study identifies the various governance dimensions for environmental, social and governance (ESG) implementations, including reporting. Subsequently, it investigates the governance structures in place to steer these dimensions in project-based and project-oriented organizations.Design/methodology/approachA systematic literature review identifies 11 organizational governance dimensions for ESG implementations, followed by a conceptual mapping of these dimensions to the most likely governance structures being set up for their implementation (i.e. single-level, multi-level and polycentric governance).FindingsEleven governance dimensions are identified and categorized under (1) organizational settings, (2) ESG strategy and (3) implementation. The conceptual mapping of these dimensions against the governance structures for their implementation identifies an inverse relationship between the governance level in the organizational hierarchy and the complexity of governance structures needed for steering these dimensions. The paper suggests a variety of context-dependent governance structures and contributes to the governance literature on the interface between projects and their parent organizations.Research limitations/implicationsAcademics benefit from an organization-wide model and the first taxonomy on the relevant governance dimensions for ESG implementation and reporting projects, thus a first approach to theorizing the governance of ESG implementations.Practical implicationsThe results are of value for practitioners by allowing them to understand the diversity of dimensions and the structural implementation of ESG and its reporting.Social implicationsOne of the first studies to address governance of ESG implementation and reporting across intra-organizational boundaries between the permanent and the project-based parts of the organization. This provides for organization-wide improvements in the governance toward the UN Sustainability Goals.Originality/valueThe paper investigates the under-researched link of governance implementations from the corporate level to individual projects in the context of ESG implementations, including reporting.
Exploring corporate financial reporting theories: a systematic approach
Authors: Rouf Md. Abdur , Siddique Md. Nur-E-Alam , Akhtaruddin Md. 
Published: December 2024

Purpose
The study aims to identify, summarize and synthesize the theories used in corporate financial reporting (CFR) and propose a conceptual framework based on those theories.

Design/methodology/approach
The study applied the systematic literature review approach to achieve the study objectives. So, the researchers systematically collected the relevant documents from the Scopus database with the help of an advanced search string containing keywords to the CFR theories. Preferred reporting items for systematic reviews and meta-analyses technique was used for the relevant document selection process. Finally, 67 documents were extracted and analyzed spanning from the year of 2017 to 2023.

Findings
The major findings of this study indicate a predominance of legitimacy, agency and stakeholder theories in CFR studies. Whereas, this study reveals that neo-institutional, signaling, resource dependency, political economics and impression management theories have been less focused on by scholars in the CFR studies. Those theories need to be reemphasized in this field in future research.

Originality/value
The study’s contributions are significant for academics, policymakers and different parties, as it enhance the understanding of CFR theoretical frameworks and suggest directions for future research to broaden the theoretical landscape. The study maps the motivations of applying a certain theory which will help the researchers to select a specific theory for the underlying context of CFR.
Influence of the main bulb’s parameters of bulbous bow vessels on heave and pitch motions for head sea
Authors: Ruiz-Capel Samuel , Romero-Tello Pablo , Gutiérrez-Romero José Enrique , Kraniotis Dimitrios , Reyes Aase 
Published: December 2024

PurposeThis paper addresses the influence of the main bulb’s parameters of a containership on heave and pitch RAO for head waves.Design/methodology/approachTo obtain the RAO curves, these parameters are scattered over the design space through latin hypercube sampling (LHS), where different bulb designs are obtained using the free form deformation (FFD) technique. Linear RAO curves are calculated based on numerical software, split into various frequency intervals and assessed according to six evaluation parameters.FindingsThe findings show that maximum, minimum and average values of the RAO curve are useful indicators to study the RAO of a ship. Average values of the curve are reduced more than 6% for heave and over 24% for pitch with respect to a vessel with a conventional bulbous bow. The best designs concentrate the volume around the mid-lower part of the bulb, whilst the worst designs concentrate the bulb volume towards the upper part of the bulb.Originality/valueIn the literature, we get an overview of the influence of different bows on seakeeping. However, the influence of the bulb or large variations of the bow in a parametric way have not been studied yet. Since most of these parameters are derived from the RAO curve and ship motions, this paper focuses on studying the RAO curve for heave and ship motions of a bulbous bow containership. The objective is to minimize the RAO values of the curves so that most derived parameters reduce their values as well.
Adapting teaching practices and enhancing intercultural competence: student teachers’ experiences in an international exchange program
Authors: Thinh Mai Phuc 
Published: December 2024

Purpose
This study aims to examine how participation in international exchange programs influences both the teaching practices and intercultural competence of student teachers. Focusing on the experiences of Vietnamese participants in Thailand, the study explores how these educators adapted their teaching methods in response to cross-cultural challenges and developed essential intercultural skills through immersion in a new educational environment.

Design/methodology/approach
Using a qualitative case study approach, this research highlights the transformative experiences of 13 Vietnamese student teachers who participated in a three-week exchange program in Thailand. Data were gathered using semi-structured interviews and reflective journals to capture rich insights into how the exchange shaped their teaching practices and intercultural competence.

Findings
The findings indicate that the program significantly impacted participants’ teaching practices, as they adapted their instructional strategies to better meet the needs of diverse students and manage cross-cultural classroom dynamics. In addition, participants demonstrated growth in intercultural competence, developing greater empathy, flexibility and cultural sensitivity. These skills not only improved their teaching but also enabled them to engage more effectively with students from different cultural backgrounds.

Originality/value
This study contributes to the understanding of how short-term international experiences can lead to both pedagogical transformations and the development of intercultural competence in a global educational context. It underscores the necessity of incorporating structured intercultural training within teacher education programs to better prepare educators for the complexities of teaching in culturally diverse settings.