bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol for a prospective, multicentre, cross-sectional cohort study to assess personal light exposure
Authors: Guidolin Carolina , Aerts Sam , Agbeshie Gabriel Kwaku , Akuffo Kwadwo Owusu , Aydin Sema Nur , Baeza Moyano David , Bolte John , Broszio Kai , Cantarero-García Guadalupe , Didikoglu Altug , González-Lezcano Roberto Alonso , Joosten-Ma Hongli , Melero-Tur Sofia , Nilsson Tengelin Maria , Pérez Gutiérrez María Concepción , Stefani Oliver , Svensson Ingemar , Udovicic Ljiljana , Zauner Johannes , Spitschan Manuel 
Published: February 2024

AbstractLight profoundly impacts many aspects of human physiology and behaviour, including the synchronization of the circadian clock, the production of melatonin, and cognition. These effects of light, termed the non-visual effects of light, have been primarily investigated in laboratory settings, where light intensity, spectrum and timing can be carefully controlled to draw associations with physiological outcomes of interest. Recently, the increasing availability of wearable light loggers has opened the possibility of studying personal light exposure in free-living conditions where people engage in activities of daily living, yielding findings associating aspects of light exposure and health outcomes, supporting the importance of adequate light exposure at appropriate times for human health. However, comprehensive protocols capturingenvironmental(e.g., geographical location, season, climate, photoperiod) andindividualfactors (e.g., culture, personal habits, behaviour, commute type, profession) contributing to the measured light exposure are currently lacking. Here, we present a protocol that combines smartphone-based experience sampling (experience sampling implementing Karolinska Sleepiness Scale, KSS ratings) and high-quality light exposure data collection at three body sites (near-corneal plane between the two eyes mounted on spectacle, neck-worn pendant/badge, and wrist-worn watch-like design) to capture daily factors related to individuals’ light exposure. We will implement the protocol in an international multi-centre study to investigate the environmental and socio-cultural factors influencing light exposure patterns in Germany, Ghana, Netherlands, Spain, Sweden, and Turkey (minimum n=15, target n=30 per site, minimum n=90, target n=180 across all sites). With the resulting dataset, lifestyle and context-specific factors that contribute to healthy light exposure will be identified. This information is essential in designing effective public health interventions.
Pathways in the brain, heart and lung influenced by SARS-CoV-2 NSP6 and SARS-CoV-2 regulated miRNAs: anin silicostudy hinting cancer incidence
Authors: Chatterjee Shrabonti , Mahata Joydeep , Kateriya Suneel , Anirudhan Gireesh 
Published: February 2024

AbstractThe influence of SARS-CoV-2 non-structural protein in the host’s tissue-specific complexities remains a mystery and needs more in-depth attention because of COVID-19 recurrence and long COVID. Here we investigated the influence of SARS-CoV-2 transmembrane protein NSP6 (Non-structural protein 6) in three major organs – the brain, heart, and lungin silico. To elucidate the interplay between NSP6 and host proteins, we analyzed the protein-protein interaction network of proteins regulated after SARS-CoV-2 infection and that are interacting with NSP6 interacting proteins. Pathway enrichment analyses provided global insights into biological pathways governed by differentially regulated genes in the three tissues after COVID-19 infection. Many drugs targeting hub genes of tissue-specific protein interactome were found that could be candidates for COVID-19 management. MiRNA-gene network for the tissue-specific regulated proteins was also deduced and comparing gene list targeted by SARS-CoV-2 regulated miRNAs, we found three and two common genes in the brain and lung respectively. Among the five common proteins revealed as potential therapeutic targets across the three tissues, Galectin3 (LGALS3) that was upregulated in the heart and brain after COVID-19 infection is reported to be influencing all the ten hallmarks of cancer positively and is found in multiple cancers. COVID-19 infection also causes myocardial inflammation and heart failure (HF). HF is observed to be increasing cancer incidence. Our bioinformatics and systems study hints probable effect of COVID-19 infection in cancer incidence and warrants in-depth studies in this direction and cancer surveillance especially with the present scenario of long COVID-19 and recurrent COVID-19 infections.Graphical Abstract
Phages reconstitute NAD+to counter bacterial immunity
Authors: Osterman Ilya , Samra Hadar , Rousset Francois , Loseva Elena , Itkin Maxim , Malitsky Sergey , Yirmiya Erez , Millman Adi , Sorek Rotem 
Published: February 2024

AbstractBacteria defend against phage infection via a variety of antiphage defense systems. Many defense systems were recently shown to deplete cellular nicotinamide adenine dinucleotide (NAD+) in response to infection, by breaking NAD+to ADP-ribose (ADPR) and nicotinamide. It was demonstrated that NAD+depletion during infection deprives the phage from this essential molecule and impedes phage replication. Here we show that a substantial fraction of phages possess enzymatic pathways allowing reconstitution of NAD+from its degradation products in infected cells. We describe NAD+reconstitution pathway 1 (NARP1), a two-step pathway in which one enzyme phosphorylates ADPR to generate ADPR-pyrophosphate (ADPR-PP), and the second enzyme conjugates ADPR- PP and nicotinamide to generate NAD+. Phages encoding the NARP1 pathway can overcome a diverse set of defense systems, including Thoeris, DSR1, DSR2, SIR2-HerA, and SEFIR, all of which deplete NAD+as part of their defensive mechanism. Phylogenetic analyses show that NARP1 is primarily encoded on phage genomes, suggesting a phage- specific function in countering bacterial defenses. A second pathway, NARP2, allows phages to overcome bacterial defenses by building NAD+via metabolites different than ADPR-PP. Our findings report a unique immune evasion strategy where viruses rebuild molecules depleted by defense systems, thus overcoming host immunity.
Antivirals for Monkeypox Virus: Proposing an Effective Machine/Deep Learning Framework
Authors: Hashemi S. Morteza , Zabihian Arash , Hajsaeedi Masih , Hooshmand Mohsen 
Published: February 2024

AbstractMonkeypox is one of the infectious viruses which caused morbidity and mortality problems in these years. Despite its danger to public health, there is no approved drug to stand and handle Monkeypox. On the other hand, drug repurposing is a promising screening method for the low-cost introduction of approved drugs for emerging diseases and viruses which utilizes computational methods. Therefore, drug repurposing is a promising approach to suggesting approved drugs for the monkeypox virus. This paper proposes a computational framework for monkeypox antiviral prediction. To do this, we have geenrated a new virus-antiviral dataset. Moreover, we applied several machine learning and one deep learning method for virus-antiviral prediction. The suggested drugs by the learning methods have been investigated using docking studies. To the best of our knowledge, this work is the first work to study deep learning methods for the prediction of monkeypox antivirals. The screening results confirm that Tilorone, Valacyclovir, Ribavirin, Favipiravir, and Baloxavir marboxil are effective drugs for monkeypox treatment.
Sociodemographic and health-related differences in non-diabetic hyperglycaemia and undiagnosed type 2 diabetes in the Health Survey for England 2013-2019
Authors: Campbell Emma , Macey Ellie , Kneebone-Hopkins Caitlin , Shine Chris , Nafilyan Vahé , Brown Nicholas , White Martin , Jones Ross , Khunti Kamlesh , Finning Katie 
Published: February 2024

AbstractBackgroundType 2 diabetes is a leading cause of morbidity and mortality but is often undiagnosed. Non-diabetic hyperglycaemia increases T2D risk, and its prevalence is increasing. Understanding the scale of undiagnosed T2D and NDH and identifying at-risk groups is important for detection and intervention.MethodsWe used the 2013-2019 Health Survey for England, an annual, nationally representative, cross-sectional survey. Respondents aged 16+who were not pregnant and had valid HbA1c measurements were included. Outcomes were undiagnosed T2D (HbA1c ≥48 mmol/mol (6·5%) and no T2D diagnosis), and NDH (HbA1c 42-47 mmol/mol (6·0-6·4%) and no diagnosis). Age-adjusted prevalence was estimated across sociodemographic and health-related characteristics. Independent associations were assessed using logistic regression.FindingsAn estimated 2·25% (95% confidence interval 2·05-2·45) of adults had undiagnosed T2D and 11·54% (11·11-11·97) had NDH; an estimated 999,700 and 5,121,800 adults respectively. Prevalence was higher in those with known risk factors for T2D, such as older age or Black or Asian ethnicity. Among those with T2D, 30·21% (28·13-32·28) were undiagnosed. Younger adults and those self-reporting better health were most likely to be undiagnosed. For women, lower BMI, and waist circumference, not being prescribed antidepressants, and living in rural areas, were associated with increased likelihood of being undiagnosed.InterpretationNearly a third of T2D cases were undiagnosed. Some groups less likely to have T2D were most likely to be undiagnosed. NDH is prevalent across all groups, even those considered low risk. Findings highlight the burden of T2D and NDH and emphasise the need for awareness across the population.
Intermittent low-intensity far-UVC irradiation inhibits growth of common mold below threshold limit value
Authors: Mogensen Emilie Hage , Holm Christian Kanstrup 
Published: February 2024

AbstractMold infestations in buildings pose significant challenges to human health, affecting both private residences and hospitals. While molds commonly trigger asthma and allergies in the immunocompetent, they can cause life-threatening diseases in the immunocompromised. Currently, there is an unmet need for new strategies to reduce or prevent mold infestations. Far-UVC technology can inactivate microorganisms while remaining safe for humans. This study investigates the inhibitory efficacy of far-UVC light at 222 nm on the growth of common mold-producing fungi, specificallyPenicillium candidum, when delivered in low-dose on-off duty cycles, a configuration consistent with its use in real-world settings. The inhibitory effect of the low-dose duty cycles was assessed on growth induced by i) an adjacent spore-producingP. candidumdonor and ii)P. candidumspores seeded directly onto agar plates. In both setups, the far-UVC light significantly inhibited both vertical and horizontal growth ofP. candidum, even when the UV doses were below the Threshold Value Limit of 23 mJ/cm2. These results suggest that far-UVC light holds the potential to improve indoor air quality by reducing or preventing mold growth, also when people are present.
Comparison of two automated CT perfusion software packages in patients with ischemic stroke presenting within 24 hours of onset
Authors: Kim Nak-Hoon , Ha Sue Young , Park Gihoon , Park Jong-Hyeok , Kim Dongmin , Sunwoo Leonard , Kye Min-Surk , Baik Sung Hyun , Jung Cheolkyu , Ryu Wi-Sun , Kim Beom Joon 
Published: February 2024

ABSTRACTBackgroundWe compared the ischemic core and hypoperfused tissue volumes estimated by RAPID and JBS-10K, a newly developed automated CT perfusion (CTP) analysis package. We also assessed agreement between ischemic core volumes by two software packages against early follow-up infarct volumes on diffusion-weighted images (DWI).MethodsThis retrospective study analyzed 327 patients admitted to a single stroke center in Korea from January 2021 to May 2023, who underwent CTP scans within 24 hours of onset. The concordance correlation coefficient and Bland-Altman plots were utilized to compare the volumes of ischemic core and hypoperfused tissue volumes between the software packages. Agreement with early (within 3 hours from CTP) follow-up infarct volumes on diffusion-weighted imaging (n=217) was also evaluated.ResultsThe mean age was 70.7±13.0 and 137 (41.9%) were female. Ischemic core volumes by JBS-10K and RAPID in the threshold of relative cerebral blood flow (rCBF) < 30% had excellent agreement (ρ = 0.958 [95% CI, 0.949 to 0.966]). Excellent agreement was also observed for time to a maximum of the residue function (Tmax) > 6 seconds between JBS-10K and RAPID (ρ = 0.835 [95% CI, 0.806 to 0.863]). Although early follow-up infarct volume showed substantial agreement in both packages (JBS-10K ρ = 0.751 and RAPID ρ = 0.632), ischemic core volumes at the threshold of rCBF <30% tended to overestimate ischemic core volumes.ConclusionJBS-10K and RAPID demonstrated remarkable concordance in estimating the volumes of the ischemic core and hypoperfused area based on CTP within 24 hours from onset.
Targeted Viromes and Total Metagenomes Capture Distinct Components of Bee Gut Phage Communities
Authors: Sbardellati Dino Lorenzo , Vannette Rachel Lee 
Published: February 2024

AbstractDespite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey beeApis melliferaand the eastern bumble beeBombus impatiens. We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low abundance and low occupancy phage, while total metagenomes were biased towards sampling temperate phage and the most prominent phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage.
RNAformer: A Simple yet Effective Model for Homology-Aware RNA Secondary Structure Prediction
Authors: Franke Jörg K.H. , Runge Frederic , Köksal Ryan , Matus Dominika , Backofen Rolf , Hutter Frank 
Published: February 2024

AbstractPredicting RNA secondary structure is essential for understanding RNA function and developing RNA-based therapeutics. Despite recent advances in deep learning for structural biology, its application to RNA secondary structure prediction remains contentious. A primary concern is the control of homology between training and test data. Moreover, deep learning approaches often incorporate complex multi-model systems, ensemble strategies, or require external data. Here, we present theRNAformer, a scalable axial-attention-based deep learning model designed to predict secondary structure directly from a single RNA sequence without additional requirements. We demonstrate the benefits of this lean architecture by learning an accurate biophysical RNA folding model using synthetic data. Trained on experimental data, our model overcomes previously reported caveats in deep learning approaches with a novel homology-aware data pipeline. The RNAformer achieves state-of-the-art performance on RNA secondary structure prediction, out-performing both traditional non-learning-based methods and existing deep learning approaches, while carefully considering sequence and structure similarities.
SpoIIDMP-driven peptidoglycan rearrangement is crucial for ribosome translocation into the spore
Authors: Iwańska Olga , Latoch Przemysław , Kovalenko Mariia , Lichocka Małgorzata , Hołówka Joanna , Serwa Remigiusz , Grzybowska Agata , Zakrzewska-Czerwińska Jolanta , Starosta Agata L. 
Published: February 2024

AbstractIn a spore-forming bacteriumBacillus subtilistranscription and translation are uncoupled and the translational machinery is located at the cell poles. During sporulation the cell undergoes morphological changes including asymmetric septation and chromosome translocation. However, the fate of translational machinery during sporulation has not been described. Here, using a combination of microscopic assays and mass spectrometry, we are tracking the ribosome localisation during sporulation inB. subtilisWT and mutants. We show that the ribosomes are associated with the asymmetric septum which is a functionally important organelle and that peptidoglycan rearrangement is essential for ribosome packing into the forespore. We also show that the feeding tube channel SpoIIIA-SpoIIQ is not required for the ribosome translocation, but is essential for maintaining the chromosome inside the spore.One-Sentence SummaryMovement of ribosomes into the spore ofB. subtilisfollows chromosome transport and is precisely orchestrated in the cell.
Transcriptional and post-transcriptional mechanisms modulate cyclopropane fatty acid synthase through small RNAs inEscherichia coli
Authors: Bianco Colleen M. , Caballero-Rothar Nancy N. , Ma Xiangqian , Farley Kristen R. , Vanderpool Carin K. 
Published: February 2024

AbstractThe small RNA (sRNA) RydC strongly activatescfa, which encodes the cyclopropane fatty acid synthase. Previous work demonstrated that RydC activation ofcfaincreases conversion of unsaturated fatty acids to cyclopropanated fatty acids in membrane lipids and changes the biophysical properties of membranes, making cells more resistant to acid stress. The conditions and regulators that control RydC synthesis had not previously been identified. In this study, we demonstrate that RydC regulation ofcfais important for resistance to membrane-disrupting conditions. We identify a GntR-family transcription factor, YieP, that repressesrydCtranscription and show that YieP indirectly regulatescfathrough RydC. YieP positively autoregulates its own transcription. We further identify additional sRNA regulatory inputs that contribute to control of RydC andcfa. The translation ofyiePis repressed by the Fnr-dependent sRNA, FnrS, making FnrS an indirect activator ofrydCandcfa.Conversely, RydC activity oncfais antagonized by the OmpR-dependent sRNA OmrB. Altogether, this work illuminates a complex regulatory network involving transcriptional and post-transcriptional inputs that link control of membrane biophysical properties to multiple environmental signals.ImportanceBacteria experience many environmental stresses that challenge their membrane integrity. To withstand these challenges, bacteria sense what stress is occurring and mount a response that protects membranes. Previous work documented the important roles of small RNA (sRNA) regulators in membrane stress responses. One sRNA, RydC, helps cells cope with membrane-disrupting stresses by promoting changes in the types of lipids incorporated into membranes. In this study, we identified a regulator, YieP, that controls when RydC is produced, and additional sRNA regulators that modulate YieP levels and RydC activity. These findings illuminate a complex regulatory network that helps bacteria sense and respond to membrane stress.
Designing ICT integrated lesson activities: an intervention to bolster tutors’ pedagogical use of ICT competences in Tanzania teacher education
Authors: Lubuva Elisei Emili , Ndibalema Placidius , Mbwambo Esther 
Published: February 2024

PurposeThe study aims to assess the effectiveness of engaging tutors in designing and using ICT integrated lesson activities in strengthening their pedagogical use of ICT competences.Design/methodology/approachSurvey data from an intervention group of 70 tutors from two teachers colleges (TCs) were used to compare their level of ICT competences and domains of professional practice before and after the intervention. Document analysis, lesson observations and feedback from the learning management system (LMS) were used to describe tutors’ experiences from the intervention.FindingsThere was a statistically significant increase in tutors’ level of pedagogical use of ICT competences and domains of professional practice associated with hands-on practice in designing and implementing the intervention.Research limitations/implicationsThe intervention focus on hands-on practice, actual teaching and learning needs, and the use of active learning strategies like flipped classroom and the LMS, were useful means for tutors to make sense of pedagogical use of ICT competences.Practical implicationsThe results offer useful insights to teacher education institutions and policymakers on how to prepare professional learning and supportive policies to enhance teaching and learning with ICT for addressing the learning needs of the subject matter.Originality/valueCreating 16 ICT integrated lesson activities helped tutors to learn pedagogical use of ICT competences by doing. Use of such intervention could be a useful strategy in teacher education institutions to reposition ICT competence development from reproducing technological competences toward developing knowledge creators who could innovate their pedagogical practice with support from mentors, digital learning resources and networks.
Key stakeholder perceived value’s influence on autonomous vehicles’ privacy and security governance – an evolutionary analysis based on the prospect theory
Authors: Lu Chao , Xin Xiaohai 
Published: February 2024

Purpose
The promotion of autonomous vehicles introduces privacy and security risks, underscoring the pressing need for responsible innovation implementation. To more effectively address the societal risks posed by autonomous vehicles, considering collaborative engagement of key stakeholders is essential. This study aims to provide insights into the governance of potential privacy and security issues in the innovation of autonomous driving technology by analyzing the micro-level decision-making processes of various stakeholders.

Design/methodology/approach
For this study, the authors use a nuanced approach, integrating key stakeholder theory, perceived value theory and prospect theory. The study constructs a model based on evolutionary game for the privacy and security governance mechanism of autonomous vehicles, involving enterprises, governments and consumers.

Findings
The governance of privacy and security in autonomous driving technology is influenced by key stakeholders’ decision-making behaviors and pivotal factors such as perceived value factors. The study finds that the governmental is influenced to a lesser extent by the decisions of other stakeholders, and factors such as risk preference coefficient, which contribute to perceived value, have a more significant influence than appearance factors like participation costs.

Research limitations/implications
This study lacks an investigation into the risk sensitivity of various stakeholders in different scenarios.

Originality/value
The study delineates the roles and behaviors of key stakeholders and contributes valuable insights toward addressing pertinent risk concerns within the governance of autonomous vehicles. Through the study, the practical application of Responsible Innovation theory has been enriched, addressing the shortcomings in the analysis of micro-level processes within the framework of evolutionary game.