bluuebunny/crossref_metadata_2025 huggingface dataset:
A dynamical system to model land use interactions by using population dynamics: application on vulnerable grasslands
Authors: Arteaga Johny , Agudelo Jhonny , Brazeiro Alejandro , Fort Hugo
Published: November 2024

We introduce a deterministic set of equations, the Lotka–Volterra (LV) generalized equations, to explain or predict the temporal dynamics and competition between land use and land cover (LULC) classes. We evaluated this new approach in two regions of Uruguay where human activities have reduced natural grasslands. We infer the interaction coefficients from the LV model through the pairwise maximum entropy method using the spatial covariance matrices obtained from annual remote-sensing LULC maps. The model performed well in predicting short-term temporal changes, with errors similar to those obtained using traditional Markov chains. This model introduces a novel avenue for assisting LULC modelling in improving the temporal dynamics.
Tracking Rayleigh–Bloch waves swapping between Riemann sheets
Authors: Matsushima Kei , Bennetts Luke G. , Peter Malte A.
Published: November 2024

Rayleigh–Bloch waves are modes localized to periodic arrays of scatterers with unbounded unit cells. Here, Rayleigh–Bloch waves are studied for line arrays of sound-hard circular scatterers embedded in a two-dimensional acoustic medium, for which it has recently been shown that Rayleigh–Bloch waves exist for higher frequencies than previously thought. Moreover, it was shown that Rayleigh–Bloch waves can cut off (disappear) and cut on (reappear), and additional Rayleigh–Bloch waves can cut on and interact with the existing ones. These complicated behaviours are reconsidered using a family of quasi-periodic Green’s functions that allow particular plane-wave components to become unbounded away from the array. The Green’s function formulation is combined with the block Sakurai–Sugiura method to trace the trajectories of the Rayleigh–Bloch wavenumbers as they swap between Riemann sheets that are categorized according to the unbounded plane wave(s). A detailed analysis is presented for three different scatterer radius values, and contrasting qualitative behaviours are identified. The findings are consistent with those published previously, extend to higher frequencies than allowed by the previous approach, and provide new understanding of Rayleigh–Bloch waves around the critical frequency intervals where they cut on/cut off/interact.
Structural dynamic characteristics of vertical axis wind and tidal current turbines
Authors: Leng Jun , Zhang Lijun , Li Ye
Published: November 2024

Vertical axis turbines have received great attention in both offshore wind and tidal current energy communities considering their advantages of economic design and unidirectional operation. However, their commercialization process is rather slow compared with the development of horizontal axis turbines due to technical challenges resulting from higher loads from unsteady aero/hydrodynamic forces, centrifugal forces and gravity of the structures. These are mainly because, while the inherent unsteady tangential pulls and fatigue loads intensify the structural vibration, aggravating structural safety and fatigue life, the relationship between the geometric parameters and the structural responses of blades remains unclear. Therefore, in order to clarify this issue, in this study, we focus on the modal and transient analysis of vertical axis turbines using multi-body dynamics, geometrically exact beam theory and detached eddy simulation. We find that the natural frequency of the rotor is directly related to the ratio of blade length and arm length. The effect of arms cannot be ignored in the structural analysis of the turbine. Moreover, an increase of blade length intensifies the deformation and vibration of the turbine’s structure, making the turbine more prone to fatigue failure. This article is expected to extend the existing knowledge of wind and tidal current turbines and provide a reference for choosing proper design parameters and developing suitable-capacity vertical axis turbines.
Host nest defence does not act as selective agent against plumage polymorphism in brood parasites
Authors: Honza Marcel , Štětková Gabriela , Požgayová Milica , Samaš Peter
Published: November 2024

Batesian mimicry in brood parasites is often viewed as an evolutionary strategy to mitigate host aggression. Female common cuckoos (
Cuculus canorus
) exhibit two morphs: the hawk-like grey and the rufous one, potentially maintained by apostatic selection. It was hypothesized that the grey morph’s predator-like appearance deters host defences, while the rufous morph benefits from its rarity by evading host attention. Previous research predominantly utilized static cuckoo dummies, lacking insights into real-world interactions. We investigated the effectiveness of the cuckoo morphs in accessing great reed warbler (
Acrocephalus arundinaceus
) nests under natural conditions. Analysing video-recorded cuckoo attempts, we found no significant difference in nest-access success between the morphs. Both experienced a similar probability of physical attacks when hosts were present, and the rufous morph did not evade host detection more often compared with the grey morph. These results fail to support the assumptions of (a) Batesian mimicry, that hawk-like mimicry enhances nest access or reduces host aggression, and (b) apostatic selection, that the rarity of the rufous morph confers an advantage in successfully accessing the host nest. Future research should aim to identify stages in the cuckoo’s life cycle or host interactions where colour polymorphism provides an evolutionary benefit.
Vertical and diel niches modulate thermal selection by rainforest frogs
Authors: Klinges David H. , Randriambololona Tsitohaina , Lange Zachary K. , Laterza-Barbosa Julia , Randrianandrasana Herizo , Scheffers Brett R.
Published: November 2024

Thermoregulatory behaviour determines an organism’s body temperature and therefore its physiological condition, and may differ for organisms situated across climate gradients. Species’ preferred or selected temperatures may be higher in warmer locations—referred to as coadaptation—or lower in warmer temperatures—countergradient variation. Here, we tested if rainforest amphibians exhibited coadaptation or countergradient thermal selection across an underappreciated spatial climate gradient (vertical height from forest floor to canopy) and separating diel activity (diurnal versus nocturnal behaviour). We captured 2534 amphibians over 216 ground-to-canopy surveys, and conducted 282 thermal selection assays for 37 species while pairing microclimate measurements and mechanistic model predictions to understand vertical and daily thermal variation in the field. Amphibians exhibited countergradient thermal selection: species occupying cool nocturnal conditions in canopies selected warmer temperatures than species occupying hot diurnal conditions at the forest floor. Furthermore, amphibians selected warmer temperatures than the average conditions that they were exposed to when active, and this divergence was especially high for nocturnal arboreal species (8.68°C). This suggests that rainforest amphibians dramatically underfill the warm end of their thermal niches, a trend across local thermal gradients that reflects recent findings across elevational and latitudinal gradients. We show that considering multidimensional climate gradients is important to evaluate thermoregulatory behaviour, and its evolutionary underpinnings, for understanding species’ niches and community assembly.
Emergence of black spot syndrome in Caribbean reefs: a century of fish collections reveal long-term increases in
Scaphanocephalus
infection
Authors: Johnson Pieter T. J. , Malawauw Rémon J. , Piaskowy Julia , Calhoun Dana M. , Kohl Zachary , ter Horst Lars J. V. , Zelmer Derek A.
Published: November 2024

Despite evidence that certain diseases of marine wildlife are increasing, long-term infection data are often lacking. Archived samples of hosts from natural history collections offer a powerful tool for evaluating temporal changes in parasitism. Using vouchered fish collections from the Southern Caribbean, we investigated long-term (1905–2022) shifts in infections by the trematode
Scaphanocephalus
spp., which causes black spot syndrome (BSS) in reef fishes. Examination of 190 museum-preserved fishes from Curaçao and Bonaire revealed that
Scaphanocephalus
infections are not new, with histologically confirmed detections from as early as 1948. However,
Scaphanocephalus
was rare among archival surgeonfish and parrotfishes, with an infection prevalence of <10% and an average abundance of 0.25 metacercariae per fish. Contemporary collections of 258 ocean surgeonfish and parrotfishes (7 species) supported a 7-fold higher prevalence (71%) and a 49-fold higher abundance (12.1). These findings offer evidence that infections by
Scaphanocephalus
spp. have increased substantially over the past century and underscore the value of biological repositories in the study of emerging parasites within marine ecosystems. We emphasize the need for additional research to evaluate the geographical extent of BSS emergence, test proposed hypotheses related to shifts in host density or environmental characteristics and assess the consequences for affected species.
Structural disorder facilitates future memory decisions
Authors: Bocheva Michaela
Published: November 2024

It is well known that perception and cognition are systematically biased towards the recent past. That is, a decision about the current state of a perceptual feature (e.g. orientation) can be predicted based on a recent state of the same feature. Such serial dependencies have been demonstrated across perception, memory and cognition, and have been jointly attributed to an adaptive mechanism meant to promote stability in a constantly changing environment. Here, we argue that this adaptive mechanism prioritizes past information on the most basic structural level, such that the strength of the attractive bias is modulated by the amount of structural coherence in stimuli. We presented visual patterns of varied structural disorder (randomness) prior to a recognition memory decision that required discriminating between trained and novel visual patterns. Both highly generic geometrical shapes and completely random patterns failed to elicit an effect on decisional response times. By contrast, we found recognition memory decisions to be significantly faster in trials where the irrelevant probe pattern was ‘optimally’ random. This result suggests that decision-making is influenced by the past’s informational worth. More importantly, it suggests an optimal amount of uncertainty to facilitate future decisions.
Empowering minorities and everyone in participatory budgeting: an agent-based modelling perspective
Authors: Carpentras Dino , Hänggli Fricker Regula , Helbing Dirk
Published: November 2024

Currently, there are increasing attempts to better involve citizens in political decision processes. A successful approach in that regard has been participatory budgeting (PB), which allows citizens to propose projects and then decide how to distribute a given budget over them. Meanwhile, the literature on collective intelligence (CI) has also shown the ability of groups to solve complex problems. Thus, by combining CI and PB, it should be possible for citizens to identify problems and create their own solutions. In this article, we study this possibility by using agent-based models. Specifically, we first show that a system combining CI and PB produces solutions that strongly penalize minorities if the solution quality depends on group size. Then, we introduce an approach that can overcome this issue. Indeed, by using a common knowledge base for the storage of partial solutions, the quality of solutions of minorities can benefit from the work of the majority, thereby promoting fairness. Interestingly, this approach also benefits majorities, as the quality of their solutions is further improved by the work of the minorities, thus reaching better solutions for everyone. This stresses the potential and importance of an open innovation approach, which is committed to information sharing.

This article is part of the theme issue ‘Co-creating the future: participatory cities and digital governance’.
Artefact design and societal worldview
Authors: Stockinger Elisabeth , Mandlmayr Michael
Published: November 2024

Technological artefacts are created in accordance with the values and worldviews of their designers. In operation, they act as a medium, facilitating and constraining human interaction with, and perception of, the world. When used on a large scale, they may lastingly affect societal ethos. If institutional structures of domination allocate the resources necessary for artefact design and development to some population groups over others, the direction and extent of such an effect may lead to increased disparity and inequity. While the direct influence of technology on opinion is well-studied, the evaluation of non-epistemic values, assumptions and presuppositions is a hurdle in the way of a deeper understanding of the large-scale effects of asymmetries in worldviews embodied by artefacts. Here, we show that artefacts have a strong potential to bias societal worldviews when they are distributed unevenly across the value spectrum. They can affect the clustering behaviour of agents with regard to worldview, both aiding and hindering intra- and inter-cluster diversity, depending on their distribution and frequency. Our findings underline the distributional sensitivity of worldview dynamics to institutional structures of domination. We highlight the importance of procedural interventions such as participatory design, which explicitly acknowledges existing asymmetries and redistributes power accordingly.

This article is part of the theme issue ‘Co-creating the future: participatory cities and digital governance’.
Navigating the cohesion-diversity trade-off: understanding the role of facilitators in co-creation using agent-based modelling
Authors: Mahajan Sachit
Published: November 2024

In the domain of participatory research and co-creation, understanding the dynamic interplay between group cohesion and diversity is pivotal for fostering innovation. While diversity fuels the generation of novel ideas, cohesion ensures these ideas are effectively synthesized and implemented. This study aims to explore the nuanced role that facilitators play in navigating the balance between cohesion and diversity, particularly in groups characterized by pronounced faultlines. Employing agent-based modeling, the study examines how facilitators affect the cohesion-diversity nexus. The findings reveal a complex facilitator’s paradox. While facilitative actions can successfully enhance group cohesion by mitigating the negative effect of faultlines, such efforts often inadvertently reduce the within-group diversity that is crucial for sparking innovative outcomes. These findings challenge the conventional view of faultlines as merely divisive and underscore the intricate role of facilitators in modulating group dynamics. This research discusses a novel framework for dynamic facilitation strategies, emphasizing the need for facilitators to skillfully balance cohesion and diversity. This framework not only enriches the theoretical understanding of group facilitation but also offers practical insights for optimizing collaborative innovation in diverse settings.

This article is part of the theme issue ‘Co-creating the future: participatory cities and digital governance’.
Analysing macroscopic traffic rhythms and city size in affluent cities: insights from a global panel data of 25 cities
Authors: Saavedra Martín , Muñuzuri Alberto P. , Menendez Monica , Balsa-Barreiro Jose
Published: November 2024

The world is undergoing a rapid process of urbanization. Currently, it is estimated that over 55% of the global population resides in urban areas, a figure projected to reach nearly 70% by 2050. This trend is accompanied by a spatial reorganization of human activities on a global scale, bringing about significant changes in mobility patterns and urban traffic management capabilities. Consequently, it is imperative to evaluate, on a broad scale, how city size influences traffic capacity. This study aims to analyse on-road traffic patterns using a diverse dataset comprising cities of varying population sizes, geographical extents and global locations. Specifically, we conduct an analysis encompassing 25 cities primarily situated in several European countries (France, Italy, Germany, Spain, Switzerland, and the United Kingdom), as well as in North America (Canada) and East Asia (Japan and Taiwan). Our findings shed light on how physical aspects related to urban form influence mobility patterns, offering insights for the implementation of more effective and sustainable traffic management policies.

This article is part of the theme issue ‘Co-creating the future: participatory cities and digital governance’.
A roadmap to account for reporting delays for public health situational awareness – a case study with COVID-19 and dengue in United States jurisdictions
Authors: Lopez Velma K. , Bastos Leonardo S. , Codeço Cláudia T. , Johansson Michael A.
Published: November 2024

Background

Decision making in public health is limited by data availability where the most recent reports do not reflect the actual trajectory of an epidemic. Nowcasting is a modeling tool that can estimate eventual case counts by accounting for reporting delays. While these tools have generated reliable predictions when designed for specific use cases, several limitations exist when scaling the models to systems composed of multiple distinct surveillance systems. We seek to identify flexible application of nowcasting models to address these problems.

Methods

We used a previously developed Bayesian nowcasting tool, which dynamically estimates delay probabilities up to a user-defined maximum delay using a user-defined training window. We tested automated approaches to select the maximum delay and training window, setting maximum delay values at the 90th, 95th, and 99thquantile distribution of the most recently reported data and training windows to the maximum delay plus one week or multiplied by 1.5 or 2.0. We generated and evaluated nowcasts for 321 datasets reflecting COVID-19 cases and dengue cases in different United States jurisdictions. We assessed prediction error and precision via logarithmic scoring and coverage metrics for the most recent three weeks of predictions in each nowcast. We used these metrics to further assess why nowcasts may fail and to compare predictions generated from three different publicly available tools.

Results

Using recent data to estimate dynamic delay and training window parameters resulted in nowcast with less error relative to nowcasts made with static parameters for long historic periods. Nowcasts likely to fail could be predicteda prioriby the relative width of the prediction intervals and the permutation entropy of the epidemic trend. More complex models do not significantly improve nowcast performance compared to simple models.

Conclusions

We tested multiple systems for scaling up nowcasts in a flexible framework. We recommend using dynamic parameter selection and creating a system to suppress nowcasts likely to fail. This requires collaboration with surveillance colleagues to implement data-driven choices to improve the utility of predictions for decision making.
The science of child and adolescent mental health in Brazil: a nationwide systematic review and compendium of evidence-based resources
Authors: Marchionatti Lauro Estivalete , Campello André Cardoso , Veronesi Jessica Azevedo , Ziebold Carolina , Tonon André Comiran , Casella Caio Borba , Schafer Julia Luiza , Madyun Aaliyah Nadirah , Caye Arthur , Kieling Christian , Rohde Luis Augusto , Polanczyk Guilherme V. , Mari Jair , Rocha Rudi , Rosa Leonardo , Rosa Dayana , Sanchez Zila M , Bressan Rodrigo A , Saxena Shekhar , Evans-Lacko Sara , Cuijpers Pim , Merikangas Kathleen R. , Kohrt Brandon A. , Bantjes Jason , Reynolds Shirley , Mneimneh Zeina , Salum Giovanni Abrahão
Published: November 2024

Background

Brazil is home to 50 million children and adolescents, whose mental health needs require context-sensitive research. Although scientific output is growing in the country, publications are scattered and often inaccessible.

Methods

This systematic review compiles prevalence estimates, assessment instruments, and interventions for child and adolescent mental health in Brazil (PROSPERO registration: CRD42023491393). We searched international (PubMed, Web of Science, PsycINFO, Google Scholar) and national (Scielo, Lilacs, Brazilian Digital Library of Theses and Dissertations) databases up to July 2024. Reference lists, reviews, and experts were consulted. Extraction followed Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) and Cochrane manuals.

Results

This review appraises 734 studies on 2,576 prevalence estimates, 908 studies on 912 instruments, and 192 studies on 173 intervention trials. Point prevalence of any mental disorder ranged from 10.8% (age 12) to 19.9% (ages 7 to 14), although a nationally-representative study is lacking. There is a rise of self-harm notifications, reaching 133.1 in 2019 (per 100,000 aged 10-19). Indigenous youth face suicide rates of 11 (age 10 to 14), far exceeding national averages (0.652). There is severe violence exposure (21% of adolescents reported domestic physical violence in the previous month), disproportionately impacting Black youth and heightening risks for depression and substance use. Reliable instruments exist for assessing psychopathology, yet most lack psychometric and cross-cultural validation. Interventions remain under-implemented; the largest trials adapted international substance-use prevention programs, showing null effects. High-quality studies are mainly funded by public investment.

Discussion

This compilation provides accessible data for professionals, facilitating translation of science to practice. Brazilian sociocultural challenges impact youth mental health, with public health priorities including violence, systemic racism, and indigenous youth suicide. National research must develop culturally-sensitive resources for mental health, including scalable interventions focused on social minorities.

Funding

The Stavros Niarchos Foundation.
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors
Authors: Vorontsov Ilya E. , Kozin Ivan , Abramov Sergey , Boytsov Alexandr , Jolma Arttu , Albu Mihai , Ambrosini Giovanna , Faltejskova Katerina , Gralak Antoni J. , Gryzunov Nikita , Inukai Sachi , Kolmykov Semyon , Kravchenko Pavel , Kribelbauer-Swietek Judith F. , Laverty Kaitlin U. , Nozdrin Vladimir , Patel Zain M. , Penzar Dmitry , Plescher Marie-Luise , Pour Sara E. , Razavi Rozita , Yang Ally W.H. , Yevshin Ivan , Zinkevich Arsenii , Weirauch Matthew T. , Bucher Philipp , Deplancke Bart , Fornes Oriol , Grau Jan , Grosse Ivo , Kolpakov Fedor A. ,   The Codebook/GRECO-BIT Consortium, Makeev Vsevolod J. , Hughes Timothy R. , Kulakovskiy Ivan V.
Published: November 2024

A DNA sequence pattern, or “motif”, is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and computational motif discovery algorithm. As a part of the Codebook/GRECO-BIT initiative, here we evaluated at large scale the cross-platform recognition performance of positional weight matrices (PWMs), which remain popular motif models in many practical applications. We applied ten different DNA motif discovery tools to generate PWMs from the “Codebook” data comprised of 4,237 experiments from five different platforms profiling the DNA-binding specificity of 394 human proteins, focusing on understudied transcription factors of different structural families. For many of the proteins, there was no prior knowledge of a genuine motif. By benchmarking-supported human curation, we constructed an approved subset of experiments comprising about 30% of all experiments and 50% of tested TFs which displayed consistent motifs across platforms and replicates. We present the Codebook Motif Explorer (https://mex.autosome.org), a detailed online catalog of DNA motifs, including the top-ranked PWMs, and the underlying source and benchmarking data. We demonstrate that in the case of high-quality experimental data, most of the popular motif discovery tools detect valid motifs and generate PWMs, which perform well both on genomic and synthetic data. Yet, for each of the algorithms, there were problematic combinations of proteins and platforms, and the basic motif properties such as nucleotide composition and information content offered little help in detecting such pitfalls. By combining multiple PMWs in decision trees, we demonstrate how our setup can be readily adapted to train and test binding specificity models more complex than PWMs. Overall, our study provides a rich motif catalog as a solid baseline for advanced models and highlights the power of the multi-platform multi-tool approach for reliable mapping of DNA binding specificities.

Abstract Figure

Graphical Abstract
Identification of methylation-sensitive human transcription factors using meSMiLE-seq
Authors: Gralak Antoni J. , Faltejskova Katerina , Yang Ally W.H. , Steiner Clemence , Russeil Julie , Grenningloh Nadia , Inukai Sachi , Demir Mustafa , Dainese Riccardo , Owen Cooper , Pankevich Eugenia ,   Codebook/GRECO-BIT Consortium, Hughes Timothy R. , Kulakovskiy Ivan V. , Kribelbauer-Swietek Judith F. , van Mierlo Guido , Deplancke Bart
Published: November 2024

Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assayed 284 mostly poorly characterized, putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 72 new DNA binding motifs. To investigate whether some of the 158 TFs for which we did not find motifs preferably bind epigenetically modified DNA (i.e. methylated CG dinucleotides), we developed methylation-sensitive SMiLE-seq (meSMiLE-seq). This microfluidic assay simultaneously probes the affinity of a protein to methylated and unmethylated DNA, augmenting the capabilities of the original method to infer methylation-aware binding sites. We assayed 114 TFs with meSMiLE-seq and identified DNA-binding models for 48 proteins, including the known methylation-sensitive binding modes for POU5F1 and RFX5. For 11 TFs, binding to methylated DNA was preferred or resulted in the discovery of alternative, methylation-dependent motifs (e.g. PRDM13), while aversion towards methylated sequences was found for 13 TFs (e.g. USF3). Finally, we uncovered a potential role for ZHX2 as a putative binder of Z-DNA, a left-handed helical DNA structure which is adopted more frequently upon CpG methylation. Altogether, our study significantly expands the human TF codebook by identifying DNA binding motifs for 98 TFs, while providing a versatile platform to quantitatively assay the impact of DNA modifications on TF binding.
Genomic characterization of a persistent, azole-resistantC. parapsilosisstrain responsible for a hospital outbreak during the first COVID-19 wave
Authors: Vumbaca Michela , Biffignandi Gherard Batisti , Cavanna Caterina , Bellinzona Greta , Corbella Marta , Cambieri Patrizia , Rhodes Johanna , Corander Jukka , Baldanti Fausto , Sassera Davide
Published: November 2024

Yeasts belonging to theCandidagenus typically reside on the mucosal surface and within the respiratory and gastrointestinal tract as commensals. Under conditions of host vulnerability,theycan act as opportunistic pathogens, leading to various forms of candidiasis, including candidemia. Such infections can be particularly problematic when caused by isolates that exhibit resistance to antifungal drugs, which is becoming more prevalent in many regions.

One hundred and seven samples ofCandidaspp. were isolated from patients with candidemia in the hospital San Matteo in Pavia (Italy) over a period of 6 years, from 2015 to the first COVID wave in spring 2020. In order to understand the epidemiology ofCandidainfections in this hospital setting, the isolates were whole-genome sequenced which identified most asC. parapsilosisandC. albicans. Comparative genomics revealed that isolates ofC. albicanswere genomically diverse, indicating repeated introductions in the hospital from the community.C. parapsilosisisolates comprised two groups of highly similar isolates representing strains capable of long-term persistence in the hospital. All isolates of the main persistent group were resistant to fluconazole and presented variable levels of resistance to voriconazole and itraconazole, resulting from the Y132F substitution in erg11 and the N455D substitution in upc2. Interestingly, with the exception of the single isolate susceptible to both voriconazole and itraconazole, all the 61 isolates presented one unreported missense mutation in mrr1 (S1907C).
Identification of Stress-induced miRNA of Microbial flora, networking, expression with chronic rhinosinusitis (CRS)
Authors: Wei Bo , He Jiaoyu , Li Jiaxin , Xian Junming , Lius Feng
Published: November 2024

All age groups are affected by one of the most prevalent chronic medical disorders globally: chronic rhinosinusitis (CRS). Its estimated incidence is 10.9% in Europe, 13% in China, and 12.3% in the United States. For many years, the 16S rRNA gene has been the backbone of sequence-based bacterial study. Still, it is only recently that the possibility of high-throughput sequencing the entire gene has been feasible. A unique gene regulation mechanism known as “RNA silencing” limits the transcript level by either starting specific RNA degradation or blocking translation. RNA interference (RNAi) is commonly induced by viruses or exogenously produced small interfering RNAs. Small RNAs like these have been utilized in biomedical research to specifically silence genes. The purpose of a short hairpin RNA is to create interference by inserting an artificial RNA molecule with a hairpin or loop-like structure into a specially designed siRNA. Every stage of life, including cell development, metabolism, the cell cycle, and signal transmission, depends on gene regulatory networks. Total fifteen mRNAs of 16SrRNA gene examined, siRNA regions is unique and isolated through 3’ to 5’ position nucleotide. Networking of both genes lies varieties of path in human being, so early to utilized siRNA technique to silence the effect of 16SrRNA gene in CRS illness. The gene encoding 16S rRNA has around ten target sites that siRNAs can attach to. The siRNAs are made to be complementary sequences to each of the target sites. Verify the 16S rRNA gene expression in CRS illness and other types across the body. Since a cystic fibrosis transmembrane conductance regulator (CFTR) mutation causes CRS illness, we isolated a mutant form of CFTR with an accession ID of 1XMJ and 16S rRNA protein quotes in 8SR6. Examine the two proteins interaction (1xmj, 8sr6) describe the inhibition of CRS illness through new way. Utilizing in-vitro exploratory approaches, both this computational study of siRNA and protein-protein interaction may be employed further to verify efficacy and appropriateness.
invertiaDB: A Database of Inverted Repeats Across Organismal Genomes
Authors: Provatas Kimonas , Chantzi Nikol , Patsakis Michail , Nayak Akshatha , Mouratidis Ioannis , Pavlopoulos Georgios A. , Georgakopoulos-Soares Ilias
Published: November 2024

Inverted repeats are repetitive elements that can form hairpin and cruciform structures. They are linked to genomic instability, however they also have various biological functions. Their distribution differs markedly across taxonomic groups in the tree of life, and they exhibit high polymorphism due to their inherent genomic instability. Advances in sequencing technologies and declined costs have enabled the generation of an ever-growing number of complete genomes for organisms across taxonomic groups in the tree of life. However, a comprehensive database encompassing inverted repeats across diverse organismal genomes has been lacking. We present InvertiaDB, the first comprehensive database of inverted repeats spanning multiple taxa, featuring repeats identified in the genomes of 118,070 organisms across all major taxonomic groups. The database currently hosts 30,067,666 inverted repeat sequences, serving as a centralized, user-friendly repository to perform searches, interactive visualization, and download existing inverted repeat data for independent analysis. invertiaDB is implemented as a web portal for browsing, analyzing and downloading inverted repeat data. invertiaDB is publicly available athttps://invertiadb.netlify.app/homepage.html.
Non-destructive transcriptomics via vesicular export
Authors: Armbrust Niklas , Geilenkeuser Julian , Grosshauser Martin , Stroppel Luisa , Schmidt Sebastian , Panne Tobias , Steinmaßl Emily , Widenmeyer Florenc , Warsing Niklas , Berezin Oleksandr , Sabry Melike , Sultanbai Asina , Santl Tobias , Theis Fabian , Gagneur Julien , Jeffery Truong Dong-Jiunn , Westmeyer Gil Gregor
Published: November 2024

Transcriptomics is a valuable technique for multiplexed monitoring of cellular states. However, its application has been predominantly limited to assays that necessitate cell fixation or lysis, which hinders real-time, longitudinal tracing of RNA expression in live cells. Here, we present non-destructive transcriptomics by vesicular export (NTVE) to enable multi-time-point monitoring of RNA expression dynamics in living inducible reporter cell lines. Stabilized RNA reporter barcodes can be selectively packaged and exported from cells via virus-like particles (VLPs) containing selective affinity handles for convenient multichannel tracking of co-cultured cells. Using an engineered RNA adapter, NTVE exports cellular transcripts from inducible human and murine reporter cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE allows monitoring of transcriptome changes in response to genetic and chemical perturbations in the same cells over time using standard sequencing workflows. NTVE can also be equipped with fusogens to deliver mRNA-encoded effectors or ribonucleoprotein gene editors from sender cells to activate gene reporters in co-cultured recipient cells. In addition, we demonstrate the utility of NTVE in monitoring hiPSC differentiation through daily NTVE analysis tracking multiple lineage-specific marker genes.
Indecision and recency-weighted evidence integration in non-clinical and clinical settings
Authors: del Río M , Trudel N , Prabhu G , Hunt LT , Moutoussis M , Dolan RJ , Hauser TU
Published: November 2024

Biases in information gathering are common in the general population and can reach pathological extremes in paralysing indecisiveness, as in obsessive-compulsive disorder (OCD). Here, we adopt a new perspective on information gathering and demonstrate an information integration bias where most recent information is over-weighted by means of evidence strength updates (ΔES). In a large, crowd-sourced sample (N=5,237), we find reduced ΔES-weighting drives indecisiveness along an OC spectrum. We replicate the attenuated ΔES- weighting in a second lab-based study (N=105) that includes a transdiagnostic OC spectrum encompassing OCD and generalised anxiety patients. Using magnetoencephalography (MEG), we trace ΔES signals to a late neural signal peaking around 920 ms. Critically, high-OC participants show an attenuated neural ΔES signal in medio-frontal areas while other decision- relevant processes remain intact. Our findings establish biased information-weighting as a key driver of information gathering, where attenuated ΔES can lead to indecisiveness across an OC spectrum.
Urban Cohabscapes: exploring European Co-Habitative landScapes diversity, in the ECOLOPES framework.
Authors: Oneto Gabriele , Perini Katia , Canepa Maria , Culshaw Victoria , Weisser Wolfgang , Mimet Anne
Published: November 2024

Urban liveability is closely related to the landscape features that support human societies. The promotion of liveability influences the well-being of both human and non-human inhabitants of the city, as the two share the same urban habitat. In this paper, we propose a classification of urban landscapes tailored to facilitate the acquisition of interdisciplinary knowledge on the multi-inhabitant liveability of urban landscapes. Our classification represents the layered urban dimensions through four different subclassifications: local and landscape Urban Form, Anthropic Imprint, and Biophysical Conditions. We developed a flexible and scalable methodology that enables us to expand to other cities, by using only opensource geospatial and remote sensing data. We modelled our four subclassifications at 10-metres through a set of automatic pipelines, running Principal Component Analysis as dimensionality reduction and KMeans unsupervised classification. In this paper we explore the application of our methodology in the framework of ECOLOPES, a project that investigates the human and non-human liveability in cities through the computational design of green building envelopes. We apply the methodology to three distinct European cities, i.e. Vienna, Munich, and Genoa. We produced a set of 12 raster maps from 64 variables, with a total of 32 classes and 1264 possible combinations. We analysed inter and intra-urban class frequencies by highlighting the primary spatial signatures over each sub-classification, and between the overall Functional Urban Areas and the core areas. In this paper we discuss how this approach could foster multidisciplinary studies on urban liveability that hold into account not just humans, but all living inhabitants in cities. From this application, we envision a second step where our methodology will be applied to the full extent of European cities.
Glioblastoma-Neuroblastoma co-cultured multicellular spheroid model for anti-cancer drug screening
Authors: Murugappan Sivasubramanian , Mali Ajay , Thorat Nanasaheb
Published: November 2024

Preclinical drug screening often relies on 2D mono-cultures and animal models, which fail to replicate the complexity of the human brain tumor microenvironment. This study presents a novel 3D co-culture spheroid model combining glioblastoma (U87-MG) and neuroblastoma (SH-SY5Y) cells to better mimic the cellular and molecular dynamics of brain tumors. Using the liquid overlay technique, reproducible and scalable spheroids were developed and characterized for growth, morphology, and drug sensitivity to temozolomide (TMZ), an FDA-approved brain cancer drug. Our findings demonstrate that glioblastoma spheroids thrive under hypoxic conditions and show significant resistance to TMZ, maintaining ∼88% viability even at 1000 µM. In contrast, neuroblastoma spheroids exhibit marked sensitivity, with viability reducing to ∼67% at the same concentration. Co-cultured spheroids displayed intermediate drug sensitivity (∼68% viability), highlighting the influence of neuroblastoma cells on glioblastoma’s drug response. Notably, neuroblastoma cells in the co-culture model exhibited neurite-like morphologies, suggesting differentiation and enhanced tumor-tumor interactions. This model addresses key limitations of existing preclinical systems by bridging the gap between simplistic 2D cultures and time-intensive organoids. It provides a biologically relevant and time-efficient platform for investigating tumor-stroma interactions, drug responses, and the role of neuron-glia dynamics in glioblastoma progression. Therefore, this co-culture spheroid system represents a critical step forward in developing more effective therapeutic strategies for brain tumors.
Targeting the tomato fruit cuticle by gene overexpression and editing with the fruit epidermis-preferentialnsLTPpromoter
Authors: Alonso Marie , Paulsen Ella , Geneix Nathalie , Pedemay Sandra , D’Orlando Angelina , Marion Didier , Lahaye Marc , Bakan Bénédicte , Rothan Christophe , Petit Johann
Published: November 2024

The thick cuticle covering and embedding epidermal cells of tomato (Solanum lycopersicum) fruit, a model for cuticle studies, plays important roles in fruit protection and quality. To further our understanding of the influence of cuticle components on cuticle architecture and properties, the next step is to engineer cuticle composition. Ideally, to avoid indirect effects at whole-plant level, a fruit-and epidermis-specific promoter should be used. Here, to overexpress and edit target genes in tomato, we selected anon-specific Lipid Transfer Protein 2promoter (pronsLTP) with preferential activity in fruit epidermis, as shown by NLS-GFP fluorescence analysis. Overexpression ofSlMYB75driven bypronsLTPinduced anthocyanin accumulation specifically in the growing fruit epidermis, consistent with the cuticle deposition pattern. In keeping with changes in anthocyanins, the cuticle composition in flavonoids and phenolic acids was altered, as shown by Raman microspectroscopy, as were several cuticle properties. We then edited the carotenoidPSY1gene with apronsLTP–drivenCRISPR/Cas9 system. DifferentPSY1knock-out alleles were detected predominantly in fruit exocarp and mesocarp of color-impairedpronsLTP::Cas9-Psy1mutants, and very little in the leaf. A mutant carrying a heritable knock-out mutation in both fruit and leaf was also detected, indicating that mutants obtained withpronsLTPmay require screening before being studied. Altogether, our results indicate thatpronsLTP2can efficiently result in gene overexpression and editing in fruit epidermis. Implications of these findings are important for the functional analysis and genetic engineering of cuticle-related genes in tomato.
Blood-tumor barrier organoids recapitulate glioblastoma microenvironment and enable high-throughput modeling of therapeutic delivery
Authors: Zhuang Pei , Scott Benjamin , Gao Shuai , Meng Wei-Min , Yin Rui , Nie Xinyu , Gaiaschi Ludovica , Lawler Sean E. , Lamfers Martine , Bei Fengfeng , Cho Choi-Fong
Published: November 2024

The blood-brain barrier (BBB) is a highly specialized system that is critical for regulating transport between the blood and the central nervous system. In brain tumors, the vasculature system is compromised, and is referred to as the blood-tumor barrier (BTB). The ability to precisely model the unique physiological properties of the BTB is essential to decipher its role in tumor pathophysiology and for the rational design of efficacious therapeutics. Here, we introduce a robust and high-throughputin vitro3D human BTB organoid model that recapitulates various key features of the BTB observedin vivoand in clinical GBM samples. The organoids are composed of patient-derived glioblastoma stem cells (GSCs), human brain endothelial cells (EC), astrocytes and pericytes, which are formed through self-assembly. Transcriptomic and functional analyses reveal that the GSCs in the BTB organoids exhibit enhanced level of stemness, mesenchymal signature, invasiveness and angiogenesis, and this is further confirmed inin vivostudies. We demonstrate the ability of the BTB organoids to model therapeutic delivery and drug efficacy on brain tumor cells. Collectively, our findings show that the BTB organoid model has broad utility as a clinically representative system for studying the BTB and evaluating brain tumor therapies.
Spatial Transcriptomics Reveals Inflammation and Trans-differentiation States of Acute Myeloid Leukemia in Extramedullary and Medullary Tissues
Authors: Dasdemir Enes , Veletic Ivo , Ly Christopher P. , Quesada Andres E. , Pacheco Christopher D. , Jelloul Fatima Z. , Borges Pamela , Basu Sreyashi , Jindal Sonali , Wang Zhiqiang , Lazar Alexander , Wani Khalida M. , Antunes Dinler A. , Reville Patrick K. , Gunaratne Preethi H. , Tower Robert J. , Sharma Padmanee , Abbas Hussein A.
Published: November 2024

Acute myeloid leukemia (AML) is a heterogeneous disease of the bone marrow (medullary) but can also involve extramedullary tissues. While single cell dynamics of AML in suspension are previously explored, a comprehensive spatial transcriptomic assessment in AML remain underexplored. Here, we used Visium spatial transcriptomics to resolve medullary and extramedullary AML environments. We reveal spatial co-localization of monocytes and granulocyte-monocyte progenitors with leukemic populations in the bone marrow, sharing molecular signatures with extramedullary sites. Cell-cell communication via the CXCL12- CXCR4 axis correlated with PI3K/AKT/mTOR signaling in high inflammatory niches. Trans- differentiation states were concentrated in AML-infiltrated regions, with committed-like AML populations present in inflammatory niches and away from the trabeculae, while primitive-like AML cells localized near the endosteal niche. We validated these findings in GeoMx-based Digital Spatial profiling (DSP). Our study applied multimodal spatial transcriptomic approaches to characterize the spatial hierarchy and microenvironmental dynamics of AML differentiation states. We also demonstrated the feasibility of applying Visium-based spatial transcriptomics in decalcified bone tissues.
Differential beta and gamma activity modulation during unimanual and bimanual motor learning
Authors: Wu Min , Schoenfeld Marleen J. , Lindersson Carl , Braeutigam Sven , Zich Catharina , Stagg Charlotte J.
Published: November 2024

Movement-related dynamics in the beta and gamma bands have been studied in relation to motor execution and learning during unimanual movements, but their roles in complex bimanual tasks remain largely unexplored. This study aimed to investigate how beta and gamma activity differs between unimanual and bimanual movements, and how these neural signatures evolve during the learning process. Our motor task incorporated varying levels of bimanual interaction: unimanual, bimanual-equal, and bimanual-unequal. Magnetoencephalography data were recorded during task performance, and beta and gamma dynamics were quantified. As expected, increasing task complexity from unimanual to bimanual-equal, and then to bimanual-unequal movements resulted in slower and less accurate performance. Across all conditions, significant beta event-related desynchronization (ERD) and gamma event-related synchronization (ERS) were observed during movement, as well as beta ERS after movement. Bimanual movements exhibited greater beta ERD, beta ERS, and gamma ERS compared to unimanual movements. With practice, participants demonstrated faster and more accurate movements, accompanied by enhanced beta ERS responses. Furthermore, learning-related reductions in errors correlated with increases in beta ERS. These findings suggest the distinct behavioural and neural demands of unimanual versus bimanual movements and highlight the important role of beta dynamics in motor performance and learning.