bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Social Isolation Due to the COVID-19 Pandemic on Cognitive Dysfunction of Patients With Alzheimer Disease
Authors: Nakamura Yu , Omori Takumi , Nishiyama Kenichi , Ishikawa Ichiro , Aoki Hiroshi , Nagakura Naoki 
Published: November 2024

Background:
Previous studies were examined effects of social restriction by COVID-19 pandemic on elderly peoples or compared difference of before/after restrictions on patients with Alzheimer disease-related dementia (ADRD). Here, we assessed the effects of restrictions on the cognitive function of the patients by comparing control group.

Methods:
We examined the impact on cognitive function using the Alzheimer Disease Assessment Scale (Japanese version) cognitive subscale (ADAS-JCOG), in patients with mild to moderate ADRD by a post hoc subgroup analysis of double-blinded, noninferiority study of donepezil 27.5 mg patches and donepezil hydrochloride 5 mg tablets (JapicCTI-194582). After demonstrating the noninferiority of both treatments, we used combined data for this analysis.

Results:
The analyzed subpopulation of the per-protocol set groups was balanced (n=126 and 135, respectively). Patient demographics were similar between subgroups. The difference of ADAS-JCOG scores [least-squares mean (95%CI)] between the groups was 0.388 (-0.377 to 1.152, not statistically significant).

Conclusion:
Social isolation affects cognitive function on ADRD and this knowledge should be considered in future.
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

AbstractBackgroundDecision 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.MethodsWe 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.ResultsUsing 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.ConclusionsWe 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

AbstractBackgroundBrazil 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.MethodsThis 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.ResultsThis 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.DiscussionThis 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.FundingThe 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

AbstractA 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 FigureGraphical 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

AbstractTranscription 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

ABSTRACTYeasts 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

AbstractAll 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

AbstractInverted 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.