bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling the daily probability of wildfire occurrence in the contiguous United States
Authors: Keeping Theodore , Harrison Sandy P , Prentice I Colin 
Published: January 2024

Abstract
The development of a high-quality wildfire occurrence model is an essential component in mapping present wildfire risk, and in projecting future wildfire dynamics with climate and land-use change. Here, we develop a new model for predicting the daily probability of wildfire occurrence at 0.1° (∼10 km) spatial resolution by adapting a generalised linear modelling (GLM) approach to include improvements to the variable selection procedure, identification of the range over which specific predictors are influential, and the minimisation of compression, applied in an ensemble of model runs. We develop and test the model using data from the contiguous United States. The ensemble performed well in predicting the mean geospatial patterns of fire occurrence, the interannual variability in the number of fires, and the regional variation in the seasonal cycle of wildfire. Model runs gave an area under the receiver operating characteristic curve (AUC) of 0.85–0.88, indicating good predictive power. The ensemble of runs provides insight into the key predictors for wildfire occurrence in the contiguous United States. The methodology, though developed for the United States, is globally implementable.
Enhancing quality control in bioprinting through machine learning
Authors: Bonatti Amedeo Franco , Vozzi Giovanni , De Maria Carmelo 
Published: January 2024

Abstract
Bioprinting technologies have been extensively studied in literature to fabricate three-dimensional constructs for tissue engineering applications. However, very few examples are currently available on clinical trials using bioprinted products, due to a combination of technological challenges (i.e. difficulties in replicating the native tissue complexity, long printing times, limited choice of printable biomaterials) and regulatory barriers (i.e. no clear indication on the product classification in the current regulatory framework). In particular, quality control (QC) solutions are needed at different stages of the bioprinting workflow (including pre-process optimization, in-process monitoring, and post-process assessment) to guarantee a repeatable product which is functional and safe for the patient. In this context, machine learning (ML) algorithms can be envisioned as a promising solution for the automatization of the quality assessment, reducing the inter-batch variability and thus potentially accelerating the product clinical translation and commercialization. In this review, we comprehensively analyse the main solutions that are being developed in the bioprinting literature on QC enabled by ML, evaluating different models from a technical perspective, including the amount and type of data used, the algorithms, and performance measures. Finally, we give a perspective view on current challenges and future research directions on using these technologies to enhance the quality assessment in bioprinting.
Light switching between localized and delocalized states in chiral moiré-like photonic lattice
Authors: He Yundong , Wen Zhixi , Tong Zhenzhu , Guan Jiahao , Xin Guoguo , Zhang Wenjing , Gao Yuanmei , Qi Xinyuan 
Published: January 2024

Abstract
We constructed a chiral moiré-like lattice pattern by the interference between two sets of plane waves and two circular polarized beams. The study shows that the intensity distributions of the lattice pattern are a moiré-like structure in the transverse direction and a spiral structure in the longitudinal direction. By tuning the relative rotation angle between two sets of beams, moiré-like lattice pattern can be switched between periodic to aperiodic systems. Further, we numerically study the impacts of relative rotation angle, the screw pitch of the lattice waveguide, the width and incident direction of the probe beam on the light behavior in chiral moiré-like photonic lattice fabricated with photon-induction method. It turns out that light propagation can be switched between localization and delocalization. Our study enriches the physical content of moiré-like lattice patterns and paves a novel way to the light modulation in photonic lattices.
Simultaneous mapping of the magnetic field components using near-field microscopy
Authors: Merlo Juan M , Ettinger-Finley Raphael J , Carhart Madeleine Hoag , Binny Florence , Merlo-Ramírez Lázaro 
Published: January 2024

Abstract
In this work, we present a near-field scanning optical microscope capable of simultaneously mapping the

x
−

,

y
−

, and

z
−

components of the magnetic field generated by a set of magnetic coils in the

kHz

range. Using this device, we present two experiments: the observation of the well-known magnetic field of a circular coil and a resolution test. The observations achieved with our instrument are supported by numerically calculated simulations, which confirm the validity of our experimental results. In addition, our instrument is capable of imaging features of the order of

15

mm

, representing a resolution of

λ

/

10
000

. Our approach establishes an important avenue for the three-dimensional mapping of the electromagnetic field in any spectral range, using the correct configuration of the probe, and opens a new discussion on the resolution of scanning probe microscopes imaging more than one component of the studied field.
Reinvigorating Social Support Systems in Rural Northwestern Ghana: Towards Affective Empathy in a Neoliberal Age
Authors: Akurugu Constance Awinpoka 
Published: January 2024

Abstract
Scholars frequently allude to the concept of a supportive extended family system that provides a lifeline to less privileged members of society, such as the indigent and the aged. Yet, the extended family and the network of support it enables have come under immense threat from neoliberalism. This article examines the constrained role of the extended family system and its implications, based on residential ethnographic fieldwork data gathered in rural northwestern Ghana. It draws on transnational discourses on empathy and local conceptions of interdependence and unity as encapsulated by African communitarian philosophies such as Ubuntu and Te jaa bonyeni of the Waala people of northwestern Ghana to explore how to generate empathy. Neoliberal individualist values have intensely undermined the support networks of the extended family system. Te jaa bonyeni philosophy, similar to Ubuntu, and many humanistic philosophies, offers important opportunities for reinvigorating debates on African indigenous support networks as important steps towards nurturing affective empathy. This study contributes to discourses on affective empathy by connecting it to communitarianism. Cultivating empathy is necessary towards imagining forms of existence that are dignifying for the marginalized and preventing them from descending into abysmal deprivation.
From G1 to M: a comparative study of methods for identifying cell cycle phases
Authors: Guo Xinyu , Chen Liang 
Published: January 2024

Abstract
Accurate identification of cell cycle phases in single-cell RNA-sequencing (scRNA-seq) data is crucial for biomedical research. Many methods have been developed to tackle this challenge, employing diverse approaches to predict cell cycle phases. In this review article, we delve into the standard processes in identifying cell cycle phases within scRNA-seq data and present several representative methods for comparison. To rigorously assess the accuracy of these methods, we propose an error function and employ multiple benchmarking datasets encompassing human and mouse data. Our evaluation results reveal a key finding: the fit between the reference data and the dataset being analyzed profoundly impacts the effectiveness of cell cycle phase identification methods. Therefore, researchers must carefully consider the compatibility between the reference data and their dataset to achieve optimal results. Furthermore, we explore the potential benefits of incorporating benchmarking data with multiple known cell cycle phases into the analysis. Merging such data with the target dataset shows promise in enhancing prediction accuracy. By shedding light on the accuracy and performance of cell cycle phase prediction methods across diverse datasets, this review aims to motivate and guide future methodological advancements. Our findings offer valuable insights for researchers seeking to improve their understanding of cellular dynamics through scRNA-seq analysis, ultimately fostering the development of more robust and widely applicable cell cycle identification methods.
Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning
Authors: Krishnan Sowmya R , Roy Arijit , Gromiha M Michael 
Published: January 2024

Abstract
Ribonucleic acids (RNAs) play important roles in cellular regulation. Consequently, dysregulation of both coding and non-coding RNAs has been implicated in several disease conditions in the human body. In this regard, a growing interest has been observed to probe into the potential of RNAs to act as drug targets in disease conditions. To accelerate this search for disease-associated novel RNA targets and their small molecular inhibitors, machine learning models for binding affinity prediction were developed specific to six RNA subtypes namely, aptamers, miRNAs, repeats, ribosomal RNAs, riboswitches and viral RNAs. We found that differences in RNA sequence composition, flexibility and polar nature of RNA-binding ligands are important for predicting the binding affinity. Our method showed an average Pearson correlation (r) of 0.83 and a mean absolute error of 0.66 upon evaluation using the jack-knife test, indicating their reliability despite the low amount of data available for several RNA subtypes. Further, the models were validated with external blind test datasets, which outperform other existing quantitative structure-activity relationship (QSAR) models. We have developed a web server to host the models, RNA-Small molecule binding Affinity Predictor, which is freely available at: https://web.iitm.ac.in/bioinfo2/RSAPred/.
‘Sedative Coping’, Contextual Maturity and Institutionalization Among Prisoners Serving Life Sentences in England and Wales
Authors: Crewe Ben 
Published: January 2024

Abstract
Based on a longitudinal study of life-sentenced prisoners in England and Wales, this article seeks to make sense of what it characterizes as ‘sedative coping’. In doing so, it brings together analytic conclusions from the existing research literature that appear highly inconsistent, but which indicate the centrality of emotion in the experience of serving a long prison sentence. Specifically, it highlights the forms of emotion management and suppression involved in coping with the trauma of such circumstances, and the post-release impact of sustained forms of emotional self-preservation. This focus helps us better understand the connection between ‘mature coping’ in custody and the post-release difficulties that life-sentenced prisoners often describe.
Influence Maximization in Social Networks Using an Improved Multi-Objective Particle Swarm Optimization
Authors: Wang Ping , Zhang Ruisheng 
Published: January 2024

Abstract
The influence maximization (IM) problem has received great attention in the field of social network analysis, and its analysis results can provide reliable basis for decision makers when promoting products or political viewpoints. IM problem aims to select a set of seed users from social networks and maximize the number of users expected to be influenced. Most previous studies on the IM problem focused only on the single-objective problem of maximizing the influence spread of the seed set, ignoring the cost of the seed set, which causes decision makers to be unable to develop effective management strategies. In this work, the IM problem is formulated as a multi-objective IM problem that considers the cost of the seed set. An improved multi-objective particle swarm optimization (IMOPSO) algorithm is proposed to solve this problem. In the IMOPSO algorithm, the initialization strategy of Levy flight based on degree value is used to improve the quality of the initial solution, and the local search strategy based on greedy mechanism is designed to improve the Pareto Frontier distribution and promote algorithm convergence. Experimental results on six real social networks demonstrate that the proposed IMOPSO algorithm is effective, reducing runtime while providing competitive solutions.
Lack of NAD(P)+ transhydrogenase activity in patients with primary adrenal insufficiency due to NNT variants
Authors: Francisco Annelise , Goler Ayse Mine Yilmaz , Navarro Claudia Daniele Carvalho , Onder Asan , Yildiz Melek , Kendir Demirkol Yasemin , Karademir Yilmaz Betul , Seven Menevse Tuba , Güran Tülay , Castilho Roger Frigério 
Published: January 2024

Abstract

Background
Pathogenic variants in the nicotinamide nucleotide transhydrogenase gene (NNT) are a rare cause of primary adrenal insufficiency (PAI), as well as functional impairment of the gonads.

Objective
Despite the description of different homozygous and compound heterozygous NNT variants in PAI patients, the extent to which the function and expression of the mature protein are compromised remains to be clarified.

Design
The activity and expression of mitochondrial NAD(P)+ transhydrogenase (NNT) were analyzed in blood samples obtained from patients diagnosed with PAI due to genetically confirmed variants of the NNT gene (n = 5), heterozygous carriers as their parents (n = 8), and healthy controls (n = 26).

Methods
NNT activity was assessed by a reverse reaction assay standardized for digitonin-permeabilized peripheral blood mononuclear cells (PBMCs). The enzymatic assay was validated in PBMC samples from a mouse model of NNT absence. Additionally, the PBMC samples were evaluated for NNT expression by western blotting and reverse transcription quantitative polymerase chain reaction and for mitochondrial oxygen consumption.

Results
NNT activity was undetectable (&lt;4% of that of healthy controls) in PBMC samples from patients, independent of the pathogenic genetic variant. In patients' parents, NNT activity was approximately half that of the healthy controls. Mature NNT protein expression was lower in patients than in the control groups, while mRNA levels varied widely among genotypes. Moreover, pathogenic NNT variants did not impair mitochondrial bioenergetic function in PBMCs.

Conclusions
The manifestation of PAI in NNT-mutated patients is associated with a complete lack of NNT activity. Evaluation of NNT activity can be useful to characterize disease-causing NNT variants.
Contact tracing in Austria, Georgia, Kyrgyzstan, Ukraine, and Kosovo during the COVID-19 pandemic: response review and good practices
Authors: Aboushady Ahmed Taha , Blackmore Claire , Nagel Anna , Janashvili Lika , Gexha Dafina , Otorbaeva Dinagul , Bugaienko Natalia , Pebody Richard , Hegermann-Lindencrone Michala 
Published: January 2024

Abstract

Background
During the COVID-19 pandemic, effective contact tracing was recognized as a crucial public health response to mitigate the spread of SARS-CoV-2 and reduce COVID-19-related morbidity and mortality, particularly before widespread vaccination. The World Health Organization (WHO) recommended implementing active surveillance strategies to trace and quarantine contacts of confirmed or suspected COVID-19 cases.

Methods
A detailed review and analysis of the COVID-19 contact tracing responses was conducted in five European countries and territories, between March 2021 and August 2022. The countries and territories were selected to ensure geographical representation across the WHO European Region and applied a mixed-methods approach of in-depth interviews with various stakeholders across different administrative levels to identify good practices in COVID-19 contact tracing. The interviews covered 12 themes, including methods and procedures for COVID-19 contact tracing, information technology, quality assurance and key performance indicators.

Results
The findings demonstrate that the policy approach, digitalization capabilities and implementation approach varied in the countries and territories and were dynamic throughout the pandemic. The analysis revealed that some practices were applicable across all countries and territories, while others were context-specific, catering to each country’s and territory’s unique needs. The study highlighted a need for all countries to institutionalize contact tracing as an essential function of existing health systems, to digitalize contact tracing practices and processes, and to build and retain contact tracing capacities for better pandemic preparedness.

Conclusion
The lessons related to COVID-19 contact tracing should be utilized to strengthen future outbreak response operations as part of epidemic and pandemic preparedness.
Divergent effects of switching from cytology to HPV-based screening in the Nordic countries
Authors: Partanen Veli-Matti , Dillner Joakim , Tropé Ameli , Ágústsson Ágúst Ingi , Lönnberg Stefan , Heinävaara Sirpa , Anttila Ahti 
Published: January 2024

Abstract

Background
Cervical cytology has been the primary method of cervical cancer screening for decades. Tests that detect viral HPV are shown in several randomized trials to provide better protection against cancer compared with cytology. HPV-based screening has been implemented alongside cytology in the Nordic countries for several years. The aim of this study was to compare cytology and HPV-based screening in the colposcopy referrals and detection rates of cervical lesions.

Methods
Individual-level screening data from Finland, Iceland, Norway and Sweden were harmonized and aggregated locally. We utilized data for tests taken during years 2015–17 and biopsies taken during years 2015–19 to allow 24 months of follow-up. Age-standardized estimates and age-adjusted risk ratios for six different outcomes of screening management were calculated.

Results
The age-standardized colposcopy rates were higher in HPV-based testing compared with cytology in Finland (3.5% vs. 0.9%) and Norway (6.0% vs. 4.1%) but lower in Sweden (3.7% vs. 4.9%). The relative detection rate of cervical intraepithelial neoplasia grade 2 and above in HPV-based testing compared with cytology was highest in Finland (RR 2.37, 95% CI 2.13–2.63) and Norway (RR 1.66, 95% CI 1.57–1.72) while in Sweden the difference was not statistically significant (RR 0.98, 95% CI 0.95–1.00).

Conclusions
The effects of implementing HPV screening varied by country as different screening algorithms were implemented. HPV-based screening increases colposcopy rates mainly through referrals from increased repeat testing and detection rate is therefore significantly higher compared with cytology. Monitoring of these indicators in subsequent rounds of HPV-based screening remains essential.
Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements
Authors: Silver Brianna D , Willett Courtney G , Maher Kelsey A , Wang Dongxue , Deal Roger B 
Published: January 2024

Abstract
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II often initiates transcription in both directions at the promoter transcription start site, but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements such as enhancers. These bidirectional RNA Polymerase II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the transcription start site or cis-regulatory elements. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both transcription start sites and cis-regulatory elements in A. thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional RNA Polymerase II initiation at both promoters and gene-proximal cis-regulatory elements of A. thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both D. melanogaster and H. sapiens, as well as cis-regulatory elements in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around transcription start sites in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.
Hepatitis C virus point-of-care microelimination approach in a vulnerable population in the South of Spain
Authors: Pinazo-Bandera José María , Aranda Jesús , García-García Alberto Manuel , Alcántara Ramiro , Ortega-Alonso Aida , Del Campo-Herrera Enrique , Clavijo Encarnación , García-Escaño M Dolores , Ruiz Ruiz Juan Jesús , Morales-Herrera Mónica , Valle-López Vanesa , Martín-Alarcón Rosa , Viciana Isabel , Jiménez Juan Bautista , Fernández-García Felix , Toro-Ortiz Juan Pedro , Sánchez-Yáñez Elena , Álvarez-Álvarez Ismael , Andrade Raúl J , Robles-Díaz Mercedes , García-Cortés Miren 
Published: January 2024

Abstract

Background
Since the introduction of direct-acting antivirals, thousands of chronic hepatitis C patients have been successfully treated. However, vulnerable populations have a higher prevalence of hepatitis C virus (HCV) infection and face barriers that impede their access to antivirals. We carried out an HCV microelimination program focused on vulnerable population groups in Malaga.

Methods
People in drug addiction treatment centers and homeless shelters in Malaga who participated in the program between October 2020 and October 2021 were included. After providing participants with educational information on HCV, a dry drop test (DDT) was used to collect blood for subsequent screening for HCV infection. The participants who were diagnosed with HCV infection were scheduled for comprehensive healthcare assessments, including blood tests, ultrasonography, elastography, and the prescription of antivirals, all conducted in a single hospital visit. Sustained viral response (SVR) was analysed 12 weeks after end of treatment.

Results
Of the 417 persons invited to participate, 271 (65%) agreed to participate in the program. These participants were screened for HCV infection and 28 of them were diagnosed with HCV infection (10%). These hepatitis C-infected patients had a mean age of 53 ± 9 years; 86% were males and 93% were or had been drug users. Among 23 patients with HCV infection, HCV genotype 1a predominated (74%). Medical exams showed that 19% (4/21) had advanced fibrosis (F3–4), and 5% (1/21) had portal hypertension. Finally, 23 infected patients received treatment with glecaprevir/pibrentasvir or sofosbuvir/velpatasvir and SVR was confirmed in 22 patients (96%).

Conclusions
Drug users and homeless people have a higher prevalence of HCV infection than the general population. The microelimination program with educational activity and screening tools achieved a high participation rate, easy healthcare access, and a high rate of SVR despite the SARS-CoV-2 pandemic.