bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene function prediction in five model eukaryotes exclusively based on gene relative location through machine learning
Authors: Pazos Obregón Flavio , Silvera Diego , Soto Pablo , Yankilevich Patricio , Guerberoff Gustavo , Cantera Rafael 
Published: July 2022

AbstractThe function of most genes is unknown. The best results in automated function prediction are obtained with machine learning-based methods that combine multiple data sources, typically sequence derived features, protein structure and interaction data. Even though there is ample evidence showing that a gene’s function is not independent of its location, the few available examples of gene function prediction based on gene location rely on sequence identity between genes of different organisms and are thus subjected to the limitations of the relationship between sequence and function. Here we predict thousands of gene functions in five model eukaryotes (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens) using machine learning models exclusively trained with features derived from the location of genes in the genomes to which they belong. Our aim was not to obtain the best performing method to automated function prediction but to explore the extent to which a gene's location can predict its function in eukaryotes. We found that our models outperform BLAST when predicting terms from Biological Process and Cellular Component Ontologies, showing that, at least in some cases, gene location alone can be more useful than sequence to infer gene function.
Nutrient intakes and telomere length of cell-free circulating DNA from amniotic fluid: findings from the Mamma & Bambino cohort
Authors: Magnano San Lio Roberta , Maugeri Andrea , La Rosa Maria Clara , Giunta Giuliana , Panella Marco , Cianci Antonio , Caruso Maria Anna Teresa , Agodi Antonella , Barchitta Martina 
Published: July 2022

AbstractPregnancy represents a crucial period in which several exposures—and especially maternal diet—might shape children’s health. Thus, identifying how maternal dietary intakes early affect biological aging in children represents a public health mission. We aimed to assess the relationship between maternal intake of nutrients in early pregnancy and telomere length of cell-free circulating DNA (cfDNA) from amniotic fluid. We used data and samples from the ongoing prospective “Mamma & Bambino” study, which recruits mother–child pairs from Catania at the first prenatal visit. Maternal nutrient intakes were assessed using a Food Frequency Questionnaire, while relative telomere length of cfDNA was assessed by real-time polymerase chain reaction. Our analysis included 174 mother–child pairs. The intakes of iron, vitamin B1, and magnesium were positively correlated with relative telomere length (p-values < 0.05). However, only the intake of magnesium was positively associated with relative telomere length, after applying a linear regression model (β = 0.002; SE = 0.001; p = 0.024). Magnesium deficiency was negatively associated with relative telomere length after adjusting for the same covariates (β = −0.467; SE = 0.176; p = 0.009). To our knowledge, this is the first evidence of a positive relationship between maternal nutrient intake and telomere length of cfDNA. Further efforts are needed for deeply investigating the effect of maternal dietary intakes on telomere length, in order to develop effective public health strategies.
Performance and reproducibility of 13C and 15N hyperpolarization using a cryogen-free DNP polarizer
Authors: Ferrari Arianna , Peters Josh , Anikeeva Mariia , Pravdivtsev Andrey , Ellermann Frowin , Them Kolja , Will Olga , Peschke Eva , Yoshihara Hikari , Jansen Olav , Hövener Jan-Bernd 
Published: July 2022

AbstractThe setup, operational procedures and performance of a cryogen-free device for producing hyperpolarized contrast agents using dissolution dynamic nuclear polarization (dDNP) in a preclinical imaging center is described. The polarization was optimized using the solid-state, DNP-enhanced NMR signal to calibrate the sample position, microwave and NMR frequency and power and flip angle. The polarization of a standard formulation to yield ~ 4 mL, 60 mM 1-13C-pyruvic acid in an aqueous solution was quantified in five experiments to P(13C) = (38 ± 6) % (19 ± 1) s after dissolution. The mono-exponential time constant of the build-up of the solid-state polarization was quantified to (1032 ± 22) s. We achieved a duty cycle of 1.5 h that includes sample loading, monitoring the polarization build-up, dissolution and preparation for the next run. After injection of the contrast agent in vivo, pyruvate, pyruvate hydrate, lactate, and alanine were observed, by measuring metabolite maps. Based on this work sequence, hyperpolarized 15N urea was obtained (P(15N) = (5.6 ± 0.8) % (30 ± 3) s after dissolution).
Phylogeography of Nasutitermes ephratae (Termitidae: Nasutitermitinae) in neotropical region
Authors: de Faria Santos Amanda , Cancello Eliana Marques , Morales Adriana Coletto 
Published: July 2022

AbstractThe neotropical region ranks third in the number of termites and includes five different families. Of these, Termitidae is the most diverse and includes the speciesNasutitermes ephratae, which is widespread in the neotropics. To date, only one study has been published about phylogeography in neotropical termites (N. corniger). Here, we explored the population genetic patterns ofN. ephrataeand also evaluated the phylogeographical processes involved in the evolutionary history of the species. We used the mitochondrial genes 16S rRNA and COII as molecular markers: these were sequenced for 128 samples ofN. ephratae. We estimated the genetic diversity and divergence time as well as the demography and genetic structure. We also performed an ancestral area reconstruction and a haplotype network. The results showed high genetic variability, recent demographic expansion, and strong genetic structure. A dispersal route for the species, that occurred in both directions between South and Central America, was inferred. The results emphasize a temporary separation between the South and Central America populations that affected the origin of the current Central America populations. These populations were formed from different phylogeographic histories.
Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats
Authors: Horta Pedro , Raposeira Helena , Baños Adrián , Ibáñez Carlos , Razgour Orly , Rebelo Hugo , Juste Javier 
Published: July 2022

AbstractCryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.
A novel inactivated virus system (InViS) for a fast and inexpensive assessment of viral disintegration
Authors: Furer Lea A. , Clement Pietro , Herwig Gordon , Rossi René M. , Bhoelan Farien , Amacker Mario , Stegmann Toon , Buerki-Thurnherr Tina , Wick Peter 
Published: July 2022

AbstractThe COVID–19 pandemic has caused considerable interest worldwide in antiviral surfaces, and there has been a dramatic increase in the research and development of innovative material systems to reduce virus transmission in the past few years. The International Organization for Standardization (ISO) norms 18,184 and 21,702 are two standard methods to characterize the antiviral properties of porous and non-porous surfaces. However, during the last years of the pandemic, a need for faster and inexpensive characterization of antiviral material was identified. Therefore, a complementary method based on an Inactivated Virus System (InViS) was developed to facilitate the early-stage development of antiviral technologies and quality surveillance of the production of antiviral materials safely and efficiently. The InViS is loaded with a self-quenched fluorescent dye that produces a measurable increase in fluorescence when the viral envelope disintegrates. In the present work, the sensitivity of InViS to viral disintegration by known antiviral agents is demonstrated and its potential to characterize novel materials and surfaces is explored. Finally, the InViS is used to determine the fate of viral particles within facemasks layers, rendering it an interesting tool to support the development of antiviral surface systems for technical and medical applications.
Exploring the molecular interaction of mebendazole with bovine serum albumin using multi-spectroscopic approaches and molecular docking
Authors: El Gammal Reem N. , Elmansi Heba , El-Emam Ali A. , Belal Fathalla , Hammouda Mohammed E. A. 
Published: July 2022

AbstractThis article presents the binding interaction between mebendazole (MBZ) and bovine serum albumin. The interaction has been studied using different techniques, such as fluorescence quenching spectroscopy, UV–visible spectroscopy, synchronous fluorescence spectroscopy, fourier transform infrared, and fluorescence resonance energy transfer in addition to molecular docking. Results from Stern Volmer equation stated that the quenching for MBZ-BSA binding was static. The fluorescence quenching spectroscopic study was performed at three temperature settings. The binding constant (kq), the number of binding sites (n), thermodynamic parameters (ΔHο, ΔSοand ΔGο), and binding forces were determined. The results exhibited that the interaction was endothermic. It was revealed that intermolecular hydrophobic forces led to the stabilization of the drug-protein system. Using the site marker technique, the binding between MBZ and BSA was found to be located at subdomain IIA (site I). This was furtherly approved using the molecular docking technique with the most stable MBZ configuration. This research may aid in understanding the pharmacokinetics and toxicity of MBZ and give fundamental data for its safe usage to avoid its toxicity.
Impact of joint interactions with humans and social interactions with conspecifics on the risk of zooanthroponotic outbreaks among wildlife populations
Authors: Balasubramaniam Krishna N. , Aiempichitkijkarn Nalina , Kaburu Stefano S. K. , Marty Pascal R. , Beisner Brianne A. , Bliss-Moreau Eliza , Arlet Malgorzata E. , Atwill Edward , McCowan Brenda 
Published: July 2022

AbstractPandemics caused by pathogens that originate in wildlife highlight the importance of understanding the behavioral ecology of disease outbreaks at human–wildlife interfaces. Specifically, the relative effects of human–wildlife and wildlife-wildlife interactions on disease outbreaks among wildlife populations in urban and peri-urban environments remain unclear. We used social network analysis and epidemiological Susceptible-Infected-Recovered models to simulate zooanthroponotic outbreaks, through wild animals’ joint propensities to co-interact with humans, and their social grooming of conspecifics. On 10 groups of macaques (Macacaspp.) in peri-urban environments in Asia, we collected behavioral data using event sampling of human–macaque interactions within the same time and space, and focal sampling of macaques’ social interactions with conspecifics and overall anthropogenic exposure. Model-predicted outbreak sizes were related to structural features of macaques’ networks. For all three species, and for both anthropogenic (co-interactions) and social (grooming) contexts, outbreak sizes were positively correlated to the network centrality of first-infected macaques. Across host species and contexts, the above effects were stronger through macaques’ human co-interaction networks than through their grooming networks, particularly for rhesus and bonnet macaques. Long-tailed macaques appeared to show intraspecific variation in these effects. Our findings suggest that among wildlife in anthropogenically-impacted environments, the structure of their aggregations around anthropogenic factors makes them more vulnerable to zooanthroponotic outbreaks than their social structure. The global features of these networks that influence disease outbreaks, and their underlying socio-ecological covariates, need further investigation. Animals that consistently interact with both humans and their conspecifics are important targets for disease control.
Multimorbidity patterns and hospitalisation occurrence in adults and older adults aged 50 years or over
Authors: Rodrigues Luciana Pereira , Vissoci João Ricardo Nickenig , França Diego Galdino , Caruzzo Nayara Malheiros , Batista Sandro Rogério Rodrigues , de Oliveira Cesar , Nunes Bruno Pereira , Silveira Erika Aparecida 
Published: July 2022

AbstractMultimorbidity is highly prevalent in older adults and can lead to hospitalisation. We investigate the prevalence, associated factors, and multimorbidity pattern associated to hospitalisation, readmission, and length of stay in the population aged 50 years and older. We analysed baseline data (2015–2016) from the ELSI-Brazil cohort, a representative sample of non-institutionalised Brazilians aged ≥ 50 years. In total, 8807 individuals aged ≥ 50 years were included. Poisson regression with robust variance adjusted for confounders was used to verify the associations with hospitalisation. Multiple linear regression was used to analyse the associations with readmission and length of stay. Network analysis was conducted using 19 morbidities and the outcome variables. In 8807 participants, the prevalence of hospitalisation was 10.0% (95% CI 9.1, 11), mean readmissions was 1.55 ± 1.191, and mean length of stay was 6.43 ± 10.46 days. Hospitalisation was positively associated with male gender, not living with a partner, not having ingested alcoholic beverages in the last month, and multimorbidity. For hospital readmission, only multimorbidity ≥ 3 chronic conditions showed a statistically significant association. Regarding the length of stay, the risk was positive for males and negative for living in rural areas. Five disease groups connected to hospitalisation, readmission and length of stay were identified. To conclude, sociodemographic variables, such as gender, age group, and living in urban areas, and multimorbidity increased the risk of hospitalisation, mean number of readmissions, and mean length of stay. Through network analysis, we identified the groups of diseases that increased the risk of hospitalisation, readmissions, and length of stay.
Pupil drift rate indexes groove ratings
Authors: Spiech Connor , Sioros George , Endestad Tor , Danielsen Anne , Laeng Bruno 
Published: July 2022

AbstractGroove, understood as an enjoyable compulsion to move to musical rhythms, typically varies along an inverted U-curve with increasing rhythmic complexity (e.g., syncopation, pickups). Predictive coding accounts posit that moderate complexity drives us to move to reduce sensory prediction errors and model the temporal structure. While musicologists generally distinguish the effects of pickups (anacruses) and syncopations, their difference remains unexplored in groove. We used pupillometry as an index to noradrenergic arousal while subjects listened to and rated drumbeats varying in rhythmic complexity. We replicated the inverted U-shaped relationship between rhythmic complexity and groove and showed this is modulated by musical ability, based on a psychoacoustic beat perception test. The pupil drift rates suggest that groovier rhythms hold attention longer than ones rated less groovy. Moreover, we found complementary effects of syncopations and pickups on groove ratings and pupil size, respectively, discovering a distinct predictive process related to pickups. We suggest that the brain deploys attention to pickups to sharpen subsequent strong beats, augmenting the predictive scaffolding’s focus on beats that reduce syncopations’ prediction errors. This interpretation is in accordance with groove envisioned as an embodied resolution of precision-weighted prediction error.
Cross-cultural differences in early expectations about third party resource distribution
Authors: Meristo Marek , Zeidler Henriette 
Published: July 2022

AbstractResearch using non-verbal looking-time methods suggests that pre-verbal infants are able to detect inequality in third party resource allocations. However, nothing is known about the emergence of this capacity outside a very narrow Western context. We compared 12- to 20-month-old infants (N = 54) from one Western and two non-Western societies. Swedish infants confirmed the pattern from previous Western samples by looking longer at the unequal distribution, suggesting that they expected the resources to be distributed equally. Samburu infants looked longer at the equal distribution, suggesting an expectation of unequal distribution. The Kikuyu infants looked equally at both distributions, and did not show any specific exactions. These results suggest that expectations of equal distributions in third party allocations are affected by experience of cultural variations of distributive norms and social interaction early in development.
A pair of primers facing at the double-strand break site enables to detect NHEJ-mediated indel mutations at a 1-bp resolution
Authors: Ijaz Faryal , Nakazato Ryota , Setou Mitsutoshi , Ikegami Koji 
Published: July 2022

AbstractThe introduction of small insertion/deletion (indel) mutations in the coding region of genes by the site-specific nucleases such as Cas9 allows researchers to obtain frameshift null mutants. Technically simple and costly reasonable genotyping methods are awaited to efficiently screen the frameshift null mutant candidates. Here, we developed a simple genotyping method called DST-PCR (Double-strand break Site-Targeted PCR) using “face-to-face” primers where the 3’ ends of forward and reverse primers face each other at the position between 3-bp and 4-bp upstream of the PAM sequence, which is generally the Cas9-mediated double-strand break site. Generated amplicons are directly subjected to TBE-High-Resolution PAGE, which contains a high concentration of bis-acrylamide, for mutant clones detection with 1-bp resolution. We present actual cases of screening of CRISPR/Cas9-engineered knockout (KO) cells for six genes, where we screen indels to obtain potential KO cell clones utilizing our approach. This method allowed us to detect 1-bp to 2-bp insertion and 1-bp to 4-bp deletion in one or both alleles of mutant cell clones. In addition, this technique also allowed the identification of heterozygous and homozygous biallelic functional KO candidates. Thus, DST-PCR is a simple and fast method to screen KO candidates generated by the CRISPR/Cas9 system before the final selection of clones with sequencing.
Dental anomaly detection using intraoral photos via deep learning
Authors: Ragodos Ronilo , Wang Tong , Padilla Carmencita , Hecht Jacqueline T. , Poletta Fernando A. , Orioli Iêda M. , Buxó Carmen J. , Butali Azeez , Valencia-Ramirez Consuelo , Restrepo Muñeton Claudia , Wehby George L. , Weinberg Seth M. , Marazita Mary L. , Moreno Uribe Lina M. , Howe Brian J. 
Published: July 2022

AbstractChildren with orofacial clefting (OFC) present with a wide range of dental anomalies. Identifying these anomalies is vital to understand their etiology and to discern the complex phenotypic spectrum of OFC. Such anomalies are currently identified using intra-oral exams by dentists, a costly and time-consuming process. We claim that automating the process of anomaly detection using deep neural networks (DNNs) could increase efficiency and provide reliable anomaly detection while potentially increasing the speed of research discovery. This study characterizes the use of` DNNs to identify dental anomalies by training a DNN model using intraoral photographs from the largest international cohort to date of children with nonsyndromic OFC and controls (OFC1). In this project, the intraoral images were submitted to a Convolutional Neural Network model to perform multi-label multi-class classification of 10 dental anomalies. The network predicts whether an individual exhibits any of the 10 anomalies and can do so significantly faster than a human rater can. For all but three anomalies, F1 scores suggest that our model performs competitively at anomaly detection when compared to a dentist with 8 years of clinical experience. In addition, we use saliency maps to provide a post-hoc interpretation for our model’s predictions. This enables dentists to examine and verify our model’s predictions.
Stimulation-related modifications of evolving functional brain networks in unresponsive wakefulness
Authors: Helmstaedter Christoph , Rings Thorsten , Buscher Lara , Janssen Benedikt , Alaeddin Sara , Krause Vanessa , Knecht Stefan , Lehnertz Klaus 
Published: July 2022

AbstractRecent advances in neurophysiological brain network analysis have demonstrated novel potential for diagnosis and prognosis of disorders of consciousness. While most progress has been achieved on the population-sample level, time-economic and easy-to-apply personalized solutions are missing. This prospective controlled study combined EEG recordings, basal stimulation, and daily behavioral assessment as applied routinely during complex early rehabilitation treatment. We investigated global characteristics of EEG-derived evolving functional brain networks during the repeated (3–6 weeks apart) evaluation of brain dynamics at rest as well as during and after multisensory stimulation in ten patients who were diagnosed with an unresponsive wakefulness syndrome (UWS). The age-corrected average clustering coefficient C* allowed to discriminate between individual patients at first (three patients) and second assessment (all patients). Clinically, only two patients changed from UWS to minimally conscious state. Of note, most patients presented with significant changes of C* due to stimulations, along with treatment, and with an increasing temporal distance to injury. These changes tended towards the levels of nine healthy controls. Our approach allowed to monitor both, short-term effects of individual therapy sessions and possibly long-term recovery. Future studies will need to assess its full potential for disease monitoring and control of individualized treatment decisions.