-
Frontiers in Genetics 2024DNA methylation is a critical epigenetic modification involving the addition of a methyl group to the DNA molecule, playing a key role in regulating gene expression...
DNA methylation is a critical epigenetic modification involving the addition of a methyl group to the DNA molecule, playing a key role in regulating gene expression without changing the DNA sequence. The main difficulty in identifying DNA methylation sites lies in the subtle and complex nature of methylation patterns, which may vary across different tissues, developmental stages, and environmental conditions. Traditional methods for methylation site identification, such as bisulfite sequencing, are typically labor-intensive, costly, and require large amounts of DNA, hindering high-throughput analysis. Moreover, these methods may not always provide the resolution needed to detect methylation at specific sites, especially in genomic regions that are rich in repetitive sequences or have low levels of methylation. Furthermore, current deep learning approaches generally lack sufficient accuracy. This study introduces the iDNA-OpenPrompt model, leveraging the novel OpenPrompt learning framework. The model combines a prompt template, prompt verbalizer, and Pre-trained Language Model (PLM) to construct the prompt-learning framework for DNA methylation sequences. Moreover, a DNA vocabulary library, BERT tokenizer, and specific label words are also introduced into the model to enable accurate identification of DNA methylation sites. An extensive analysis is conducted to evaluate the predictive, reliability, and consistency capabilities of the iDNA-OpenPrompt model. The experimental outcomes, covering 17 benchmark datasets that include various species and three DNA methylation modifications (4mC, 5hmC, 6mA), consistently indicate that our model surpasses outstanding performance and robustness approaches.
PubMed: 38689652
DOI: 10.3389/fgene.2024.1377285 -
European Thyroid Journal Jun 2024Maternal thyroid autoimmunity and thyroid function in early pregnancy may impact fetal neurodevelopment. We aimed to investigate how thyroid autoimmunity and thyroid...
OBJECTIVE
Maternal thyroid autoimmunity and thyroid function in early pregnancy may impact fetal neurodevelopment. We aimed to investigate how thyroid autoimmunity and thyroid function in early pregnancy were associated with language acquisition in offspring at 12-36 months of age.
METHODS
This study was embedded in the prospective Odense child cohort. Mother-child dyads were excluded in case of maternal intake of thyroid medication during pregnancy. The parents completed MacArthur-Bates Communicative Development Inventories (MB-CDI) every third month to assess their offspring's productive vocabulary. All completed reports for each child were included in the analyses. Logistic growth curve models evaluated associations between MB-CDI scores and levels of maternal thyroid peroxidase antibodies (TPOAb), free thyroxine (FT4), and thyrotropin, respectively, measured in early pregnancy (median gestational week 12). All models were stratified by offspring sex and adjusted for maternal age, education, pre-pregnancy body mass index, parity, breastfeeding, and offspring age.
RESULTS
The study included 735 mother-child dyads. Children born to mothers with TPOAb ≥11 kIU/L, opposed to TPOAb <11 kIU/L, had a lower probability of producing words at age 18-36 months for girls (OR = 0.78, P < 0.001) and 33-36 months for boys (OR = 0.83, P < 0.001). The probability of producing words was higher in girls at 30-36 months of age with low-normal maternal FT4 vs high-normal FT4 (OR = 0.60, P < 0.001), and a similar trend was seen in boys. Results were ambiguous for thyrotropin.
CONCLUSION
In women without known thyroid disease, TPOAb positivity in early pregnancy was negatively associated with productive vocabulary acquisition in girls and boys. This association was not mediated by a decreased thyroid function, as low-normal maternal FT4, unexpectedly, indicated better vocabulary acquisition. Our results support that maternal thyroid autoimmunity per se may affect fetal neurodevelopment.
Topics: Humans; Female; Pregnancy; Male; Infant; Child, Preschool; Prospective Studies; Adult; Autoimmunity; Iodide Peroxidase; Autoantibodies; Language Development; Thyroxine; Thyrotropin; Prenatal Exposure Delayed Effects; Thyroid Gland; Pregnancy Complications
PubMed: 38688317
DOI: 10.1530/ETJ-23-0233 -
Frontiers in Psychiatry 2024Alexithymia is common among patients with generalized anxiety disorder (GAD) and may negatively affect the efficacy of treatment. This case report described a sole...
Alexithymia is common among patients with generalized anxiety disorder (GAD) and may negatively affect the efficacy of treatment. This case report described a sole short-term psychotherapy focusing on alexithymia for a GAD patient. The intervention extends over 3 weekly 50-minute sessions and incorporates components of: (a) understanding the basic categories of emotions and the importance of processing them consciously and building one's own vocabulary of emotions; (b) developing skills in identifying and labeling emotions and learning to register both positive and negative emotions in daily life; (c) observing and interpreting emotion-related body sensations and learning to get in touch with, be empathetic to, and take care of one's own inner feelings in daily life. The Hamilton Rating Scale for Depression (HRSD), Hamilton Anxiety Rating Scale (HAMA), and Toronto Alexithymia Scale (TAS) were used to evaluate depression, anxiety, and alexithymia before and after the sessions. The results suggested that the treatment was not only effective in reducing alexithymia helping the patient to clarify, identify and describe her feelings, but also effective in reducing anxiety and depression.
PubMed: 38686127
DOI: 10.3389/fpsyt.2024.1342398 -
Journal of Experimental Child Psychology Aug 2024Children's emergent literacy skills are essential for the development of later literacy abilities and school success. However, children with migration background often...
Children's emergent literacy skills are essential for the development of later literacy abilities and school success. However, children with migration background often show poorer language skills in the majority language and are at a greater risk of developing literacy deficits. In addition, there is evidence for the predictive role of emergent literacy skills in reading comprehension, but there has been relatively little research concerning the association between preschool emergent literacy skills and word reading and spelling in Germany, especially for children with migration background. This study examines the associations of emergent literacy skills (vocabulary, phonological awareness [PA], letter knowledge, and rapid naming) with word reading and spelling from kindergarten to the end of Grade 2 and evaluates the role of migration background (i.e., use of the majority or minority language at home) in these associations. Data from 187 preschool children were obtained before school entry (M = 63.58 months, SD = 4.45). The results show that vocabulary and letter knowledge were strong predictors of word reading, whereas letter knowledge and PA were significant predictors of spelling. Furthermore, children's migration background was negatively associated with preschool vocabulary and PA. For children with migration background, vocabulary was a significant predictor of word reading, whereas letter knowledge was the best predictor of word reading for children without migration background. The results reflect the complexity of language development and the relevance of emergent literacy skills as predictors for word reading and spelling. Specific interventions should be developed to promote children's literacy abilities.
Topics: Humans; Germany; Reading; Male; Literacy; Female; Child, Preschool; Child; Vocabulary; Phonetics; Comprehension
PubMed: 38678807
DOI: 10.1016/j.jecp.2024.105927 -
Scientific Reports Apr 2024Brain-computer interfaces (BCIs) that reconstruct and synthesize speech using brain activity recorded with intracranial electrodes may pave the way toward novel...
Brain-computer interfaces (BCIs) that reconstruct and synthesize speech using brain activity recorded with intracranial electrodes may pave the way toward novel communication interfaces for people who have lost their ability to speak, or who are at high risk of losing this ability, due to neurological disorders. Here, we report online synthesis of intelligible words using a chronically implanted brain-computer interface (BCI) in a man with impaired articulation due to ALS, participating in a clinical trial (ClinicalTrials.gov, NCT03567213) exploring different strategies for BCI communication. The 3-stage approach reported here relies on recurrent neural networks to identify, decode and synthesize speech from electrocorticographic (ECoG) signals acquired across motor, premotor and somatosensory cortices. We demonstrate a reliable BCI that synthesizes commands freely chosen and spoken by the participant from a vocabulary of 6 keywords previously used for decoding commands to control a communication board. Evaluation of the intelligibility of the synthesized speech indicates that 80% of the words can be correctly recognized by human listeners. Our results show that a speech-impaired individual with ALS can use a chronically implanted BCI to reliably produce synthesized words while preserving the participant's voice profile, and provide further evidence for the stability of ECoG for speech-based BCIs.
Topics: Humans; Brain-Computer Interfaces; Amyotrophic Lateral Sclerosis; Male; Speech; Middle Aged; Electrodes, Implanted; Electrocorticography
PubMed: 38671062
DOI: 10.1038/s41598-024-60277-2 -
Nutricion Hospitalaria Apr 2024The objective of this review is to study the relationship between food insecurity (FI) and malnutrition in schoolchildren from low-and middle-income countries (LMIC)....
The objective of this review is to study the relationship between food insecurity (FI) and malnutrition in schoolchildren from low-and middle-income countries (LMIC). The review was conducted using the databases PubMed, MEDLINE, CENTRAL, LILACS and SCiELO during the months of March to April 2022 without language or publication date restrictions. The search strategy consisted of combinations of text words and controlled vocabulary (MeSH terms and DeCS) related to "schoolchildren", "low- and middle-income countries" and "food insecurity". Fifteen studies were included in this review. Studies assessing FI and undernutrition in LMIC schoolchildren have indicated that FI is associated with lower height-for-age and higher prevalence of undernutrition overall. Only two studies identified a positive risk association between FI and overweight and obesity, the remaining studies suggested that schoolchildren with FI have a lower risk of overweight and obesity than those without FI. The review suggests a link between FI and undernutrition in schoolchildren from LMIC, with controversial results on overweight and obesity. Comprehensive public health policies should consider contextual and population-specific factors in addressing FI's impact on nutritional status.
PubMed: 38666331
DOI: 10.20960/nh.04847 -
Data in Brief Jun 2024There is a growing interest in milk oligosaccharides (MOs) because of their numerous benefits for newborns' and long-term health. A large number of MO structures have...
There is a growing interest in milk oligosaccharides (MOs) because of their numerous benefits for newborns' and long-term health. A large number of MO structures have been identified in mammalian milk. Mostly described in human milk, the oligosaccharide richness, although less broad, has also been reported for a wide range of mammalian species. The structure of MOs is particularly difficult to report as it results from the combination of 5 monosaccharides linked by various glycosidic bonds forming structurally diverse and complex matrices of linear and branched oligosaccharides. Exploring the literature and extracting relevant information on MO diversity within or across species appears promising to elucidate structure-function role of MOs. Currently, given the complexity of these molecules, the main issues in exploring literature to extract relevant information on MO diversity within or across species relate to the heterogeneity in the way authors refer to these molecules. Herein, we provide a thesaurus (MilkOligoThesaurus) including the names and synonyms of MOs collected from key selected articles on mammalian milk analyses. MilkOligoThesaurus gathers the names of the MOs with a complete description of their monosaccharide composition and structures. When available, each unique MO molecule is linked to its ID from the NCBI PubChem and ChEBI databases. MilkOligoThesaurus is provided in a tabular format. It gathers 245 unique oligosaccharide structures described by 22 features (columns) including the name of the molecule, its abbreviation, the chemical database IDs if available, the monosaccharide composition, chemical information (molecular formula, monoisotopic mass), synonyms, its formula in condensed form, and in abbreviated condensed form, the abbreviated systematic name, the systematic name, the isomer group, and scientific article sources. MilkOligoThesaurus is also provided in the SKOS (Simple Knowledge Organization System) format. This thesaurus is a valuable resource gathering MO naming variations that are not found elsewhere for (i) Text and Data Mining to enable automatic annotation and rapid extraction of milk oligosaccharide data from scientific papers; (ii) biology researchers aiming to search for or decipher the structure of milk oligosaccharides based on any of their names, abbreviations or monosaccharide compositions and linkages.
PubMed: 38665156
DOI: 10.1016/j.dib.2024.110404 -
PloS One 2024In recent years, with the trend of open science, there have been many efforts to share research data on the internet. To promote research data sharing, data curation is...
In recent years, with the trend of open science, there have been many efforts to share research data on the internet. To promote research data sharing, data curation is essential to make the data interpretable and reusable. In research fields such as life sciences, earth sciences, and social sciences, tasks and procedures have been already developed to implement efficient data curation to meet the needs and customs of individual research fields. However, not only data sharing within research fields but also interdisciplinary data sharing is required to promote open science. For this purpose, knowledge of data curation across the research fields is surveyed, analyzed, and organized as an ontology in this paper. As the survey, existing vocabularies and procedures are collected and compared as well as interviews with the data curators in research institutes in different fields are conducted to clarify commonalities and differences in data curation across the research fields. It turned out that the granularity of tasks and procedures that constitute the building blocks of data curation is not formalized. Without a method to overcome this gap, it will be challenging to promote interdisciplinary reuse of research data. Based on the analysis above, the ontology for the data curation process is proposed to describe data curation processes in different fields universally. It is described by OWL and shown as valid and consistent from the logical viewpoint. The ontology successfully represents data curation activities as the processes in the different fields acquired by the interviews. It is also helpful to identify the functions of the systems to support the data curation process. This study contributes to building a knowledge framework for an interdisciplinary understanding of data curation activities in different fields.
Topics: Data Curation; Information Dissemination; Humans; Knowledge; Internet
PubMed: 38662657
DOI: 10.1371/journal.pone.0301772 -
ELife Apr 2024We are unresponsive during slow-wave sleep but continue monitoring external events for survival. Our brain wakens us when danger is imminent. If events are...
We are unresponsive during slow-wave sleep but continue monitoring external events for survival. Our brain wakens us when danger is imminent. If events are non-threatening, our brain might store them for later consideration to improve decision-making. To test this hypothesis, we examined whether novel vocabulary consisting of simultaneously played pseudowords and translation words are encoded/stored during sleep, and which neural-electrical events facilitate encoding/storage. An algorithm for brain-state-dependent stimulation selectively targeted word pairs to slow-wave peaks or troughs. Retrieval tests were given 12 and 36 hr later. These tests required decisions regarding the semantic category of previously sleep-played pseudowords. The sleep-played vocabulary influenced awake decision-making 36 hr later, if targeted to troughs. The words' linguistic processing raised neural complexity. The words' semantic-associative encoding was supported by increased theta power during the ensuing peak. Fast-spindle power ramped up during a second peak likely aiding consolidation. Hence, new vocabulary played during slow-wave sleep was stored and influenced decision-making days later.
Topics: Humans; Sleep, Slow-Wave; Male; Female; Memory, Long-Term; Adult; Young Adult; Brain; Decision Making; Vocabulary; Electroencephalography
PubMed: 38661727
DOI: 10.7554/eLife.89601 -
Heliyon Apr 2024This study investigated the relationship between the EFL teachers' beliefs about oral. corrective feedback (OCF) and their actual teaching practices in the context of....
This study investigated the relationship between the EFL teachers' beliefs about oral. corrective feedback (OCF) and their actual teaching practices in the context of. synchronous computer-mediated communication (SCMC). It aimed to understand the. extent of in/consistency between the teachers' OCF practices and beliefs. regarding the significance of OCF, types of OCF strategies and the types of errors. receiving OCF.Data were collected through two instruments: observations for the. purpose of exploring the teachers' actual OCF practices and a questionnaire to. uncover OCF beliefs.It was found that the teachers expressed strong beliefs. about their awareness of the significance of OCF, which, however, was not. reflected in the frequency of OCF provision. The results also indicated that recasts. were the most frequently employed form of feedback, which is in line with the overall. preferences reported by the teachers in the questionnaire. Additionally, the teachers considered. pronunciation errors the most significant target of OCF. Nevertheless, vocabulary errors had a substantially higher frequency of corrections. It was also noted that the. teachers stated to adapt their OCF provision in SCMC contexts compared to F2F. classroom settings. The observed in/consistencies were discussed considering the. impact of various belief systems on classroom behaviors and several contextual factors.
PubMed: 38660293
DOI: 10.1016/j.heliyon.2024.e29507