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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 -
Genome Biology and Evolution Apr 2024Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved...
Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts.
Topics: Animals; Fishes; Evolution, Molecular; Conserved Sequence; Phylogeny; Genome; Synteny
PubMed: 38648507
DOI: 10.1093/gbe/evae061 -
Frontiers in Psychology 2024This article concerns two types of word meanings: nonverbal meanings which appear to be associated with neurological representations and verbally-based meanings which...
This article concerns two types of word meanings: nonverbal meanings which appear to be associated with neurological representations and verbally-based meanings which appear to depend in part on other words to construct meanings. Using word use data from Hart and Risley's study of children aged 19 to 36 months, and word meaning knowledge data from Biemiller and Slonim's studies of children between aged 5 to 11, meanings were classified as nonverbal or verbally-based. Biemiller and Slonim used sampled word meanings reported known from grade levels 2 to 12 reported by Dale and O'Rourke in their Living Word Vocabulary. Virtually all meanings used at age 3 or known at age 5 (preschool) were classified nonverbal. By grade two, and even more by grade five, children had added many verbally-defined meanings, although by grade five the majority of the word meanings known were still nonverbal. Evidence for neurological meaning associates are cited. Implications for vocabulary support and instruction at various ages suggest that for children under 6, supporting larger nonverbal vocabularies while after age 6 should prioritize verbally-defined meanings.
PubMed: 38646119
DOI: 10.3389/fpsyg.2024.1280568 -
MedRxiv : the Preprint Server For... Apr 2024Brain-computer interfaces can enable rapid, intuitive communication for people with paralysis by transforming the cortical activity associated with attempted speech into...
Brain-computer interfaces can enable rapid, intuitive communication for people with paralysis by transforming the cortical activity associated with attempted speech into text on a computer screen. Despite recent advances, communication with brain-computer interfaces has been restricted by extensive training data requirements and inaccurate word output. A man in his 40's with ALS with tetraparesis and severe dysarthria (ALSFRS-R = 23) was enrolled into the BrainGate2 clinical trial. He underwent surgical implantation of four microelectrode arrays into his left precentral gyrus, which recorded neural activity from 256 intracortical electrodes. We report a speech neuroprosthesis that decoded his neural activity as he attempted to speak in both prompted and unstructured conversational settings. Decoded words were displayed on a screen, then vocalized using text-to-speech software designed to sound like his pre-ALS voice. On the first day of system use, following 30 minutes of attempted speech training data, the neuroprosthesis achieved 99.6% accuracy with a 50-word vocabulary. On the second day, the size of the possible output vocabulary increased to 125,000 words, and, after 1.4 additional hours of training data, the neuroprosthesis achieved 90.2% accuracy. With further training data, the neuroprosthesis sustained 97.5% accuracy beyond eight months after surgical implantation. The participant has used the neuroprosthesis to communicate in self-paced conversations for over 248 hours. In an individual with ALS and severe dysarthria, an intracortical speech neuroprosthesis reached a level of performance suitable to restore naturalistic communication after a brief training period.
PubMed: 38645254
DOI: 10.1101/2023.12.26.23300110 -
Genome Biology Apr 2024Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility...
Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines have led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.
Topics: Reproducibility of Results; Metadata; Research Design
PubMed: 38641812
DOI: 10.1186/s13059-024-03223-9 -
PloS One 2024The use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient...
BACKGROUND
The use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient outcomes, and guides policy. This secondary data, as found in electronic medical records (EMRs), can be optimised through conversion into a uniform data structure to enable analysis alongside other comparable health metric datasets. This can be achieved with the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), which employs a standardised vocabulary to facilitate systematic analysis across various observational databases. The concept behind the OMOP-CDM is the conversion of data into a common format through the harmonisation of terminologies, vocabularies, and coding schemes within a unique repository. The OMOP model enhances research capacity through the development of shared analytic and prediction techniques; pharmacovigilance for the active surveillance of drug safety; and 'validation' analyses across multiple institutions across Australia, the United States, Europe, and the Asia Pacific. In this research, we aim to investigate the use of the open-source OMOP-CDM in the PATRON primary care data repository.
METHODS
We used standard structured query language (SQL) to construct, extract, transform, and load scripts to convert the data to the OMOP-CDM. The process of mapping distinct free-text terms extracted from various EMRs presented a substantial challenge, as many terms could not be automatically matched to standard vocabularies through direct text comparison. This resulted in a number of terms that required manual assignment. To address this issue, we implemented a strategy where our clinical mappers were instructed to focus only on terms that appeared with sufficient frequency. We established a specific threshold value for each domain, ensuring that more than 95% of all records were linked to an approved vocabulary like SNOMED once appropriate mapping was completed. To assess the data quality of the resultant OMOP dataset we utilised the OHDSI Data Quality Dashboard (DQD) to evaluate the plausibility, conformity, and comprehensiveness of the data in the PATRON repository according to the Kahn framework.
RESULTS
Across three primary care EMR systems we converted data on 2.03 million active patients to version 5.4 of the OMOP common data model. The DQD assessment involved a total of 3,570 individual evaluations. Each evaluation compared the outcome against a predefined threshold. A 'FAIL' occurred when the percentage of non-compliant rows exceeded the specified threshold value. In this assessment of the primary care OMOP database described here, we achieved an overall pass rate of 97%.
CONCLUSION
The OMOP CDM's widespread international use, support, and training provides a well-established pathway for data standardisation in collaborative research. Its compatibility allows the sharing of analysis packages across local and international research groups, which facilitates rapid and reproducible data comparisons. A suite of open-source tools, including the OHDSI Data Quality Dashboard (Version 1.4.1), supports the model. Its simplicity and standards-based approach facilitates adoption and integration into existing data processes.
Topics: Humans; Australia; Biomedical Research; Databases, Factual; Electronic Health Records; Europe; Pharmacovigilance; Primary Health Care
PubMed: 38635655
DOI: 10.1371/journal.pone.0301557 -
Heliyon Apr 2024Rotenone is a toxic chemical found in various plants, including some used as food. Rotenone poisoning can be fatal and there is no antidote. Mechanistically, rotenone...
CONTEXT
Rotenone is a toxic chemical found in various plants, including some used as food. Rotenone poisoning can be fatal and there is no antidote. Mechanistically, rotenone inhibits mitochondrial complex I, leading to reduced ATP production, compensatory glycolytic upregulation and secondary lactate production, and oxidative stress. Our literature review examined acute rotenone poisoning in humans, including exposure scenarios, clinical presentations, and treatments.
METHODS
We searched five databases for relevant literature from database inception through the search date: July 12, 2022, pairing controlled vocabulary and keywords for "rotenone" with terms relating to human exposures and outcomes, such as "ingestion," "exposure," and "poisoning." We included all peer-reviewed reports found using the search terms where the full English text was available. Data abstracted included the number, age, weight, and sex of the exposed person(s), country where exposure happened, exposure scenario, ingestion context, estimated dose, clinical features, whether hospitalization occurred, treatments, and outcomes.
RESULTS
After removing non-qualifying sources from 2,631 publications, we identified 11 case reports describing 18 victims, 15 of whom were hospitalized and five died. Most cases occurred in private quarters where victims unknowingly consumed rotenone-containing plants. Vomiting and metabolic acidosis occurred most commonly. Some patients exhibited impaired cardiopulmonary function. Supportive treatment addressed symptoms and included gastric lavage and/or activated charcoal to remove rotenone from the stomach, vasopressors for hypotension, mechanical ventilation for respiratory insufficiency, and sodium bicarbonate for acidosis. Some patients received N-acetylcysteine to counter oxidative stress.
CONCLUSIONS
Rotenone poisoning, though rare, can be fatal. Exposure prevention is impractical since rotenone is found in some plants used as food or pesticides. Cases may be under-diagnosed because symptoms are non-specific and under-reported in English-language journals since most cases occurred in non-English speaking countries. Treatments are supportive. Exploring antioxidant therapy in animal models of rotenone poisoning may be indicated considering rotenone's mechanism of toxicity.
PubMed: 38633629
DOI: 10.1016/j.heliyon.2024.e28334 -
BMC Public Health Apr 2024This article is a continuation of the Musafir study published in 2020. Following the results of this study, we designed an educational website with Urdu-speaking...
BACKGROUND
This article is a continuation of the Musafir study published in 2020. Following the results of this study, we designed an educational website with Urdu-speaking volunteers, using a participatory approach. This type of approach aimed at bringing out situated knowledge around taboo/sensitive topics such as sexual and mental health, by considering the cultural, religious, economic, family, and social background of young Urdu-speaking men. This approach allowed us to build culturally-appropriate content matching the needs of targeted population. We report here the lessons learned from our approach.
METHODS
Urdu-speaking volunteers were recruited via outreach strategies, for participation in focus groups. Four focus group discussions were conducted on three distinct themes: 1/ Sexual Health Promotion, 2/Hepatitis and sexually transmitted infections, and 3/ Mental Health. The focus groups were recorded, with the written consent of the users. Thematic analysis was conducted after transcription of the focus-group discussion.
RESULTS
We succeeded in mobilizing 4 Pakistani users, aged between 19 and 30 years. The group dynamics was very rich and allowed us to highlight numerous social aspects related to the importance of the group belonging, the family, and others points of view on these topics. Many Urdu vocabulary had to be redefined and revealed the extent of the pre-existing taboo.
CONCLUSIONS
Notwithstanding the extreme difficulty of mobilizing an invisible target population on a sensitive topic such as sexual and mental health, our experience highlights the need to consider the knowledge of the people concerned. The participative approach allowed us to fit the content of our medium to, for instance: the collectivist type of society of the target population; the level of literacy in their mother tongue; and to the embodiment of some taboo in their vocabulary. Although time and energy consuming, our approach seems relevant and could be replicated to other communities.
Topics: Male; Humans; Young Adult; Adult; Mental Health; Sexual Behavior; Qualitative Research; Focus Groups; Sexual Health
PubMed: 38632597
DOI: 10.1186/s12889-024-18479-w -
Genome Research Apr 2024Mitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a...
Mitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a pathogenic variant, variant allele frequency (VAF), must reach a threshold before a biochemical defect occurs, termed the biochemical threshold. Whether the often-cited biochemical threshold of >60% VAF is similar across mtDNA variants and cell types is unclear. In our systematic review, we sought to identify the biochemical threshold of mtDNA variants in relation to VAF by human tissue/cell type. We used controlled vocabulary terms to identify articles measuring oxidative phosphorylation (OXPHOS) complex activities in relation to VAF. We identified 76 eligible publications, describing 69, 12, 16, and 49 cases for complexes I, III, IV, and V, respectively. Few studies evaluated OXPHOS activities in diverse tissue types, likely reflective of clinical access. A number of cases with similar VAFs for the same pathogenic variant had varying degrees of residual activity of the affected complex, alluding to the presence of modifying variants. Tissues and cells with VAFs <60% associated with low complex activities were described, suggesting the possibility of a biochemical threshold of <60%. Using Kendall rank correlation tests, the VAF of the m.8993T > G variant correlated with complex V activity in skeletal muscle (τ = -0.58, = 0.01, n = 13); however, no correlation was observed in fibroblasts ( = 0.7, n = 9). Our systematic review highlights the need to investigate the biochemical threshold over a wider range of VAFs in disease-relevant cell types to better define the biochemical threshold for specific mtDNA variants.
Topics: Humans; DNA, Mitochondrial; Gene Frequency; Genetic Variation; Mitochondria; Mitochondrial Diseases; Oxidative Phosphorylation
PubMed: 38627095
DOI: 10.1101/gr.278200.123 -
Global Health, Science and Practice Apr 2024Community-based health information systems (CBISs) can provide critical insights into how community health systems function, and digitized CBISs may improve the quality... (Review)
Review
BACKGROUND
Community-based health information systems (CBISs) can provide critical insights into how community health systems function, and digitized CBISs may improve the quality of community-level data and facilitate integration and use of CBISs within the broader health system. This scoping review aims to understand how CBISs have been implemented, integrated, and used to support community health outcomes in low- and middle-income countries (LMICs).
METHODS
Both peer-reviewed and gray literature were included; relevant articles were identified using key terms and controlled vocabulary related to community/primary health care, health information systems, digital health, and LMICs. A total of 11,611 total records were identified from 5 databases and the gray literature. After deduplication, 6,985 peer-reviewed/gray literature were screened, and 95 articles/reports were included, reporting on 105 CBIS implementations across 38 countries.
RESULTS
Findings show that 55% of CBISs included some level of digitization, with just 28% being fully digitized (for data collection and reporting). Data flow from the community level into the health system varied, with digitized CBISs more likely to reach national-level integration. National-level integration was primarily seen among vertical CBISs. Data quality challenges were present in both paper-based and digitized CBISs, exacerbated by fragmentation of the community health landscape with often parallel reporting systems. CBIS data use was constrained to mostly vertical and digitized (partially or fully) CBISs at national/subnational levels.
CONCLUSION
Digitization can play a pivotal role in strengthening CBIS use, but findings demonstrate that CBISs are only as effective as the community health systems they are embedded within. Community-level data are often not being integrated into national/subnational health information systems, undermining the ability to understand what the community health needs are. Furthermore, stronger investments within community health systems need to be in place broadly to reduce fragmentation and provide stronger infrastructural and systemic support to the community health workforce.
Topics: Humans; Primary Health Care; Community Health Services; Health Information Systems; Developing Countries
PubMed: 38626945
DOI: 10.9745/GHSP-D-23-00429