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1.
Article in English | MEDLINE | ID: mdl-39035636

ABSTRACT

Objectives: Although color information is important in gastrointestinal endoscopy, there are limited studies on how endoscopic images are viewed by people with color vision deficiency. We aimed to investigate the differences in the visibility of blood vessels during endoscopic submucosal dissection (ESD) among people with different color vision characteristics and to examine the effect of red dichromatic imaging (RDI) on blood vessel visibility. Methods: Seventy-seven pairs of endoscopic images of white light imaging (WLI) and RDI of the same site were obtained during colorectal ESD. The original images were set as type C (WLI-C and RDI-C), a common color vision. These images were computationally converted to simulate images perceived by people with color vision deficiency protanope (Type P) or deutanope (Type D) and denoted as WLI-P and RDI-P or WLI-D and RDI-D. Blood vessels and background submucosa that needed to be identified during ESD were selected in each image, and the color differences between these two objects were measured using the color difference (ΔE 00) to assess the visibility of blood vessels. Results: ΔE 00 between a blood vessel and the submucosa was greater under RDI (RDI-C/P/D: 24.05 ± 0.64/22.85 ± 0.66/22.61 ± 0.64) than under WLI (WLI-C/P/D: 22.26 ± 0.60/5.19 ± 0.30/8.62 ± 0.42), regardless of color vision characteristics. This improvement was more pronounced in Type P and Type D and approached Type C in RDI. Conclusions: Color vision characteristics affect the visibility of blood vessels during ESD, and RDI improves blood vessel visibility regardless of color vision characteristics.

2.
Siglo cero (Madr.) ; 54(4): 11-27, oct.-dic. 2024. tab, graf
Article in Spanish | IBECS | ID: ibc-EMG-556

ABSTRACT

La formación docente es esencial dentro del proceso de educación inclusiva permitiendo responder a la diversidad de los estudiantes a partir de estrategias que promuevan su aprendizaje y participación. Este estudio analiza la formación en inclusión de 253 docentes de instituciones públicas mediante el Cuestionario de Valoración Docente de la Inclusión Educativa (CEFI-R). Los resultados indican niveles bajos de formación en las dimensiones concepciones, apoyos y metodologías. Lo que sugiere que no existe una preparación integral del profesorado para la inclusión y los planes de formación deben abordar desde aspectos conceptuales hasta la implementación de ajustes en el aula. (AU)


Teacher training is essential within the inclusive education process, allowing students to respond to diversity through strategies that promote their learning and participation. This study analyzes the inclusion training of 253 teachers in public institutions, through the Cuestionario de Valoración Docente de la Inclusión Educativa (CEFI-R). The results indicate low levels of training in the conceptual dimensions, supports and methodologies. This suggests that there is no comprehensive preparation of teachers for inclusion and training plans should address conceptual aspects to the implementation of adjustments in the classroom. (AU)


Subject(s)
Humans , Teacher Training/statistics & numerical data , Cross-Sectional Studies
3.
Siglo cero (Madr.) ; 54(4): 11-27, oct.-dic. 2024. tab, graf
Article in Spanish | IBECS | ID: ibc-229226

ABSTRACT

La formación docente es esencial dentro del proceso de educación inclusiva permitiendo responder a la diversidad de los estudiantes a partir de estrategias que promuevan su aprendizaje y participación. Este estudio analiza la formación en inclusión de 253 docentes de instituciones públicas mediante el Cuestionario de Valoración Docente de la Inclusión Educativa (CEFI-R). Los resultados indican niveles bajos de formación en las dimensiones concepciones, apoyos y metodologías. Lo que sugiere que no existe una preparación integral del profesorado para la inclusión y los planes de formación deben abordar desde aspectos conceptuales hasta la implementación de ajustes en el aula. (AU)


Teacher training is essential within the inclusive education process, allowing students to respond to diversity through strategies that promote their learning and participation. This study analyzes the inclusion training of 253 teachers in public institutions, through the Cuestionario de Valoración Docente de la Inclusión Educativa (CEFI-R). The results indicate low levels of training in the conceptual dimensions, supports and methodologies. This suggests that there is no comprehensive preparation of teachers for inclusion and training plans should address conceptual aspects to the implementation of adjustments in the classroom. (AU)


Subject(s)
Humans , Teacher Training/statistics & numerical data , Cross-Sectional Studies
4.
Environ Monit Assess ; 196(10): 916, 2024 Sep 10.
Article in English | MEDLINE | ID: mdl-39254906

ABSTRACT

Soil and water characteristics in micro basins with different land uses/land cover (LULC) can influence riparian vegetation diversity, stream water quality, and benthic diatom diversity. We analyzed 18 streams in the upper part of the La Antigua River basin, México, surrounded by cloud forests, livestock pastures, and coffee plantations. Concentrations of P, C, and N were elevated in the humus of forested streams compared to other land uses. In contrast, cations, ammonium, and total suspended solids (TSS) of water streams were higher in pastures and coffee plantations. These results indicate that LULC affects stream chemistry differently across land uses. Vegetation richness was highest (86-133 spp.) in forest streams and lowest in pastures (46-102), whereas pasture streams had the greatest richness of diatoms (9-24), likely due to higher light and temperatures. Some soil and water characteristics correlated with both true diversity and taxonomic diversity; soil carbon exchange capacity (CEC) correlated with vegetation diversity (r = 0.60), while water temperature correlated negatively (r = - 0.68). Diatom diversity was related to soil aluminum (r = - 0.59), magnesium (r = 0.57), water phosphorus (r = 0.88), and chlorophyll (r = 0.75). These findings suggest that land use affects riparian vegetation, while physical and chemical changes influence diatom diversity in stream water and soil. The lack of correlation between vegetation and diatom diversity indicates that one cannot predict the other. This research is an essential first step in understanding how land use changes impact vegetation and diatom diversity in mountain landscapes, providing valuable insights for environmental monitoring and conservation efforts in tropical cloud forests.


Subject(s)
Biodiversity , Diatoms , Environmental Monitoring , Forests , Soil , Mexico , Soil/chemistry , Rivers/chemistry , Plants , Phosphorus/analysis
5.
Cult Health Sex ; : 1-16, 2024 Sep 04.
Article in English | MEDLINE | ID: mdl-39228323

ABSTRACT

As Australia considers legislative reform regarding the rights of religious schools to discriminate against LGBT students and staff, claims are often made that religious parents or those enrolling children in religious schools do not affirm diversity of sexuality or gender. Using a national dataset of parents (n = 2418), attitudes towards sexual orientation, gender diversity, homophobia and transphobia were examined. Across all religiosities, school sectors and attitudinal statements, significant majorities of parents reported positive attitudes (62.7%-93.5%). Only small minorities expressly reported negative attitudes (1.6%-20.2%). Pairwise religiosity comparisons between parents with children only at a secular school, versus any religious school, revealed few differences. Amongst Catholic parents, those with children at Catholic schools and those with children only at secular schools, held similar attitudes towards LGBT issues and a majority held favourable attitudes, suggesting most Catholic parents who enrol their children in Catholic schools do so despite or in ignorance of Catholic doctrine. Findings suggest a significant majority of parents sending children to religious schools hold supportive attitudes towards diverse sexual orientations, gender diversity, and actions to address homophobia and transphobia. This empirical evidence contradicts religious schools' calls for the rights to discriminate against LGBT persons based on parental values and attitudes.

6.
J Homosex ; : 1-21, 2024 Sep 04.
Article in English | MEDLINE | ID: mdl-39230396

ABSTRACT

This study evaluated the prevalence and associated factors of depression and generalized anxiety among LGBTQ+ in five medical schools in Thailand. The Patient Health Questionnaire-9 (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7) were used to assess major depressive disorder (MDD) and generalized anxiety disorder (GAD), respectively, and multivariable logistic regression was employed to identify associated factors. Of 1,322 students, 412 (31.16%) identified as LGBTQ+. The prevalence for MDD and GAD among LGBTQ+ students were 32.77% and 17.23%, respectively. Significant associated factors for both MDD and GAD were a history of psychiatric illness (AOR for MDD = 2.32, p = .020; AOR for GAD = 3.67, p < .001), educational problems (AOR for MDD = 6.62, p < .001; AOR for GAD = 5.12, p < .001), and dissatisfaction with gender identity or sexual orientation (AOR for MDD = 1.92, p = .019; AOR for GAD = 2.47, p = .005). Additional factors associated with MDD were preclinical years (AOR = 2.30, p = .023), financial struggles (AOR = 2.05, p = .021), and inadequate peer support (AOR = 2.57, p = .044). In conclusion, nearly one-third and one-fifth of Thai LGBTQ+ medical students suffer from MDD and GAD, respectively. Our findings suggest that Thai medical schools should promote LGBTQ+ inclusivity to enhance students' identity satisfaction. Peer support groups should be encouraged, especially for preclinical LGBTQ+ students who face educational and financial challenges.

7.
Ecol Evol ; 14(9): e70199, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39219573

ABSTRACT

Hybrid speciation plays an important role in species diversification. The establishment of reproductive isolation is crucial for hybrid speciation, and the identification of diverse types of hybrids, particularly homoploid hybrid species, contributes to a comprehensive understanding of this process. Reaumuria songarica is a constructive shrub widespread in arid Central Asia. Previous studies have inferred that the R. songarica populations in the Gurbantunggut Desert (GuD) originated from homoploid hybridizations between its eastern and western lineages and may have evolved into an incipient species. To further elucidate the genetic composition of different hybrid populations and to determine the species boundary of this hybrid lineage, we investigated the overall phylogeographic structure of R. songarica based on variation patterns of five cpDNA and one nrITS sequences across 32 populations. Phylogenetic analyses demonstrated that within the GuD lineage, the Wuerhe population evolved directly from ancestral lineages, whereas the others originated from hybridizations between the eastern and western lineages. PCoA and genetic barrier analysis supported the subdivision of the GuD lineage into the southern (GuD-S) and northern (GuD-N) groups. Populations in the GuD-S group had a consistent genetic composition and the same ancestral female parent, indicating that they belonged to a homoploid hybrid lineage. However, the GuD-N group experienced genetic admixture of the eastern and western lineages on nrITS and cpDNA, with some populations inferred to be allopolyploid based on ploidy data. Based on cpDNA haplotypes, BEAST analyses showed that the GuD-S and GuD-N groups originated after 0.5 Ma. Our results suggest that multiple expansions and contractions of GuD, driven by Quaternary climatic oscillations and the Kunlun-Yellow River tectonic movement, are important causes of the complex origins of R. songarica populations in northern Xinjiang. This study highlights the complex origins of the Junggar Basin flora and the underappreciated role of hybridization in increasing its species diversity.

8.
Ecol Evol ; 14(9): e70206, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39219572

ABSTRACT

Most plant phylogeographic studies in China have focused on the importance of genetic divergence and where should the shelter be located. Little attention has been paid to range expansion and recolonization routes in this region. In this study, two cpDNA fragments (psbK-psbI and trnL-F), two pairs of nuclear gene sequences (ITS and ETS), and nine pairs of SSR molecular markers were used, combined with Bayesian Skyline Plot method, gene barrier analysis, and species distribution models to explore the phylogeographical pattern, potential expansion routes and population dynamic history of Pinellia ternata from 22 population. The results showed that phylogeograhical pattern and genetic structure for P. ternata are effected by environmental heterogeneity and climate fluctuation, and it can be divided into two groups (Southwest group, Central and Eastern group) and thus there are at least two glacial refugia in China. Three expanding routes within groups were explored to contribute to the phylogeogrephic pattern of P. ternata based on the geographical distribution and network analysis of haplotypes. In a word, our study reveals repeated range expansions and inter/postglacial recolonization routes on the fragmented distribution pattern in China and resolves the refugia distributing in China and has also certain reference value for the protection of the medicinal plant P. ternata.

9.
Front Plant Sci ; 15: 1428364, 2024.
Article in English | MEDLINE | ID: mdl-39220013

ABSTRACT

Luculia yunnanensis is a vulnerable species endemic to Yunnan Province, Southwestern China, which has high ornamental value. Its wild population has not been fully protected and utilized for a long time, which is not conducive to the long-term stable development of this species. Genetic diversity assessment is the basis and prerequisite for the conservation of rare species. In this study, 21 phenotypic traits and 17 highly polymorphic EST-SSR markers were used to analyze the genetic diversity and genetic structure of 164 individuals from six L. yunnanensis populations. The coefficient of variation of 21 phenotypic traits ranged from 11.76% to 52.58% (mean=21.72%), and the coefficient of variation of 18 traits was less than 30%. The average values of Ne, I, Ho and He were 1.710, 0.619, 0.384, and 0.352, respectively. The genetic diversity of LLO (Ho = 0.476 and He = 0.426) and LCM (Ho = 0.424 and He = 0.381) populations in Lushui County was highest. The GDX populations (Ho = 0.335 and He = 0.269) isolated by Gaoligong Mountain had the lowest genetic diversity. The AMOVA results showed that 13.04% of the genetic variation was among populations and 86.96% was within populations. The average phenotypic differentiation coefficient of phenotypic traits among populations was 18.69%. The results of phenotypic and genetic variation analysis were consistent, indicating that the most of variation exists within population. Genetic structure, UPGMA clustering and PCA analysis results showed that the populations of L. yunnanensis had obvious geographical divisions, and the populations distributed in the southern region and distributed in the northern region of the Nujiang River clustered into one group respectively. Combining the results of phenotypic and molecular markers, we recommend that give priority to the protection of LLO, LCM and GDX population, in order to ensure the sustainable utilization of L. yunnanensis germplasm resources.

10.
MethodsX ; 13: 102875, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39221015

ABSTRACT

Enteromonas hominis, a human intestinal protozoan parasite of the diplomonad group, has been overlooked because of its commensal features; therefore, molecular studies on this parasite are limited. To address this gap, we designed a molecular screening protocol using polymerase chain reaction (PCR) and DNA sequencing targeting the 18S small subunit ribosomal RNA gene and applied this screening method to the molecular epidemiological analysis of Enteromonas spp. in humans and various livestock. We validated our methodology using stool samples collected from 215 humans and 270 animal hosts (buffaloes, pigs, dogs, goats, horses, rodents, chickens, and ducks) during an annual epidemiological investigation conducted from 2013 to 2016 on Sumba Island, Indonesia. The overall prevalences of Enteromonas spp. were 33.9 % (n = 73/215) in humans and 25.2 % (n = 68/270) in mammals and avians. The positive predictive value of this PCR method for Enteromonas spp., as evaluated through sequencing, was 90.1 % in human samples and 58.1 % in non-human samples (particularly low, 11.4 % in rodents). Although the specificity of the PCR approach may not be perfect, in combination with DNA sequencing, it was effective in detecting and identifying a partial sequence (1458 bp) of the target gene region in Enteromonas species.

11.
Cureus ; 16(8): e66028, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39221340

ABSTRACT

BACKGROUND AND OBJECTIVES:  Addressing the issues of workplace advancement, resilience, and retention within medicine is crucial for creating a culture of equity, respect, and inclusivity especially towards women and nonbinary (WNB) providers including advanced practice providers (APPs), most notably those from marginalized groups. This also directly impacts healthcare quality, patient outcomes, and overall patient and employee satisfaction. The purpose of this study was to amplify the voices on challenges faced by WNB providers within a pediatric academic healthcare organization, to rank workplace interventions addressing advancement, resilience, and retention highlighting urgency towards addressing these issues, and, lastly, to provide suggestions on how to improve inclusivity. METHODS:  Participants were self-identified WNB providers employed by a pediatric healthcare organization and its affiliated medical university. An eligibility screener was completed by 150 qualified respondents, and 40 WNBs actually participated in study interviews. Interviews were conducted using a semi-structured interview guide to rank interventions targeted at improving equity, with time allotted for interviewees to discuss their personal lives and how individual circumstances impacted their professional experiences. RESULTS:  WNB providers called for efficient workflows and reducing uncompensated job demands. Support for family responsibilities, flexible financial/compensation models, and improved job resources all were endorsed similarly. Participants ranked direct supervisor and leader support substantially lower than other interventions.  Conclusions: Career mentorship and academic support for WNB individuals are recognized interventions for advancement and retention but were not ranked as top priorities. Respondents focused on personal supports as they relate to family, job resources, and flexible compensation models. Future studies should focus on implementing realistic expectations and structures that support whole lives including professional ambitions, time with family, personal pursuits, and self-care.

12.
Can Assoc Radiol J ; : 8465371241275204, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-39219175

ABSTRACT

Background: The importance of mentorship in medicine is well-established. Access to mentors is pivotal in enhancing career opportunities and networking, increasing research productivity, and overall wellness and resilience at all career stages. Our study aims to assess the current status of radiology mentorship programs for Canadian medical students and radiology residents. Methods: We distributed an anonymous survey to Canadian radiology program directors in December 2022. The questions pertained to the existing mentorship programs' specific goals, structure, and success. Our null hypothesis was that medical students and residents have similar mentorship opportunities. Results: We have received 12 responses (a response rate of 12/16 = 75%), 9 of which had formal mentorship programs and 3 (25%) did not. Comparing the mentorship program for medical students and residents yielded a P-value = .11 > .05. This result does not reject our null hypothesis, indicating there is no significant difference between these 2 groups. Using qualitative analysis, we categorized the responses into 4 main themes: mentorship programs' goals, structures, evaluation methods, and their results. Conclusion: Although our result did not reach statistical significance (P-value = .11 > .05), the observed trend shows that one third of Canadian medical schools do not offer a radiology mentorship program for medical students, highlighting a potentially significant opportunity for improvement. Qualitative analysis shows that despite various methods for assigning mentees to mentors, developing formalized yet flexible mentorship models that allow students and residents to self-select their mentors might be more beneficial than randomly assigning mentors to them.

14.
J Environ Manage ; 370: 122428, 2024 Sep 10.
Article in English | MEDLINE | ID: mdl-39260281

ABSTRACT

Soil microbial diversity is crucial for regulating biogeochemical cycles, including soil carbon (C) dynamics and nutrient cycling. However, how climate, plants, and soil properties influence the microbiome in forests remains unclear, especially at the continental scale, hindering us to better understand forest C-climate change feedback. Here, we investigated the spatial patterns of microbial diversity across China's forests and explored the controlling factors of microbial ß diversity and network complexity. Our results showed that soil pH strongly influenced bacterial and fungal ß diversity compared to climate, soil nutrient and plant properties. To further investigate the environmental preference of the microbial networks, we classified the amplicon sequence variants (ASVs) into five groups ranging from acidic to alkaline soils. Co-occurrence network analysis revealed that the topological structure of the bacterial network (e.g., edge and degree) increased with pH and was negatively correlated with ß diversity but not for fungal diversity. Soil fungi exhibited higher ß diversity and network complexity (i.e., degree and betweenness) than bacteria in acidic soils (pH < 5.1), and vice versa in neutral and alkaline soils (pH > 5.5). Within the pH range of 5.1-5.5, the bacterial-fungal network displayed the highest network complexity with the lowest fungal ß diversity, and significant positive correlations were found between fungal ß diversity and soil properties. In addition, bacterial growth in acidic soil (pH < 5.5) showed positive correlations with acid phosphatase (AP), but negative ones with ß-1,4-glucosidase (BG), and vice versa in neutral and alkaline soils (pH > 5.5). Furthermore, 46 bacterial core species were identified, and their abundance had significant correlation with soil pH. These findings highlight the critical role of soil pH in driving soil microbial ß diversity across China's forests and reveal the effects of pH thresholds on changes in the soil microbial network and core species.

15.
Clin Dermatol ; 2024 Sep 09.
Article in English | MEDLINE | ID: mdl-39260457

ABSTRACT

Mentorship is a critical aspect of personal and professional development throughout anyone's life. Unlike many other fields, a medical career is a long multistep process that can begin in high school and continue throughout a physician's career. When considering competitive specialties such as dermatology, mentors are increasingly crucial in helping students successfully match to programs of their choice, but the variability and extent of mentorship can raise ethical concerns. We discuss the evolution of mentorship in dermatology and the potential ethical issues involved. We propose possible solutions to the ethical conflict between mentor and mentee.

16.
Sci Total Environ ; : 176178, 2024 Sep 09.
Article in English | MEDLINE | ID: mdl-39260478

ABSTRACT

Mining is a major threat to vegetation and soil in the tropical forests. Reforestation of degraded surface mines is critically dependent on the recovery of soil health, where the nematodes play an important role. However, the key determinants of community assembly of soil nematodes during mine-restoration remain unknown in the tropical rainforests. Here, the recovery of taxonomic diversity of nematode communities and their trophic groups during reforestation of an extremely degraded tropical open-mining area is studied. The factors that may impact their recovery, such as root traits (length, area and tissue density), soil properties (pH and soil organic matter content (SOM)), and taxonomic diversities of soil bacterial and fungal communities are investigated. Differences in these parameters were evaluated in the three soil types: (i) mined soil - the erstwhile soil that was removed during mining and stock-piled for 10 years at the foot of an extremely degraded open-mining area; (ii) reforested soil, sampled from a 10-year successful restoration, which used the mined soil for reforestation; and (iii) undisturbed soil, collected from an adjacent undisturbed/not-mined tropical rainforest. A total of 11, 34 and 29 nematode-genera were identified in mined-, undisturbed-, and reforested soils, respectively. The taxonomic diversities of the 5 nematode groups in the mined soil were 1.5-5.2 times lower than in the undisturbed soil, but were similar in the restored and undisturbed soils. Taxonomic diversities of phytophagous and predator nematodes were correlated to restored root traits; whereas of bacterivores, fungivores, and omnivores were correlated to pH, SOM, soil bacterial and fungal communities. Consequently, complete loss of roots during mining likely severely reduced the nematodes, but their recovery after reforestation led to the restoration of taxonomic diversity of nematode communities. The mix-planting fast-growing tree species may be appropriate for recovering soil health, including nematode diversity, during reforestation of open tropical mines.

17.
Article in English | MEDLINE | ID: mdl-39261114

ABSTRACT

It is a well-known fact in veterinary medicine that the field has struggled to diversify the profession and is one of the most homogenous careers in the United States. Discrimination is still quite common in the United States, despite decades of policy changes and implementation of DEI practices. This study discusses how veterinary medicine can benefit from an intersectional approach to diversity, equity, and inclusion. It discusses the need of intersectional data to better understand the disparities that exist within veterinary medicine to make a more significant impact.

18.
Prog Biophys Mol Biol ; 193: 19-34, 2024 Sep 06.
Article in English | MEDLINE | ID: mdl-39245215

ABSTRACT

Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions.

19.
BMC Genomics ; 25(1): 842, 2024 Sep 09.
Article in English | MEDLINE | ID: mdl-39251911

ABSTRACT

BACKGROUND: DNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads. RESULTS: We show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~ 4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were ≤ 1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12-15 h of sequencing. CONCLUSION: Our results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.


Subject(s)
DNA Barcoding, Taxonomic , High-Throughput Nucleotide Sequencing , Nanopores , DNA Barcoding, Taxonomic/methods , Animals , High-Throughput Nucleotide Sequencing/methods , INDEL Mutation , Nanopore Sequencing/methods , Electron Transport Complex IV/genetics , Zooplankton/genetics , Zooplankton/classification , Sequence Analysis, DNA/methods
20.
Data Brief ; 56: 110821, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39252785

ABSTRACT

Fruits are mature ovaries of flowering plants that are integral to human diets, providing essential nutrients such as vitamins, minerals, fiber and antioxidants that are crucial for health and disease prevention. Accurate classification and segmentation of fruits are crucial in the agricultural sector for enhancing the efficiency of sorting and quality control processes, which significantly benefit automated systems by reducing labor costs and improving product consistency. This paper introduces the "FruitSeg30_Segmentation Dataset & Mask Annotations", a novel dataset designed to advance the capability of deep learning models in fruit segmentation and classification. Comprising 1969 high-quality images across 30 distinct fruit classes, this dataset provides diverse visuals essential for a robust model. Utilizing a U-Net architecture, the model trained on this dataset achieved training accuracy of 94.72 %, validation accuracy of 92.57 %, precision of 94 %, recall of 91 %, f1-score of 92.5 %, IoU score of 86 %, and maximum dice score of 0.9472, demonstrating superior performance in segmentation tasks. The FruitSeg30 dataset fills a critical gap and sets new standards in dataset quality and diversity, enhancing agricultural technology and food industry applications.

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