Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagenesis and porosity development associated with major sea level fluctuations, Upper Permian, Jameson land, east Greenland

The Upper Permian of Jameson Land includes two major carbonate sequences, represented by the Karstryggen and Wegener Halvoe formations. The initial Karstryggen transgression led to the development of a shallow marine platform with structurally controlled evaporite basins (salinas) separated by stromatolitic, peloidal, or micritic carbonate depositional areas. The Wegener Havloe sequence reflects more rapid and extensive transgression with the deposition of three subcycles of fully marine, platform, or biohermal carbonates containing minor evaporites near the basin margins. Bioherms (bryozoan-brachiopod-marine cement mounds) show > 100 m of relief, indicating that large relative sea level changes were involved. Both the Karstryggen and Wgener Havloe cycles were terminated by major regressions, which led to karstic and/or fluvial incision of the underlying sequences. Not surprisingly, carbonate and evaporite diagenesis was greatly affected by these regional or eustatic sea level fluctuations. Evaporites dissolved or were replaced by calcite and celestite under the influence of meteoric waters. Limestones show collapse brecciation, grain leaching, soil development, and characteristic vadose and phreatic cements. Most significantly meteoric flushing led to massive dissolution of botryoidal marine cements (aragonite and probable high-Mg calcite) within biohermal facies on the Wegener Peninsula. This early porosity resurrection led to the preservation of porous biohermmore » core zones until hydrocarbon migration. Only late (posthydrocarbon), probably hydrothermal fluid flow led to cementation of the bioherm cores while expelling most of the reservoired hydrocarbons. If the sea level changes affecting the Greenlandic Permian are eustatic, then this study may provide significant clues to porosity development throughout the largely unexplored northern Zechstein basin. « less
Modelling marine connectivity in the Great Barrier Reef and exploring its ecological implications

The dispersal of coral larvae away from their natal habitats is an important process for coral reef ecosystems, but remains poorly understood and hard to gauge. This thesis presents a spatially explicit numerical modelling approach to simulate larval dispersal in Australia's Great Barrier Reef (GBR), and in doing so to estimate connectivity between the thousands of reefs that comprise it. A high resolution, finite element ocean model, SLIM, is used to build a biophysical model of larval dispersal capable of estimating larval exchange between reefs in large sections of the the GBR. Tools from network science are employed to investigate the community structure of the GBR's connectivity network, and these tools are used to reveal the presence of clusters of highly inter-connected reefs. Subsequently, the model is used to estimate the extent of connectivity between reefs of different morphologies and depths in the GBR. Finally, the possible impacts of climate change on connectivity in the GBR are assessed, and estimates are made of the likely changes to coral larval dispersal patterns over the coming century.
UvA-DARE ( Digital Academic Repository ) Advances in colonoscopic imaging and the approach to dysplasia in IBD

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Map Building for Cluttered Environment

This paper presents a novel approach to scene localization and mapping in indoor environments from the concept of the Image Bag of Words (BOW) technique, where a group of native feature descriptors represents images and are subsequently transformed to a separate set of image words. This approach uses the famed algorithm called Scale invariant Feature Transform (SIFT). To extract distinctive invariant feature for reliable matching, we normalized the images as illumination changes affect the feature extraction. To achieve robust and efficient matching the environment is modelled. Clustering is shown to be appropriate for quantizing these descriptors into clusters based on selected threshold. In this work, we developed an efficient SLAM using images captured from a highly cluttered background. The result indicates a promising trend in using the camera for SLAM implementation. Keywords—Image Bag of words (BOW), Scale Invariant Feature Transform (SIFT), Clustering, Simultaneous Localization and mapping (SLAM), Images, Environment
Distribution and main characteristics of eclogite in the northern Dabie Mountains, Anhui

Eclogite discovered in the northern Dabie Mountains, Anhui, mainly occurs in granite gneiss and basic ultrabasic rocks. It is very similar to the eclogite in the southern Dabie Mountains with repect to the country rocks, mineral composition and geochemical characteristics. The current distribution of more eclogite in the south than in the north is mainly due to violent differential uplift and erosion in the Mesozoic thermal uplift regime and extensive emplacement of Mesozoic granites.
The pre-Permo-Carboniferous Rocks and Structures from Southern Kirwanveggen, Dronning Maud Land, Antarctica

The basement of southern Kirwanveggen (western Dronning Maud Land) is formed by a SSW-dipping section consisting of (from SW to NE): migmatic gneisscs; granitoid; low-grade/prograde meta-pelites, meta-psammites and meta-basalts (= "Polaris Formation"); ortho-gneiss; quartzite mylonite; Polaris Formation; quartzite mylonite; meta-turbidites. ment of the Grunehogna Craton is exposed scarcely west of the Borgmassivet (Annandagstoppane). The Grunehogna Craton in turn is thought to be part of the African Kalahari Craton (e.g. GROENEWALD et al. 1995).
Application of Next-Generation Sequencing in Microbiology

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis, and for outbreak investigations. We evaluated the performance of long-(LR) and/or short-read (SR) sequencing for anti-TB-drug resistance prediction using the TBProfiler and Mykrobe tools, the fraction of genome recovery, assembly accuracies and the robustness of two typing approaches based on core genome single nucleotide polymorphism (cgSNP) typing and core genome multi-locus sequence typing (cgMLST). Most of the discrepancies between phenotypic DST and drug resistance prediction were observed for the first-line drugs rifampicin, isoniazid, pyrazinamide, and ethambutol, mainly with LR sequence data. Resistance prediction to second-line drugs made by both TBProfiler and Mykrobe tools with SR-and LR-sequence data were in complete agreement with phenotypic DST except for one isolate. The SR assemblies were more accurate than the LR assemblies, having significantly (p<0.05) fewer indels and mismatches per 100 kbp. However, the hybrid and LR assemblies had slightly higher genome fractions. For LR assemblies, Canu followed by Racon, and Medaka polishing was the most accurate approach. The cgSNP approach, based on either reads or assemblies, was more robust than the cgMLST approach, especially for LR sequence data. In conclusion, anti-TB drug resistance prediction, particularly with only LR sequence data, remains challenging, especially for first-line drugs. In addition, SR assemblies appear more accurate than LR ones, and reproducible phylogeny can be achieved using cgSNP approaches.
THEMED ISSUE: GPCR REVIEW Agonism and allosterism: the pharmacology of the free fatty acid receptors FFA2 and FFA3

The free fatty acid receptors FFA2 and FFA3 are recently de-orphanized G protein-coupled receptors that share a group of short-chain free fatty acids as endogenous ligands. The expression of FFA2 and FFA3 by immune cells, in parts of the gastro-intestinal tract and by white adipocytes has suggested their potential as therapeutic targets in conditions including inflammation and obesity. However, although FFA2 and FFA3 display distinct structure–activity relationships for stimulation by short-chain free fatty acids, the overlap between these endogenous agonists and the lack of synthetic small molecule ligands that display selectivity between these two receptors has, until recently, hindered efforts to resolve their individual functions. Recently, chloro-a-(1-methylethyl)-N-2-thiazolylbenzeneacetamide has been described as an FFA2 selective ago-allosteric ligand, not only being a direct agonist but also acting as a positive allosteric modulator of the function of short-chain free fatty acids at FFA2. Mutation of a pair of key arginine residues near the top of transmembrane domains V and VII of both FFA2 and FFA3 eliminates the function of short-chain free fatty acids but is without effect on the direct agonist action of chloro-a-(1methylethyl)-N-2-thiazolylbenzeneacetamide at FFA2, confirming the distinct nature of the binding site of the ago-allosteric regulator from the orthosteric binding site for free fatty acids. An understanding of structure–activity relationships for ligands related to chloro-a-(1-methylethyl)-N-2-thiazolylbenzeneacetamide is likely to provide greater insight into the mode of action and site of binding of this ligand, but further FFA2 and FFA3 selective ligands, preferably with higher potency/affinity, will be required to fully explore the physiological function of these receptors. British Journal of Pharmacology (2009) 158, 146–153; doi:10.1111/j.1476-5381.2009. 00421.x
PSYCHOLOGICAL THERAPIES FOR CHILDREN WITH CHRONIC PAIN Systematic review and meta-analysis of psychological therapies for children with chronic pain

Objectives This systematic review and meta-analysis examined the effects of psychological therapies for management of chronic pain in children. Methods Randomized controlled trials of psychological interventions treating children (<18 years) with chronic pain conditions including headache, abdominal, musculoskeletal, or neuropathic pain were searched for. Pain symptoms, disability, depression, anxiety, and sleep outcomes were extracted. Risk of bias was assessed and quality of the evidence was rated using GRADE. Results Thirty-five included studies revealed that across all chronic pain conditions, psychological interventions reduced pain symptoms and disability post-treatment. Individual pain conditions were analyzed separately. Sleep outcomes were not reported in any trials. Optimal dose of treatment was explored. For headache pain, higher treatment dose led to greater reductions in pain. No effect of dosage was found for other chronic pain conditions. Conclusions Evidence for psychological therapies treating chronic pain is promising. Recommendations for clinical practice and research are presented. The analyses of 37 included studies showed that psychological therapies were effective in improving pain symptoms for both headache and non-headache pain conditions at post-treatment compared to control conditions, and at follow-up for the headache group. Disability also significantly improved in the non-headache group at post-treatment. Finally, mood (including depression and anxiety) significantly improved in the headache group at follow-up. meta-analysis. No conclusions can be drawn.
Research and FPGA Implementation of Convolutional Neural Network Accelerator

Compared with CPU and GPU, FPGA has high performance, low power consumption, and flexible deployment characteristics. Nowadays, the convolutional neural network (CNN) is updated rapidly, and using the high-level synthesis (HLS) technology to design CNN image recognition accelerators has high efficiency. However, the operating speed and the energy efficiency ratio (EER) of the existing CNN accelerators designed by HLS technology are relatively low. We designed an FPGA-based CNN accelerator using HLS technology, which further improved acceleration efficiency through pipeline optimization, perfect loop, and multiplication split operation. We also realized the custom reusing of intellectual property (IP) cores. The CNN accelerator is verified on an 8-bit LeNet-5 model, and it has a recognition accuracy rate of 97.95% on the MNIST dataset, a single recognition time of 21.5ms, and a platform power consumption of 1.965W. And it reduces the recognition time by at least 5ms compared with other existing works. Its energy efficiency ratio is 23.67(s • W)-1, which is 2.3 times and 4 times that of ARM and CPU respectively. These reflect the advantages of the FPGA-based CNN image recognition accelerator in that it can be flexibly deployed and has a high energy efficiency ratio under limited deployment power consumption.
Frontiers in Dentistry

Article type: Original Article Objectives: The combination of mineral trioxide aggregate (MTA) and 2% chlorhexidine (CHX) has been recently introduced as an intracanal medicament. The aim of this study was to evaluate the potential cytotoxic effects of MTA mixed with 2% chlorhexidine gel on human periodontal ligament stem cells (PDLSCs) and compare it with other common endodontic regeneration medicaments. Materials and Methods: Minimum inhibitory concentration and minimum bactericidal concentration of six experimental groups against Enterococcus faecalis was determined. The study groups consisted of RetoMTA mixed with 2% chlorhexidine gel (MTA+CHX), calcium hydroxide (CH), CH mixed with CHX gel, two concentrations of double antibiotic paste, and 2% CHX. The direct cytotoxic effect of minimum bactericidal concentration was evaluated by MTT on PDLSCs on days 1, 3, and 7. One-way ANOVA and post hoc tests were used for data analysis (P<0.05). Results: The viability of cells treated with MTA+CHX decreased significantly over time (P<0.05) making this group the most cytotoxic intracanal medicament on the 3rd and 7th days of treatment. On day one, the highest viability percentage was detected in the CH+CHX group followed by the CHX group. On day 3, CH+CHX and CHX groups displayed the highest viability percentage. On day 7, the highest viability was observed in the CHX group, which showed no significant difference with the control group (P=0.12). Conclusion: Regarding the antimicrobial potency of intracanal medicaments at minimum bactericidal concentration levels, CHX gel appears to be the least cytotoxic drug, while MTA+CHX shows the highest reduction in viability percentage.
Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities

Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.
Autocorrelation structure of monthly streamflows

The autocorrelation structure of monthly streamflows, a nonstationary process, is developed from a mathematical model that assumes that monthly precipitation is an independent series and that the base flow of the stream is derived from a linear aquifer. Under these assumptions the first-order autocorrelation coefficients of streamflow are found to vary seasonally, as do other statistics such as monthly means and standard deviations. Comparison of the autocorrelation coefficients predicted by the model with those computed from an actual streamflow record of 58 years indicates that the seasonality of streamflow is well represented by the model.
Frontiers in Dentistry

Article type: Original Article Objectives: This study aimed to evaluate the effect of an educational intervention on oral health-related knowledge, attitude, and practice of medical students. Materials and Methods: This study was performed on the fifth-year medical students attending an elective oral health course at the Faculty of Dentistry of Tehran University (intervention group) and 25 other students attending another elective course (control group) in 2018. A 2-week internship program including 6 sessions of a workshop program plus 2 days of school field and 2 days of attending dental departments was designed for the intervention group. Before and after the intervention, students completed a questionnaire and their simplified debris index was calculated. Statistical analysis was performed using SPSS version 24 by pairedsample t-test and general linear regression. Results: The mean age of the participants was 24.84±1.31 years in the intervention group and 23.64±1.28 years in the control group. There were 14 (56%) males in the intervention group and 16 (64%) males in the control group. At baseline, the mean knowledge, attitude and practice scores of the control and intervention groups were 26.28, 14.20 and 10.88, and 27.84, 15.80, and 9.36, respectively. After the intervention, the knowledge, attitude, debris index and willingness to adhere to oral health measures significantly improved (P<0.05). Conclusion: Oral health-related knowledge, attitude and practice of medical students were not desirable at baseline. The present study showed that even a shortterm intervention in this field was effective to improve the oral health concepts in this group.
Frontiers in Dentistry

Article type: Review Article The choice of an appropriate autogenous source of stem cells has not been adequately addressed especially for intraoral bone regeneration. The current review aims to assess the clinical success of various human stem cells in oral bone regeneration. Articles studying the potential of various stem cells utilized for reconstruction of intraoral bone defects in humans were included in this review. Relevant articles were electronically searched in MEDLINE-PubMed database using keywords with different combinations. Only the articles published in English between 2006 and 2020 were included in this review. It was concluded that intra and extraoral stem cells can be successfully used for bone regeneration of various jaw defects. Depending on the origin, quantity, and quality, each cell type has its own advantages and disadvantages. Also, it brings to the fore the need for more clinical studies to validate and adopt the use of stem cells in regular clinical practice.
Please Scroll down for Article International Journal of Audiology towards Understanding the Specifics of Cochlear Hearing Loss: a Modelling Approach

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UvA-DARE ( Digital Academic Repository ) High reading skills mask dyslexia in gifted children

This study investigated how gifted children with dyslexia might be able to mask literacy problems and the role of possible compensatory mechanisms. The sample consisted of 121 Dutch primary school children that were divided over four groups (typically developing [TD] children, children with dyslexia, gifted children, gifted children with dyslexia). The test battery included measures of literacy (reading/spelling) and cognitive abilities related to literacy and language (phonological awareness [PA], rapid automatized naming [RAN], verbal short-term memory [VSTM], working memory [WM], grammar, and vocabulary). It was hypothesized that gifted children with dyslexia would outperform children with dyslexia on literacy tests. In addition, a core-deficit model including dyslexia-related weaknesses and a compensational model involving giftedness-related strengths were tested using Bayesian statistics to explain their reading/spelling performance. Gifted children with dyslexia performed on all literacy tests in between children with dyslexia and TD children. Their cognitive profile showed signs of weaknesses in PA and RAN and strengths in VSTM, WM, and language skills. Findings indicate that phonology is a risk factor for gifted children with dyslexia, but this is moderated by other skills such as WM, grammar, and vocabulary, providing opportunities for compensation of a cognitive deficit and masking of literacy difficulties.
Effects of long-term experimental warming on three High Arctic plant communities

Arctic regions are experiencing faster rates of atmospheric warming than any other biome. Increasing temperatures will affect the biomass, phenology, and composition of Arctic vegetation, which in turn will alter ecosystem functions such as greenhouse gas flux and nutrient cycling. These functional changes are likely to affect feedbacks to terrestrial and atmospheric systems. Responses are expected to occur at a range of scales and are likely to show close coupling to environmental conditions. In this thesis I compare ecosystem response in three plant communities after 18 years of experimental warming on Ellesmere Island, Canada. Warming response was measured at peak season in a dry, mesic and wet community. Biomass, height, and composition were measured using a point-intercept method and CO2 flux was measured using an infrared gas analyzer and a custom made chamber. Environmental and NDVI data were collected from all three communities as well as being sampled across the entire lowland to map environmental heterogeneity and identify predictors of NDVI. All three plant communities showed structural responses to warming. Total above-ground biomass and height did not show significant changes but growth form composition shifted in all cases. Increases were observed for graminoids and forbs at the dry site; graminoids, deciduous shrubs and bryophytes at the mesic site; and deciduous shrubs and bryophytes at the wet site. Lichen abundance decreased at all sites. CO2 flux responses were largely explained by compositional changes. All sites were CO2 sinks at peak season and the dry and wet sites became stronger sinks as a result of warming. Landscape scale mapping successfully displayed the variation in environmental variables and NDVI across the landscape. Soil moisture was identified as an important determinant of