Miracle-dz/UniFAR-FTUs huggingface dataset:
Mangrove Typology: A Proposal for Mapping based on High Spatial Resolution Orbital Remote Sensing

ABSTRACT Almeida, P.M. M. ; Cruz, C.B. M. ; Amaral, F.G. ; Furtado, L.F. A. ; Duarte, G.S. ; Silva, G.F. ; Barros, R.S. ; Marques, J.V.F.P.A. ; Rosário, E.S. ; Santos, V.F. ; Alves, A. ; Chaves, F.O. , and Soares, M.L. G. , 2020. Mangrove typology: A proposal for mapping based on high spatial resolution orbital remote sensing. In: Malvárez, G. and Navas, F. (eds.), Global Coastal Issues of 2020. Journal of Coastal Research, Special Issue No. 95, pp. 1-5. Coconut Creek (Florida), ISSN 0749-0208. Solutions to improve environmental management strategies increasingly require the adoption of new techniques, such as Geotechnologies. All this effort must be carried out in a multidisciplinary way, using different concepts, techniques and scientific visions about the same phenomenon. In response to the cartographic demands, one of the primordial steps for a good mapping starts before the processing of the images to be used. This step is based on the definition of a legend related to the scale and purpose of the mapping. This work aims to contribute in the definition of a typology adapted to the use of high spatial resolution remote sensing data for the mapping of mangrove phytophysiognomies in the Brazilian Equatorial Coast. The final mapping covered more than 27,000 ha of forests divided into the following classes: (i) Forest dominated by Avicennia schaueriana; (ii) Forest dominated by Rhizophora spp. ; (iii) Mixed Forests; all indicating differences in structural development (high, medium or low). Through this reflexive process, this work contributes to the mapping with effectively transdisciplinary strategies.
Estimation of Water Surface Flow Velocity in Coastal Video Imagery by Visual Tracking with Deep Learning

ABSTRACT Kim, J. and Kim, J., 2020. Estimation of water surface flow velocity using coastal video imagery by visual tracking with deep learning. In: Malvárez, G. and Navas, F. (eds.), Global Coastal Issues of 2020. Journal of Coastal Research, Special Issue No. 95, pp. 522-526. Coconut Creek (Florida), ISSN 0749-0208. This paper describes the method of flow velocity estimation of water surface in video imagery by tracking waves using deep neural network for visual object tracking with unsupervised learning. The model of deep neural network consists of two stages for scene separation and image registration to extract waves only and track the propagated waves, respectively. The dataset of video imagery acquired at Anmok beach of south Korea has been used to training the model and it learns the behavior of propagated waves. The performance of model is evaluated by measuring image similarity using test dataset. And the estimated flow velocity of water surface in propagated waves is compared with the flow from conventional image processing method of particle image velocity. The results show that our proposed approach with deep learning method is very promising to measure and predict coastal waves especially in the surf zone.
Identifying users based on their eye tracker calibration data

The purpose of the paper is to test the possibility of identifying people based on the input they provide to an eye tracker during the calibration process. The most popular eye trackers require the calibration before their first usage. The calibration model that is built can recalculate the subsequent eye tracker’s output to genuine gaze points. It is well known that the model is idiosyncratic (individual for the person). The calibration should be repeated every time the person uses the eye tracker. However, there is evidence that the models created for the same persons may be reused by them (but obviously with some loss of accuracy). The general idea investigated in this paper is that if we take an uncalibrated eye tracker’s output and compare it with the genuine gaze points, the errors will be repeatable for the same person. We tested this idea using three datasets with an eye tracker signal recorded for 52 users. The results are promising as the accuracy of identification (1 of N) for the datasets varied from 49% to 71%.
Assessing the Potential of Minho and Lima Estuaries for Aquaculture

ABSTRACT Picado, A. ; Oliveira, V. ; Pereira, H. ; Sousa, M.C. ; Costa, L. ; Almeida, A. , and Dias, J.M. , 2020. Assessing the potential of Minho and Lima estuaries for aquaculture. In: Malvárez, G. and Navas, F. (eds.), Global Coastal Issues of 2020. Journal of Coastal Research, Special Issue No. 95, pp. 148-152. Coconut Creek (Florida), ISSN 0749-0208. This work aims the identification of the best potential areas to develop aquaculture activities in Minho and Lima estuaries, especially for the species with the highest commercial value. The Analytic Hierarchy Process (AHP) methodology was applied to the results of an annual simulation with Delft3D model (including the hydrodynamic and water quality modules). After, each variable used in AHP was crossed with the environmental thresholds for development/growth of one bivalve (Portuguese Oyster) and one fish (Gilthead Seabream) species. In this way, an Exploration Index (EI) was defined in order to identify the most suitable regions according to water biophysical properties. This EI was mapped for both estuaries and results show that, in general, the low and middle estuaries present the best conditions for aquaculture development of bivalve and fish. In addition, the upper areas of both estuaries are unsuitable for aquaculture, due to the low salinity of these regions.
Hot Rolled Ti6321 Alloy Sheets With Different Initial Microstructures: Microstructure, Mechanical Properties, and Anisotropy Characteristics

The microstructure, mechanical properties, and texture characteristics of marine titanium alloy Ti6321 sheets with four different initial microstructures were investigated contrastively in this paper. The results indicate that the strength of hot-rolled, equiaxed, and bimodal microstructure sheets exhibits significant anisotropy in the RD and TD directions. The hot rolled sheet shows the strongest anisotropy of tensile properties, that is, the transverse yield strength is 91 MPa higher than that of the rolling direction. The morphology characteristics of the macroscopic tensile fracture are also significantly different in RD and TD. The strength anisotropy of Ti6321 alloy sheet decreases with the increase of annealing temperature. The mechanical properties of the widmanstätten microstructure sheet are close to isotropic, and the plasticity is the worst among the four initial microstructures. The root cause for the properties anisotropy was analyzed by XRD and EBSD. There is a strong (1¯21¯0)[101¯0] prismatic texture and a relatively weak (1¯21¯0)[0001] basal texture in the anisotropic sheet. The anisotropic characteristics of the tensile deformation of Ti6321 alloy sheet at room temperature are mainly attributed to the difference in the Schmid factor of the basal slip system and prismatic slip system in TD and RD specimens.
TNFRSF12A and CD38 Contribute to a Vicious Circle for Chronic Obstructive Pulmonary Disease by Engaging Senescence Pathways

Pathogenesis of chronic obstructive pulmonary disease (COPD) is dependent on chronic inflammation and is hypothesized to represent organ-specific senescence phenotype. Identification of senescence-associated gene drivers for the development of COPD is warranted. By employing automated pipeline, we have compiled lists of the genes implicated in COPD (N = 918) and of the genes changing their activity along with cell senescence (N = 262), with a significant (p < 7.06e–60) overlap between these datasets (N = 89). A mega-analysis and a partial mega-analysis were conducted for gene sets linked to senescence but not yet to COPD, in nine independent mRNA expression datasets comprised of tissue samples of COPD cases (N = 171) and controls (N = 256). Mega-analysis of expression has identified CD38 and TNFRSF12A (p < 2.12e–8) as genes not yet explored in a context of senescence–COPD connection. Functional pathway enrichment analysis allowed to generate a model, which explains accelerated aging phenotypes previously observed in COPD patients. Presented results call for investigation of the role of TNFRSF12A/CD38 balance in establishing a vicious cycle of unresolvable tissue remodeling in COPD lungs.
Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

I present here an in-depth, although non-exhaustive, review of two topics in molecular dating. Clock models, which describe the evolution of the rate of evolution, are considered first. Some of the shortcomings of popular approaches—uncorrelated clock models in particular—are presented and discussed. Autocorrelated models are shown to be more reasonable from a biological perspective. Some of the most recent autocorrelated models also rely on a coherent treatment of instantaneous and average substitution rates while previous models are based on implicit approximations. Second, I provide a brief overview of the processes involved in collecting and preparing fossil data. I then review the main techniques that use this data for calibrating the molecular clock. I argue that, in its current form, the fossilized birth-death process relies on assumptions about the mechanisms underlying fossilization and the data collection process that may negatively impact the date estimates. Node-dating approaches make better use of the data available, even though they rest on paleontologists' intervention to prepare raw fossil data. Altogether, this study provides indications that may help practitioners in selecting appropriate methods for molecular dating. It will also hopefully participate in defining the contour of future methodological developments in the field.
Structure, Function, Regulation and Phylogenetic Relationship of ZIP Family Transporters of Plants

Zinc (Zn) is an essential micronutrient for plants and humans. Nearly 50% of the agriculture soils of world are Zn-deficient. The low availability of Zn reduces the yield and quality of the crops. The zinc-regulated, iron-regulated transporter-like proteins (ZIP) family and iron-regulated transporters (IRTs) are involved in cellular uptake of Zn, its intracellular trafficking and detoxification in plants. In addition to Zn, ZIP family transporters also transport other divalent metal cations (such as Cd2+, Fe2+, and Cu2+). ZIP transporters play a crucial role in biofortification of grains with Zn. Only a very limited information is available on structural features and mechanism of Zn transport of plant ZIP family transporters. In this article, we present a detailed account on structure, function, regulations and phylogenetic relationships of plant ZIP transporters. We give an insight to structure of plant ZIPs through homology modeling and multiple sequence alignment with Bordetella bronchiseptica ZIP (BbZIP) protein whose crystal structure has been solved recently. We also provide details on ZIP transporter genes identified and characterized in rice and other plants till date. Functional characterization of plant ZIP transporters will help for the better crop yield and human health in future.
Impact of Plasma Exposure of Statins and Their Metabolites With Major Adverse Cardiovascular Events in Chinese Patients With Coronary Artery Disease

The selection of optimum statin intensity is inconclusive, and the association of plasma exposure of statins and metabolites with major adverse cardiovascular events (MACEs) is unclear. This study sought to compare the effect of low (quartile 1), intermediate (quartiles 2 and 3), and high (quartile 4) plasma exposure of statins and metabolites on MACE, re-ischemia events and death in patients with coronary artery disease (CAD) at 5 years. A total of 1,644 patients in atorvastatin (AT) cohort and 804 patients in rosuvastatin (RST) cohort were included, and their plasma concentration of statins and metabolites was categorized as low-, mid-, or high-group. The association between the plasma levels of statins and metabolites and the incidence of primary endpoint in patients was assessed by Cox proportional hazard models. Intensive AT exposure (Q4 > 5.32 ng/ml) was significantly associated with increased risk of death compared with low (hazard ratio [HR]: 1.522; 95% confidence interval [CI]: 1.035–1.061; P = 0.0022) or moderate exposure (HR: 2.054; 95% CI: 1.348–3.130; P = 0.0008). This association was also found in AT’s five metabolites (all P < 0.01). In patients with RST treatment, moderate RST concentration (0.53–4.29 ng/ml) versus low concentration had a significantly lower risk of MACE and re-ischemia events. (HR: 0.532, 95% CI: 0.347–0.815, P = 0.0061 and HR: 0.505, 95% CI: 0.310–0.823, P = 0.0061, respectively). A higher plasma exposure of AT and metabolites has a significantly higher risk of death, and moderate RST exposure has a significantly lower risk of MACE and re-ischemia events in Chinese patients with CAD. The harms of high plasma exposure should be considered when prescribing statins to patients because it may be a risk factor for having poor prognosis in patients with CAD.
Effects of the corpora allata on sexual receptivity and completion of oocyte development in females of the cricket, Gryllus bimaculatus

Abstract Allatectomy of young penultimate nymphs of Gryllus bimaculatus De Geer (Gryllidae) resulted in prothetelic creatures which exhibited reproductive competence. The same operation performed on young last instar nymphs resulted in moulting to morphologically normal adults. Allatectomized morphologically normal adult females, as well as prothetelic ones, showed the same level of sexual receptivity as untreated control females. Allatectomized morphologically normal and prothetelic females laid viable eggs, but rate of egg laying and number of eggs produced by these females were much reduced in comparison with the controls. Administration of methoprene (a Juvenile Hormone analogue) to allatectomized females restored egg production to a more or less normal rate. Removal of the spermatophore within 10 min of copulation had no effect on subsequent sexual receptivity of the females, nor on the reduced rate of egg laying by the allatectomized females, but did affect the rate of egg laying by control females.
Bam32/DAPP1-Dependent Neutrophil Reactive Oxygen Species in WKYMVm-Induced Microvascular Hyperpermeability

B cell adaptor molecule of 32 kDa (Bam32), known as dual adapter for phosphotyrosine and 3-phosphoinositides 1 (DAPP1), has been implicated in regulating lymphocyte proliferation and recruitment during inflammation. However, its role in neutrophils during inflammation remains unknown. Using intravital microscopy, we examined the role of Bam32 in formyl peptide receptor agonist WKYMVm-induced permeability changes in post-capillary venules and assessed simultaneously neutrophil adhesion and emigration in cremaster muscles of Bam32-deficient (Bam32−/−) and wild-type (WT) control mice. We observed significantly reduced WKYMVm-induced microvascular hyperpermeability accompanied by markedly decreased neutrophil emigration in Bam32−/− mice. The Bam32-specific decrease in WKYMVm-induced hyperpermeability was neutrophil-dependent as this was verified in bone marrow transplanted chimeric mice. We discovered that Bam32 was critically required for WKYMVm-induced intracellular and extracellular production of reactive oxygen species (ROS) in neutrophils. Pharmacological scavenging of ROS eliminated the differences in WKYMVm-induced hyperpermeability between Bam32−/− and WT mice. Deficiency of Bam32 decreased WKYMVm-induced ERK1/2 but not p38 or JNK phosphorylation in neutrophils. Inhibition of ERK1/2 signaling cascade suppressed WKYMVm-induced ROS generation in WT neutrophils and microvascular hyperpermeability in WT mice. In conclusion, our study reveals that Bam32-dependent, ERK1/2-involving ROS generation in neutrophils is critical in WKYMVm-induced microvascular hyperpermeability during neutrophil recruitment.
Individualized Dosing With High Inter-Occasion Variability Is Correctly Handled With Model-Informed Precision Dosing—Using Rifampicin as an Example

Rifampicin exhibits complexities in its pharmacokinetics (PK), including high inter-occasion variability (IOV), which is challenging for dose individualization. Model-informed precision dosing (MIPD) can be used to optimize individual doses. In this simulation-based study we investigated the magnitude of IOV in rifampicin PK on an exposure level, the impact of not acknowledging IOV when performing MIPD, and the number of sampling occasions needed to forecast the dose. Subjects with drug-susceptible tuberculosis (TB) were simulated from a previously developed population PK model. To explore the magnitude of IOV, the area under the plasma concentration-time curve from time zero up to 24 h (AUC0–24h) after 35 mg/kg in the typical individual was simulated for 1,000 sampling occasions at steady-state. The impact of ignoring IOV for dose predictions was investigated by comparing the prediction error of a MIPD approach including IOV to an approach ignoring IOV. Furthermore, the number of sampling occasions needed to predict individual doses using a MIPD approach was assessed. The AUC0–24h in the typical individual varied substantially between simulated sampling occasions [95% prediction interval (PI): 122.2 to 331.2 h mg/L], equivalent to an IOV in AUC0–24h of 25.8%, compared to an inter-individual variability of 25.4%. The median of the individual prediction errors using a MIPD approach incorporating IOV was 0% (75% PI: −14.6% to 0.0%), and the PI for the individual prediction errors was narrower with than without IOV (median: 0%, 75% PI: −14.6% to 20.0%). The most common target dose in this population was forecasted correctly in 95% of the subjects when IOV was included in MIPD. In subjects where doses were not predicted optimally, a lower dose was predicted compared to the target, which is favorable from a safety perspective. Moreover, the imprecision (relative root mean square error) and bias in predicted doses using MIPD with IOV decreased statistically significant when a second sampling occasion was added (difference in imprecision: −9.1%, bias: −7.7%), but only marginally including a third (difference in imprecision: −0.1%, bias: −0.1%). In conclusion, a large variability in exposure of rifampicin between occasions was shown. In order to forecast the individual dose correctly, IOV must be acknowledged which can be achieved using a MIPD approach with PK information from at least two sampling occasions.
Identification of a Pathogenic TGFBR2 Variant in a Patient With Loeys–Dietz Syndrome

Loeys–Dietz syndrome (LDS) is a rare connective tissue genetic disorder that is caused by a pathogenic variant in genes of transforming growth factor (TGF) beta receptor 1 (TGFBR1), TGFBR2, mothers against decapentaplegic homolog 2 (SMAD2), SMAD3, TGFB2, or TGFB3. It is characterized by aggressive vascular pathology, aneurysms, arterial tortuosity, bifid uvula, hypertelorism, and cleft palate. Here we present a 42-year-old female patient with LDS. The patient underwent rapidly progressing artery aneurysms and life-threatening aortic dissection. Spontaneous fracture of the first metatarsal bone was noted in her medical record. Physical examination revealed a delayed wound healing on her left abdomen. Considering these clinical manifestations, we speculated that there was a genetic defect in the connective tissue, which provides strength and flexibility to structures such as bones, skins, ligaments, and blood vessels. Thus, whole exome sequencing (WES) was performed on the proband and revealed a heterozygous missense pathogenic variant (c.1613T > C/p.Val538Ala) in TGFBR2, which was a de novo variant in the proband as confirmed by the segregation analysis in parental samples. Although this variant was discovered and associated with the phenotype of LDS previously, the pathogenicity of the variant had not been confirmed by cellular functional assay yet. To further validate the effects of the variant in vitro, we assessed the canonical TGF-β signaling pathway in mutant cells. Our results showed that the p.Val538Ala variant significantly decreased TGF-β-induced gene transcription and the phosphorylation of Smad2, which were consistent with other pathogenic variants of TGFBR2. In conclusion, this study demonstrates that the p.Val538Ala pathogenic variant in TGFBR2 leads to aberrant TGF-β signaling and LDS in this patient.
Mapping Stem Rust (Puccinia graminis f. sp. secalis) Resistance in Self-Fertile Winter Rye Populations

Rye stem rust caused by Puccinia graminis f. sp. secalis can be found in all European rye growing regions. When the summers are warm and dry, the disease can cause severe yield losses over large areas. To date only little research was done in Europe to trigger resistance breeding. To our knowledge, all varieties currently registered in Germany are susceptible. In this study, three biparental populations of inbred lines and one testcross population developed for mapping resistance were investigated. Over 2 years, 68–70 genotypes per population were tested, each in three locations. Combining the phenotypic data with genotyping results of a custom 10k Infinium iSelect single nucleotide polymorphism (SNP) array, we identified both quantitatively inherited adult plant resistance and monogenic all-stage resistance. A single resistance gene, tentatively named Pgs1, located at the distal end of chromosome 7R, could be identified in two independently developed populations. With high probability, it is closely linked to a nucleotide-binding leucine-rich repeat (NB-LRR) resistance gene homolog. A marker for a competitive allele-specific polymerase chain reaction (KASP) genotyping assay was designed that could explain 73 and 97% of the genetic variance in each of both populations, respectively. Additional investigation of naturally occurring rye leaf rust (caused by Puccinia recondita ROEBERGE) revealed a gene complex on chromosome 7R. The gene Pgs1 and further identified quantitative trait loci (QTL) have high potential to be used for breeding stem rust resistant rye.