Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Exploitation Rates in the Alabama Red Snapper Fishery Using a High‐Reward Tag–Recapture Approach

Accurate estimates of exploitation are essential to managing an exploited fishery. However, these estimates are often dependent on the area and vulnerable sizes of fish considered in a study. High-reward tagging studies offer a simple and direct approach to estimating exploitation rates at these various scales and in examining how model parameters impact exploitation rate estimates. These methods can ultimately provide a better understanding of the spatial dynamics of exploitation at smaller local and regional scales within a fishery—a measure often needed for more site-attached species, such as the Red Snapper Lutjanus campechanus. We used this approach to tag 724 Red Snapper during 2016 in the Alabama Artificial Reef Zone within the northern Gulf of Mexico to estimate recreational exploitation rates in Alabama waters. We fitted a series of tag return models, analyzed using maximum likelihood, to examine how release depth, movement between depth strata, fish length, and the rate at which anglers released fish impacted estimates of exploitation rate under a range of assumed natural and tagging mortality rates. Our model results suggested higher fishing mortality in the shallower depth stratum than in the deep stratum, constant movement rates with release depth, and constant release rates across fish lengths. Exploitation rate for the aggregate tagged population across the entire sample area was estimated at 0.14. Exploitation rates estimated for each depth stratum were 0.20 (shallow stratum: <36.5 m) and 0.06 (deep stratum: 36.5–61.0 m). In addition, length-based vulnerability to harvest was dome-shaped, with peak exploitation rates of 0.37 (shallow stratum) and 0.12 (deep stratum) occurring at 600–700 mm TL. Although previous studies have suggested higher exploitation rates in shallower waters compared to deeper waters, few estimates exist at these smaller spatial scales. Accurate estimates of exploitation rate are essential to managing an exploited fishery, as these estimates will have drastic impacts on the health of the fishery, the local economy, and stakeholder livelihoods (SEDAR 2013). One difficulty in estimating exploitation is that estimates are dependent on the area and vulnerable sizes considered Subject editor: Patrick Sullivan, Cornell University, Ithaca, New York *Corresponding author: dks0017@auburn.edu Present address: Coastal Research and Extension Center, Mississippi State University, 1815 Popps Ferry Road, Biloxi, Mississippi 39532, USA. Received November 27, 2017; accepted September 7, 2018 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 10:536–549, 2018 © 2018 The Authors. Marine and Coastal Fisheries published by Wiley Periodicals, Inc. on behalf of American Fisheries Society. ISSN: 1942-5120 online DOI: 10.1002/mcf2.10049
How a Novel Zinc Finger Domain Improves Target Gene Selection by TCF in WNT/ß-Catenin Signaling.

The evolutionarily conserved Wnt/-catenin (Wnt/-cat) pathway plays an important role in animal development in metazoans. Many Wnt targets are regulated by members of the TCF/LEF1 (TCF) family of transcription factors. All TCFs contain a High Mobility Group (HMG) domain that bind specific DNA sequences. Invertebrate TCFs and some vertebrate TCF isoforms also contain another domain, called the C-clamp, which allows TCFs to recognize an additional DNA motif known as the Helper site. While the Cclamp has been shown to be important for regulating several Wnt reporter genes in cell culture, its physiological role in regulating Wnt targets is less clear. In addition, little is known about this domain, except that two of the four conserved cysteines are functionally important. Here, we carried out a systematic mutagenesis and functional analysis of the C-clamp from the Drosophila TCF/Pangolin (TCF/Pan) protein. We found that the Cclamp is a zinc-binding domain that is sufficient for binding to the Helper site. In addition to this DNA-binding activity, the C-clamp also inhibits the HMG domain from binding its cognate DNA site. Point mutations were identified that specifically affected DNA-binding or reduced the inhibitory effect. These mutants were characterized in TCF/Pan rescue assays. The specific DNA-binding activity of the C-clamp was essential
Analysis of Non-Intrusive Rotor Speed Estimation Techniques for Inverter-Fed Induction Motors

Most non-intrusive induction motor (IM) efficiency estimation methods rely on the machine slip to compute the output power and the efficiency. To achieve the overall non-intrusive nature of the entire process, it is vital to utilize a reliable and non-intrusive rotor speed measurement technique in order to obtain the slip of an in-service motor. A number of rotor speed estimation techniques have been proposed in literature. This article focusses on the review and analysis of different techniques in terms of intrusiveness, relative accuracy, sensitivity and computational overhead particularly when the IM is fed by an inverter supply. An experimental accuracy and sensitivity analysis of some motor current and vibration-based techniques is carried out to check the accuracy trends reported in literature and the robustness of these techniques. Potential techniques for non-intrusive rotor speed estimation of inverter-fed induction motors are recommended.
Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes

Abstract A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark spots on their body. We examined the species limits in this system using comparative specimen‐based approaches, a mitochondrial gene (COI), more than 800 nuclear loci (Ultraconserved Elements), and abiotic niche comparisons. The results indicate there is a complete overlap of meristic counts and morphometric measurements between the two species. Further, we detected multiple individuals with intermediate spotting patterns suggesting that coloration is not diagnostic. Mitochondrial data recovered a single main haplotype shared between the species and all locations resulting in a complete lack of structure (ΦST = 0). Genomic analyses also suggest low levels of genetic differentiation (F ST = 0.013), and no alternatively fixed SNPs were detected between the two phenotypes. Furthermore, niche comparisons could not reject niche equivalency or similarity between the species. These results suggest that these two phenotypes are conspecific and widely distributed in the TEP. Here, we recognize Prionurus punctatus Gill 1862 as a junior subjective synonym of P. laticlavius (Valenciennes 1846). The underlying causes of phenotypic variation in this species are unknown. However, this system gives insight into general evolutionary dynamics within the TEP.
Automated Recognition of Sincere Apologies from Acoustics of Speech

Sincerity is an important characteristic of communicative behavior which represents an honest, truthful, and genuine display of verbal and non-verbal expressions. Individuals who are deemed sincere often appear more charismatic and can influence a large number of people. In this paper, we propose a multi-model fusion framework to identify sincerely delivered apologies by modelling difference between acoustics of sincere and insincere utterances. The efficacy of this framework is benchmarked using the Sincere Apology Corpus (SAC). We show that our proposed methods can improve the baseline classification performance (in terms of unweighted average recall) for SAC from 66.02% to 70.97% for the validation partition and 66.61% to 75.49% for the test partition. Moreover, as part of our investigation, we found that gender dependency can influence the classification performance of machine learning models, with models trained for male subjects performing better than those trained for female subjects.
Cold storage of juçara (Euterpe edulis Martius) fruits: stability of the bioactive compounds and antioxidant activity

Euterpe edulis Martius, known as juçara, is a palm tree threatened with extinction. The sustainable use of its perishable fruits, a promising source of bioactive compounds, would help to preserve this plant. In this study the authors evaluated the effect of temperature and storage time on the physicochemical, microbiological and colorimetric characteristics and on the bioactive compounds of the juçara. Major changes were found in the physicochemical and microbiological characteristics of the fruits stored at 5 °C and at 25 °C for 14 days, but fruits stored at -18 °C maintained most of their characteristics throughout 180 days. The bioactive compound was maintained, the antioxidant capacity increased (61%) and the coliform count reduced during this period. The results showed that juçara fruits frozen could be stored for up to 6 months, which is important in order to overcome problems related to the seasonality and short harvesting period of this fruit. Brazilian Journal of Development Braz. J. of Develop. , Curitiba, v. 6, n. 7 , p.43147-43160, jul. 2020. ISSN 2525-8761 43148
Robust-Oriented Optimization Design for Permanent Magnet Motors Considering Parameter Fluctuation

In this article, a robust-oriented optimization design method is proposed for the permanent magnet (PM) motors. The key of the method is to introduce the concept of parameter fluctuation into motor design process, which aims at solving the uncertainties during motor manufacturing process. The optimization design process is purposely divided into two layers. In the Layer I, except for the motor performance objectives, the influence of parameters fluctuation on motor performances is also served as the design objectives to obtain the deterministic motor structure. In the Layer II, the allowable manufacture errors caused by the parameter fluctuation and the manufacturing qualification rate of the motor with the errors are calculated and optimized simultaneously. Then, an interior PM (IPM) motor is chosen as a design example during robust optimization process. For verifying the effectiveness of the optimization design, the performances are evaluated in detail and the prototype motor is built. Finally, both theoretical analysis and experimental results validate the effectiveness of design method and the rationality of PM motor.
ANTIPREDATOR TRAINING FOR CAPTIVE-REARED MISSISSIPPI SANDHILL CRANECHICKS

Captive-bred Mississippi sandhill cranes (Grus canadensis pulla) suffer from low recruitment in nature, and poor nest defense ability may significantly contribute to the problem. We hypothesized that a lack of opportunities for social learning by young birds prior to release inhibits the development of appropriate nest defense in later life. Here we report the results of preliminary experiments on conditioning of antipredator behavior in young birds prior to release using predator models. Observing agonistic displays by either costumed technicians or parent birds toward a model raccoon (Procyon lotor) promoted aggressive displays to a wild raccoon, but additional exposure to wild raccoons outside of training sessions instead promoted habituation. Pre-release conditioning of crane chicks can induce antipredator behavior useful in nest defense, but optimal procedures remain to be determined. PROCEEDINGS OF THE NORTH AMERICAN CRANE WORKSHOP 14:137-141
The Effect of ACE2 Inhibitor MLN-4760 on the Interaction of SARS-CoV-2 Spike Protein with Human ACE2: A Molecular Dynamics Study

A previous study shows that an ACE2 enzymatic activity inhibitor efficiently blocks the interaction of SARS-CoV spike protein with human ACE2 and may be effective in preventing the coronavirus membrane fusion and entry to human cells. The report suggests that potent ACE2 inhibitors can be used to treat hypertension as well as for controlling SARS-CoV infection. We here studied the effect of a selective and highly potent ACE2 inhibitor (MLN-4760) on the interaction of the SARS-CoV-2 spike receptor-binding domain (RBD) with human ACE2 by molecular dynamics (MD) simulation. To this end, we docked the RBD of SARS-CoV-2 to the human native ACE2 and the ACE2 complexed with MLN-4760, and analyzed the dynamics, protein-protein and ligand-protein interactions of the complexes by MD simulation in a simulated biological condition for 100 ns. Analyzing crystallographic structures of SARS-CoV-2 and SARS-CoV RBDs in the complexes with human ACE2 showed that RBD of SARS-CoV-2 binds to ACE2 with a higher affinity than that of SARS-CoV. Results also revealed that MLN-4760 binds to ACE2 at the enzymatic active site with a high affinity and significantly alters the ACE2 protein conformation. MLN-4760 also changes the binding site and the residues involved in hydrogen and hydrophobic binding between RBD and ACE2, however, it had no major effect on the binding affinity of the interaction between RDB and ACE2. Interestingly, binding RBD to the ACE2 complexed with MLN-4760 abrogated the inhibitory effect of MLN-4760 and rescued the conformation of the ACE2 enzymatic site by reforming the closed conformation to the open native conformation. This was due to the disassociation of MLN-4760 from the enzymatic active site of the ACE2 in the result of RBD binding. Overall, these results show that MLN-4760 does neither block nor increase the binding of SARS-CoV-2 spike RBD to human ACE2 and probably had no effect on the viral entry. However, binding the spike protein to ACE2 can rescue the enzymatic function of ACE2 from its inhibitor.
PP2A methylesterase PME‐1 suppresses anoikis and is associated with therapy relapse of PTEN ‐deficient prostate cancers

While organ-confined PCa is mostly therapeutically manageable, metastatic progression of PCa remains an unmet clinical challenge. Resistance to anoikis, a form of cell death initiated by cell detachment from the surrounding extracellular matrix, is one of the cellular processes critical for PCa progression towards aggressive disease. Therefore, further understanding of anoikis regulation in PCa might provide therapeutic opportunities. Here, we discover that PCa tumors with concomitantly compromised function of two tumor suppressor phosphatases, PP2A and PTEN, are particularly aggressive, having less than 50% 5-year secondary-therapy free patient survival. Functionally, overexpression of PME-1, a PP2A inhibitor protein, inhibits anoikis in PTEN-deficient PCa cells. In vivo, PME-1 inhibition increased apoptosis in in ovo PCa tumor xenografts, and attenuated PCa cell survival in zebrafish circulation. Molecularly, PME-1 deficient PCa cells display increased trimethylation at lysines 9 and 27 of histone H3 (H3K9me3 and H3K27me3), a phenotype corresponding to increased apoptosis sensitivity. In summary, we discover that PME-1 overexpression supports anoikis resistance in PTEN-deficient PCa cells. Clinically, the results identify PME-1 as a candidate biomarker for a subset of particularly aggressive PTEN-deficient PCa.
Hyper-parameter handling for gaussian processes in efficient global optimization

In simulation-based optimization, a common issue with many meta-heuristic algorithms is the limited computational bud-get. Performing a simulation is usually considerably more time-consuming than evaluating a closed mathematical function. Surrogate-assisted algorithms alleviate this problem by using representative models of the simulation which can be evaluated much faster. One of the most promising surrogate-assisted optimization approaches is Efficient Global Optimization, which uses Gaussian processes as surrogate-models. In this paper, the importance of carefully chosen hyper-parameters for Gaussian process kernels and a way of self-configuration is shown. Based on properties of the training set, e.g. distances between observed points, observed target values, etc., the hyper-parameters of the used kernels are initialized and bounded accordingly. With these initial values and bounds in mind, hyper-parameters are then optimized, which results in improved Gaussian process models that can be used for regression. The goal is to provide an automated way of hyper-parameter initialization, which can be used when building Kriging models in surrogate-assisted algorithms, e
Green Turtles Nesting at Their Northern Range Limit in the United States Represent a Distinct Subpopulation

Abstract. Green turtle nesting has been recorded in North Carolina, since 1980, but how these nesting females fit into the broader regional context genetically has not been determined. Genetic tagging through microsatellite genotyping of clutches laid in northern South Carolina, North Carolina, and Delaware from 2010 through 2014 identified at least 52 individual nesting females. The mitochondrial control region haplotype frequencies of these individuals were significantly different from all northern Greater Caribbean subpopulations, including those in Florida, suggesting that these northern US females represent an incipient subpopulation that warrants distinct management unit status.
Agroinfiltration of Phytoene Desaturase and Lycopene Β-Cyclase Genes from Bacterial Source in Tomato (Solanum Lycopersicum L.) Enhances Nutritional and Processing Quality of its Juice

ABSTRACT There has been considerable interest in the value of carotenoids due to their high nutritional and nutraceutical properties. We have earlier shown that agroinfiltration with Agrobacterium tumifaciens GV 3101 containing binary vector pRI 101(I) harboring CrtI gene (Phytoene desaturase) and binary vector pRI 101(Y) harboring CrtY gene (Lycopene β-cyclase) from bacterial sources increases carotenoids in tomatoes. In the present study, the juice prepared from fruits having CrtY gene had higher content of β-carotene (0.60 mg 100 mL−1), lycopene (0.40 mg 100 mL−1) and total phenolics (11.41 μg GAE mL−1) compared to juice prepared from control fruits (0.47 mg 100 mL−1, 0.32 mg 100 mL−1 and 11.22 μg GAE mL−1, respectively), and it showed better antioxidant potential (DPPH IC50 value of 27.6) than that of non-transgenic fruit juice (56.4 μL mL−1). The juice from fruits having CrtY gene also had lower Bostwick value (7.5 cm min−1) than control fruits (9.8 cm min−1), indicating improvement in processing quality because of gene integration. Juice prepared from agroinfiltrated tomatoes may benefit both consumers as well as juice processing industry due to their high nutritional value and better processing quality.
Joint Data Collection and Fusion Using Mobile Sink in Heterogeneous Wireless Sensor Networks

Using a mobile sink for data collection from the sensors has been considered as a good way to prolong the network lifetime of wireless sensor networks (WSNs). To avoid the problems of long delay and data non-fresh, some previous studies selected a set of data collection points (CPs) and all the other sensors transmit their data to the closest CP in a multi-hop manner. Then the mobile sink only needs to visit and collect data from the selected CPs, reducing the path length of the mobile sink and the time required for collecting data from all sensors. This paper proposes a data collection mechanism, called DDCF, which uses a mobile sink to collect data in a heterogeneous WSN(HWSN), aiming to prolong the network lifetime while improving the surveillance coverage. The proposed DDCF mainly consists of CP selection and tree topology construction phases in each round. The CP selection phase takes into consideration multiple parameters including remaining energy, coverage contribution as well as data fusion degree and then dynamically selects CPs in each round for balancing the lifetime of CPs and improving the surveillance quality. In the tree topology construction phase, each sensor selects its parent by considering the remaining energy, data fusion degree and transmission success ratio, which aims to dynamically construct a tree topology for further reducing and balancing the energy consumptions of sensor nodes. Performance study shows that the proposed DDCF outperforms existing studies in terms of network lifetime, fairness as well as surveillance quality.
An Isolated Active Balancing and Monitoring System for Lithium Ion Battery Stacks Utilizing a Single Transformer Per Cell

An active battery management system for lithium ion battery stacks is described, that is robust and scalable. The architecture is based on an isolation unit consisting of a small equal turns ratio high isolation transformer with two diodes. One isolation unit is connected to each series connected cell in the battery stack and enables both accurate cell voltage monitoring and active cell balancing. The output of the isolation unit is completely galvanically isolated and thus suitable for high voltage packs with stringent safety requirements such as automotive and industrial electrical vehicles. Detailed measurements results are presented and a complete prototype for a LiFePO4 16s2p 2-kWh battery module is constructed and its performance measured.
Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection

Crop wild relatives contain great levels of genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops become more resistant and resilient, and adapt to the new conditions that they will experience due to climate change. An impressive global effort occurs for the conservation of various wild crop relatives and facilitates their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage) is a species native to coastal southern and western Europe that has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. is a wild relative crop in the brassica group and B. cretica subsp. nivea has been suggested as a separate subspecies. The species B. cretica has been proposed as a potential gene donor to a number of crops in the brassica group, including broccoli, Brussels sprout, cabbage, cauliflower, kale, swede, turnip and oilseed rape. Here, we present the draft de novo genome assemblies of four B. cretica individuals, including two B. cretica subsp. nivea and two B. cretica. De novo assembly of Illumina MiSeq genomic shotgun sequencing data yielded 243,461 contigs totalling 412.5 Mb in length, corresponding to 122 % of the estimated genome size of B. cretica (339 Mb). According to synteny mapping and phylogenetic analysis of conserved genes, B. cretica genome based on our sequence data reveals approximately 30.360 proteins. Furthermore, our demographic analysis based on whole genome data, suggests that distinct populations of B. cretica are not isolated. Our findings suggest that the classification of the B. cretica in distinct subspecies is not supported from the genome sequence data we analyzed.
Morphological and molecular characterization of predatory aquatic and semi-aquatic bugs of India

In the present study, a total of eight species of aquatic and semi-aquatic Hemiptera collected from India were identified based on morphology and mitochondrial cytochrome oxidase gene I (COI). Details of morphology based identification and the utility of COI gene to identify the aquatic Hemiptera is discussed in this paper.