Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys crocea)

High-density single-nucleotide polymorphism (SNP) genotyping array is an essential tool for genetic analyses of animals and plants. Large yellow croaker (Larimichthys crocea) is one of the most commercially important marine fish species in China. Although plenty of SNPs have been identified in large yellow croaker, no high-throughput genotyping array is available. In this study, a high-throughput SNP array named NingXin-I with 600K SNPs was developed and evaluated. A set of 82 large yellow croakers were collected from different locations of China and re-sequenced. A total of 9.34M SNPs were identified by mapping sequence reads to the large yellow croaker reference genome. About 1.98M candidate SNPs were selected for further analyses by using criteria such as SNP quality score and conversion performance in the final array. Finally, 579.5K SNPs evenly distributed across the large yellow croaker genome with an average spacing of 1.19 kb were proceeded to array production. The performance of NingXin-I array was evaluated in 96 large yellow croaker individuals from five populations, and 83.38% SNPs on the array were polymorphic sites. A further test of the NingXin-I array in five closely related species in Sciaenidae identified 26.68–56.23% polymorphic SNP rate across species. A phylogenetic tree inferred by using the genotype data generated by NingXin-I confirmed the phylogenetic distance of the species in Sciaenidae. The performance of NingXin-I in large yellow croaker and the other species in Sciaenidae suggested high accuracy and broad application. The NingXin-I array should be valuable for quantitative genetic studies, such as genome-wide association studies (GWASs), high-density linkage map construction, haplotype analysis, and genome-based selection.
A Data-Driven Framework for Consistent Financial Valuation and Risk Measurement

Abstract In this paper, we propose a general data-driven framework that unifies the valuation and risk measurement of financial derivatives, which is especially useful in markets with thinly-traded derivatives. We first extract the empirical characteristic function from market-observable time series for the underlying asset prices, and then utilize Fourier techniques to obtain the physical nonparametric density and cumulative distribution function for the log-returns process, based on which we compute risk measures. Then we risk-neutralize the nonparametric density and distribution functions to model-independently valuate a variety of financial derivatives, including path-independent European options and path-dependent exotic contracts. By estimating the state-price density explicitly, and utilizing a convenient basis representation, we are able to greatly simplify the pricing of exotic options all within a consistent model-free framework. Numerical examples, and an empirical example using real market data (Brent crude oil prices) illustrate the accuracy and versatility of the proposed method in handling pricing and risk management of multiple financial contracts based solely on observable time series data.
BGP Beacons, Network Tomography, and Bayesian Computation to Locate Route Flap Damping

Pinpointing autonomous systems which deploy specific inter-domain techniques such as Route Flap Damping (RFD) or Route Origin Validation (ROV) remains a challenge today. Previous approaches to detect per-AS behavior often relied on heuristics derived from passive and active measurements. Those heuristics, however, often lacked accuracy or imposed tight restrictions on the measurement methods. We introduce an algorithmic framework for network tomography, BeCAUSe, which implements Bayesian Computation for Autonomous Systems. Using our original combination of active probing and stochastic simulation, we present the first study to expose the deployment of RFD. In contrast to the expectation of the Internet community, we find that at least 9% of measured ASs enable RFD, most using deprecated vendor default configuration parameters. To illustrate the power of computational Bayesian methods we compare BeCAUSe with three RFD heuristics. Thereafter we successfully apply a generalization of the Bayesian method to a second challenge, measuring deployment of ROV.
Fatty Acids Compositions And Profiles In Traditional Sun-Dried Nile Fish In Sudan

This study was designed to clarify the content of lipid classes and the fatty acid composition of the traditional sundried Nile fish (Kajaike) in Sudan namely: Lates niloticus, Tetraodon lineatus, Heterotis niloticus, Mormyrus niloticus, Clarias lazera and Protopterus annectens. Saturated Fatty Acids (SFA) formed 16.4% 67%, highest in P. annectens and least in C. lazera, dominated by palmitic and stearic acids. Monounsaturated Fatty Acids (MUFA) formed 21.3% 34.4%, dominated by oleic and palmitoleic acids. Polyunsaturated Fatty Acids (PUFA) formed 6.3% 56.8%, dominated by linoleic acid. Linolenic, lenolenic and eicosatrienoic were the highest PUFA in C. lazera. Omega-6 was 6.3% 31.8%, with highest value in C. lazera. Omega-3 was 10.8%, 7.3% and 21.4% in H. niloticus, M. niloticus and C. lazera, respectively. The range of (EPA+DHA) was 2.3% 10.5%. The ratios UFA/SFA was (0.5 to 5.1), a range considered adequate for normal health. It was low (0.5) in P. annectens but high (5.5) in the dry product of C. lazera, higher than 3 recommended by nutritionists. The results indicated that the sun-dried product (Kajaike) of Nile fish is a good source of essential fatty acids for healthy diet.
Who Touched My Browser Fingerprint?: A Large-scale Measurement Study and Classification of Fingerprint Dynamics

Browser fingerprints are dynamic, evolving with feature values changed over time. Previous fingerprinting datasets are either small-scale with only thousands of browser instances or without considering fingerprint dynamics. Thus, it remains unclear how an evolution-aware fingerprinting tool behaves in a real-world setting, e.g., on a website with millions of browser instances, let alone how fingerprint dynamics implicate privacy and security. In this paper, we perform the first, large-scale study of millions of fingerprints to analyze fingerprint dynamics in a real-world website. Our measurement study answers the question of how and why fingerprints change over time by classifying fingerprint dynamics into three categories based on their causes. We also observed several insights from our measurement, e.g., we show that state-of-the-art fingerprinting tool performs poorly in terms of F1-Score and matching speed in this real-world setting.
Prokineticin 2 via Calcium-Sensing Receptor Activated NLRP3 Inflammasome Pathway in the Testicular Macrophages of Uropathogenic Escherichia coli-Induced Orchitis

Reproductive tract infections contribute to the development of testicular inflammatory lesions, leading to male infertility. Previous research shows that the activation of the NLRP3 inflammasome in orchitis promotes the secretion and maturation of IL-1β and, thus, decreases male fertility. The calcium-sensing receptor (CaSR) is closely related to the secretion of proinflammatory cytokines. An increase in the CaSR level promotes the assembly and activation of the NLRP3 inflammasome. However, the role of CaSRs in orchitis is unknown. We first constructed a uropathogenic Escherichia Coli (UPEC) rat orchitis model and then detected the expression of CaSR and NLRP3 inflammatory pathway proteins in testicular macrophages (TM) through RT-PCR and WB, calcium levels in TM through flow cytometry, and proinflammatory factor IL-1β through ELISA. In addition, testosterone levels in the serum samples were detected using liquid chromatography–mass spectrometry (LC-MS). Here, we show that CaSR upregulation after infection in TM in a rat model of UPEC induces the activation of the NLRP3 inflammasome pathway and thereby enhances IL-1β secretion and reduces the testosterone level in the blood. Moreover, CaSR inhibitors can alleviate inflammatory impairment. After UPEC challenge in vitro, CaSR promoted NLRP3 expression and released IL-1β cleaved from TM into the supernatant. Overall, elevated CaSR levels in TM in testes with UPEC-induced orchitis may impair testosterone synthesis through the activation of the NLRP3 pathway and PK2 is an upstream regulatory protein of CaSR. Our research further shows the underlying mechanisms of inflammation-related male infertility and provides anti-inflammatory therapeutic targets for male infertility.
NER‐RAKE: An improved rapid automatic keyword extraction method for scientific literatures based on named entity recognition

The proposing of an accurate and efficient model for automatic keyword extraction of scientific literature is conducive to promoting the development of academic text mining research, such as literature retrieval optimization, research topic discovery, topic evolution analysis, emerging trend detection and so on, with the continuous expansion of digital academic resources. A keyword extraction method is proposed called NER‐RAKE which combines Named Entity Recognition (NER) process with Rapid automatic keyword extraction (RAKE), Bidirectional Long Short‐Term Memory Network Conditional Random Field (BiLSTM‐CRF) is used to recognize the domain entities in the scientific literature so as to enrich the list of candidate keywords divided by RAKE, and the frequency threshold is set to ensure the validity of candidate keywords. NER‐RAKE is better than RAKE in accuracy and recall rate through the keyword extraction experiment in the computer science field. It is effective to combine the process of NER with RAKE, which can improve the efficiency of keyword extraction.
Enzymes of the Alternative Terpenoid Pathway in Escherichia coli

Enzymes of the alternative terpenoid biosynthesis in Escherichia coli were purified to homogeneity from wild type and recombinant strains by column chromatography. Convenient assay methods for the measurement of enzymes activities were established. The enzymes were characterized in detail. New intermediates and putative inhibitors of the deoxyxylulose phosphate pathway were revealed. The purified recombinant enzymes were used as tools for the preparation of large amount of intermediates in order to elucidate the late steps leading to isopentenyl diphosphate.
Automated Segmentation of User Interface Logs Using Trace Alignment Techniques (Extended Abstract)

—Robotic Process Automation (RPA) is a fast-emerging automation technology that allows organizations to automate high volume routines. RPA tools are able to capture in dedicated User Interface (UI) logs the execution of routines previously performed by a human user on the UI of a computer system, and then emulate their enactment in place of the user by means of a software (SW) robot. The issue to automatically understand which user actions contribute to a speciﬁc routine inside the UI log is also known as segmentation . The proposed research investigates how to leverage trace alignment techniques in Process Mining to automatically derive the boundaries of a routine by analyzing the UI log that keeps track of its execution, thus tackling the segmentation issue.
Antibacterial Effects of Methanol Extracts of Some Plant Species Belonging to Lamiaceae Family

Species belonging to Lamiaceae family are used as an antibacterial agent among medical plants. The aim of the present study was to determinate the antibacterial effects of the methanolic extracts of some plant species belonging Lamiaceae family which distributed to different ecological conditions in Amasya. The antibacterial effects of Stachys annua , Scutellaria salviifolia and Nepata nuda plant extracts were determined by disc diffusion and micro dilution methods. The antibacterial effects of plant extracts were tested against standard strains of Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 35218, Klebsiella pneumoniae ATCC 70600, Pseudomonas aeruginosa ATCC 27853 and Salmonella enteritidis ATCC 13076. We observed that plant extracts had antibacterial effect when they compared with control group antibiotics. According to the results of disc diffusion method, the highest antibacterial effect was identified in Scutellaria salviifolia , Stachys annua and Nepata nuda , respectively. The microdilution method was studied concentration range from 6.25 - to 50 mg/ml. MICs of the most effective Scutellaria salviifolia plant extract were 12.5 mg/ml for S. aureus , S. enteritidis and E. coli ; 25 mg/ml for K. pneumoniae and P. aeruginosa . The MICs of Stachys annua extract were 12.5 mg/ml for P. aeruginosa , S. enteritidis and E. coli ; 25 mg/ml for S. aureus and 50 mg/ml for K. pneumoniae . MICs of Nepata nuda were 12.5 mg/ml K. pneumonia ; 25 mg/ml for S. aureus ; 50 mg/ml for P. aeruginosa , S. enteritidis and E. coli. This study showed that Scutellaria salviifolia, Stachys annua and Nepata nuda species have in vitro antibacterial activities.
Retinal Lesions Detection for Screening of Diabetic Retinopathy

Diabetic retinopathy is an eye disease, which causes blindness in diabetic patients. Early detection and periodic screening of diabetic retinopathy can reduce the progress of the disease and reduce vision loss. Due to diabetic retinopathy, there are lesions in the retina. Retinal lesions are mainly dark and bright lesions. Lesions have different properties such as colour, shape, and size. Microaneurysms (MAs) and hemorrhages (HEMs) are dark lesions and exudates(EXs) are bright lesions. This work proposes a retinal lesions detection system for screening diabetic retinopathy. Top hat and bottom hat transform are used for the enhancement of the image for the dark lesion detection. The optic disc is suppressed first to facilitate further processing of bright lesion detection. Morphological opening and closing are used for the detection of the bright lesion. Two SVMs are used in this work, one SVM is used to classify the dark lesion into microaneurysms and hemorrhages, and other one classify the bright lesion into hard exudates and non-hard exudates.
Characterisation of three Alphabaculovirus isolates from the gypsy moth, Lymantria dispar dispar (Lepidoptera: Erebidae), in Turkey

ABSTRACT In this study, Lymantria dispar dispar larvae, collected from three different localities in Turkey, were examined for the presence of inclusion bodies under phase contrast and electron microscopes. Inclusion bodies from infected larvae were subjected to polymerase chain reaction using the conserved primers for polyhedrin (polh), late expression factor 8 (lef-8) and late expression factor 9 (lef-9) genes. Sequence analysis confirmed that larvae collected from the three different localities contained multiple nucleopolyhedrosis viruses (MNPVs). These isolates were designated LdMNPV-T1, LdMNPV-T2 and LdMNPV-T3. Phylogenetic analyses of these isolates were performed using target genes polh, lef-8 and lef-9. Restriction endonuclease analysis of the three geographic isolates with EcoRI and PstI enzymes demonstrated some differences existed among the isolates. According to the EcoRI profile, the mean estimated size for the complete genome of each isolate (LdMNPV-T1, LdMNPV-T2 and LdMNPV-T3) was calculated to be approximately 170, 153 and 170 kb, respectively. Insecticidal activities of each isolate were tested on L. d. dispar larvae using four different viral concentrations between 103 and 106 OBs/ml. Results showed that the mortalities for LdMNPV-T1, -T2 and -T3 ranged between 13–53%, 47–100% and 46–93%, respectively. The LC50 and LC95 values of LdMNPV-T2 were not significantly different from the respective corresponding values of the other two isolates. However, isolate LdMNPV-T2 killed larvae with a LC50 value that was lower than the other two isolates. Our results suggested there are promising LdMNPV isolates in Turkey that can be used for microbial control of L. d. dispar larvae.
Assessment of Genetic Diversity of Narra (Pterocarpus indicus Willd.) Populations From Various Seed Sources in the Philippines Using RAPD

Pterocarpus indicus Willd. (narra), a critically endangered group, is one of the priority species for conservation and reforestation in the Philippines due to its economic, industrial, and ecological importance. A range of 29 to 40 individual samples from each of six seed sources from the Philippines were tested for genetic diversity using 11 RAPD markers. A total of 134 loci were detected, 129 of which were polymorphic. The mean genetic diversity within population was found to be moderate at 0.3183, which could be attributed to the deciduous and outcrossing nature of narra. The genetic differentiation among populations (0.0575) and Wright’s Fixation Index (0.1528) suggests nearness of the populations to each other and distance from fixation of alternative alleles in the populations. The genetic distance and cluster analysis did not conform to geographical distribution, but revealed the relationships and the possible origin/s of the individuals of the populations. The results of the study is useful in the selection of sources of good planting materials for the improvement of narra tree in the Philippines.
Conditioning alleviates reduced yield of smaller plugs of ‘Albion’ strawberry (Fragaria X ananassa Duch.) in off-season plasticulture production

ABSTRACT The influences of plug size, planting density, and mulch colour on responses to photoperiod and nitrogen conditioning of ‘Albion’ strawberry (Fragaria x ananassa Duch.) plants were evaluated in off-season field production in New Jersey, USA. Three different sized plug plants (7.6 cm square pots, 24-cell plug trays, or 50-cell plug trays) were conditioned with natural days (ND, natural daylength) or long days (LD, natural daylength supplemented with 24 h incandescent radiation) for one week followed by ND plus 100 ppm nitrogen (N) for 4 weeks or LD plus 800 ppm N for 4 weeks. Plants were then established in plasticulture on black, white, or silver mulch. In a second experiment, plug plants (439 cm3) were conditioned with LD and nitrogen then established in plasticulture on black, white, or silver mulch at 3 planting densities (0.46, 0.23, and 0.16 m2•plant−1 (2, 4, and 6 plants•m−2)). Fruit were harvested from August through October in both experiments. Conditioning enhanced off-season fall production. White plastic enhanced survival, productivity, and fruit size and larger plugs were more productive than smaller ones. If smaller plugs are desired, conditioning prevents the reduction in yield observed with non-conditioned smaller plugs.
Pharmacokinetics and allometric scaling of antimalarial drugs

s and presentations Senarathna S.M.D.K. G, Batty Kevin T. Allometric scaling of antimalarial drugs. In Joint Australasian Society of Clinical and Experimental Pharmacologist and Toxicologist and Australasian Pharmaceutical Sciences Association 2012 conference. Sydney, Australia, 2-5 December 2012 Senarathna S.M.D.K. G, Batty Kevin T. Allometric scaling of antimalarial drugs. Mark Liveris Research Seminar, Faculty of Health Sciences, Curtin University, Australia, 11 November 2013 Senarathna S.M.D.KG. Page-Sharp Madhu, Crowe A. In-vitro drug transport of antimalarials; amodiaquine, mefloquine and methylene blue. In 63 Annual meeting of American Society of Tropical Medicine and Hygiene, New Orleans, USA, American Society of Tropical Medicine and Hygiene,2-6 November 2014. Senarathna S.M.D.KG, Crowe A. Development of a robust Caco-2 cell model for drug transport studies. In Science on the Swan Inaugural Conference 2015, Perth, Australia, 21-23 April 2015. Crowe A, Senarathna S.M.D.KG. Page-Sharp Madhu. The interactions of Pglycoprotein with antimalarial drugs, including substrate affinity and inhibition. In Science on the Swan Inaugural Conference 2015, Perth, Australia, 21-23 April 2015
3D spatial conservation prioritisation: Accounting for depth in marine environments

While marine environments are three‐dimensional (3D) in nature, current approaches and tools for planning and prioritising actions in the ocean are predominantly two dimensional. Here, we develop a novel 3D marine spatial conservation prioritisation approach, which explicitly accounts for the inherent vertical heterogeneity of the ocean. This enables both vertical and horizontal spatial prioritisation to be performed simultaneously. To our knowledge, this is the first endeavour to develop prioritisation of conservation actions in 3D. We applied the 3D spatial conservation prioritisation approach to the Mediterranean Sea as a case study. We first subdivided the Mediterranean Sea into 3D planning units by assigning them a z coordinate (representing depth). We further partitioned these 3D planning units vertically into three depth layers; this allowed us to quantify biodiversity (1,011 species and 19 geomorphic features) and the cost of conservation actions at different depths. We adapted the prioritisation software Marxan to identify 3D networks of sites where biodiversity conservation targets are achieved for the minimum cost. Using the 3D approach presented here, we identified networks of sites where conservation targets for all biodiversity features were achieved. Importantly, these networks included areas of the ocean where only particular depth layers along the water column were identified as priorities for conservation. The 3D approach also proved to be more cost‐efficient than the traditional 2D approach. Spatial priorities within the networks of sites selected were considerably different when comparing the 2D and 3D approaches. Prioritising in 3D allows conservation and marine spatial planners to target specific threats to specific conservation features, at specific depths in the ocean. This provides a platform to further integrate systematic conservation planning into the wider ongoing and future marine spatial planning and ocean zoning processes.
An improbable opportunistic predator: the functional morphology of Pinna nobilis (Bivalvia: Pterioida: Pinnidae)

The functional morphology of Pinna nobilis is described, with special reference to the uniquely pinnid pallial organ, the similarly unique buccal (formerly pallial) gland, the stomach and its contents. The pallial gland produces sulphuric acid which as well as functioning as a shell cleaning swab may be involved in prey capture. The buccal gland discharging into the oesophagus has proteolytic digestive functions while the stomach is adapted for the reception and digestion of captured, mucous-bound, mesozooplanktonic and epi- and endo-benthic, prey items. Pinna nobilis is thus not simply either an accidental or incidental predator of such species but is opportunistic. The buccal glands and stomachs of other Pinnidae are not so specialized as in P. nobilis, possibly indicating that in the particular, oligotrophic, environment of the Mediterranean and Adriatic Seas, and in which it is endemic, P. nobilis has, in addition to being a typical ctenidial suspension feeder, become an opportunistic predator. Although the deep sea representatives of the Septibranchia (Anomalodesmata) and Propeamussidae are obligate predators, this is the first record of any bivalve functioning as an opportunistic predator with unique morphological adaptations to facilitate this.