Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in the structure of the phytoplankton community in a Nile tilapia fishpond

Abstract Aim Our objectives were to recognize species that can serve as biological descriptors and evaluate the changes in the phytoplankton community throughout the grow-out period of the Nile tilapia (Oreochromis niloticus Linnaeus 1758) related to management practices and to limnological variables. Methods Samples from the inflow water and the fishpond were collected for the analysis of limnological variables and the structure of the phytoplankton community. Results In the fishpond, we registered a 1.5 times increase in nitrogen and total suspended solids and a 2 times increase in phosphorous compared to the inflow water. During the grow-out period (113 days), 134 taxa belonging to 10 taxonomic classes were registered. Chlorophyceae (60 taxa) and Cyanobacteria (26 taxa) showed the greatest diversity and abundance of species. The largest biovolumes were recorded in the fishpond. Nanoplanktonic species were the most abundant and represented 35% of the descriptor species in the phytoplankton community of the fishpond. Conclusions The instability of the system associated with the control of the hydraulic retention time as a consequence of management practices, favored the presence of species with small cellular dimensions. The decrease in air and water temperature registered at the end of the grow-out period probably favored the increase and persistence of diatoms. Graphical abstract Spatial variation of the main phytoplanktonic taxa in the fishpond.
The complete mitochondrial genome of Sargassum siliquastrum (Phaeophyceae) and its phylogenetic analysis

Abstract The complete S. siliquastrum mitogenome length was 34,765 bp. The mitogenome contains 67 genes, including 37 protein-coding, three rRNA, 25 tRNA genes, and two conserved open reading frames (ORFs). The overall GC content of the genome is 36.59%. The complete mitogenome sequence provided herein would help understand Sargassum evolution.
Genome-wide identification, classification and expression pattern of LBD gene family in Camellia sinensis

Abstract The plant-specific LBD (LATERAL ORGAN BOUNDARIES DOMAIN) genes belong to a major family of transcription factors that encode a zinc finger-like domain. This family plays crucial roles in plant development, including lateral organ development, pathogen response, pollen development, plant regeneration and hormone response. However, there is no detailed information of LBD genes in the tea plant. Tea plant [Camellia sinensis (L.) O. Kuntze] is a perennial evergreen woody crop that is cultivated worldwide. Tea leaves are used as a non-alcoholic beverage, which is known for its beneficial ingredients and multiple flavours. In this study, a total of 31 CsLBD genes were identified and characterized based on the genome of C. sinensis. CsLBD factors and Arabidopsis counterparts were clustered into 10 subgroups after phylogenetic analysis. Conserved motif analysis revealed that CsLBD proteins with a close evolutionary relationship possessed uniform or similar motif compositions. The interaction networks of LBD proteins in C. sinensis were established according to the data in Arabidopsis. Seven CsLBD genes were examined through qRT-PCR (quantitative real time polymerase chain reaction) in tea plant cultivar, ‘Longjing43’. The expression profiles of these CsLBD genes were investigated in different tissues (i.e. root, stem, leaf and flower) and subjected to five hormonal stimuli (i.e. abscisic acid, gibberellin acid, ethephon, methyl jasmonate and salicylic acid). This study provides an extensive overview of the CsLBD family genes and a valuable foundation for future functional studies of CsLBD factors.
Evidence of coastal trapped wave scattering using high-frequency
radar data in the Mid-Atlantic Bight

Abstract. Coastal trapped waves (CTWs) become scattered when they encounter irregular coastlines and bathymetry during propagation. Analytical and modeling studies have provided some information about the different types of shelf geometries that can induce scattering, but much of the CTW scattering process generally remains a large knowledge gap. Furthermore, CTW scattering has never before been directly identified with observations. High-frequency radar surface velocity data covering the Mid-Atlantic Bight (MAB) continental shelf provides unprecedented observations of CTWs within a region with a highly complex coastline and bathymetry. A combination of velocity vector maps from real vector empirical orthogonal function (R-EOF) analysis and phase maps from complex empirical orthogonal function (C-EOF) analysis allow the identification of CTW scattering by assuming each EOF mode corresponds to a CTW mode. Abrupt jumps in phase in association with magnitude amplification/reduction or directional rotation of velocity vectors are indications of scattering. Using these guidelines, Georges Bank, Hudson Shelf Valley, Delaware Bay mouth, Chesapeake Bay mouth, and the North Carolina shelf are identified as high scattering regions within the MAB. Furthermore, stratification is confirmed to increase scattering into progressively higher order modes through a cascading process by comparing winter and summer cases, which supports previous theoretical and numerical model predictions. The simple methodology used here can be applied to observations of CTWs on other coastlines around the world to identify additional scattering regions and help close the knowledge gap.
Effect of building-up core material’s kind on location of fracture for endodontically treated teeth restored using glass Fiber post (in-vitro study)

Introduction: The quality of the material used to build-up the cores of the treated and restored teeth with fiberglass posts affect the location of fracture, as it plays an important role in the durability and durability of the coronary root restoration under different oral environment conditions. The aim of the study: Study of the effect of the core building-up material quality of three different materials on the location of fracture for a group of lower premolars after treating the core and restoring them with fiberglass posts. Research materials and methods: The research sample consisted of (30) lower first laughs, as these teeth were extracted in the course of orthodontic treatment (free from any defects) and stored with distilled water. The clinical crowns of these teeth were cut so that a coronary tissue was kept 2mm high above the enamel-cemento junction. These teeth were treated with pulp and restored with fiberglass posts. The research sample was divided into three groups, each consisting of (10) premolars, according to the type of core building-up material. 1. Composite Resin (IVOCLAR, T-Econom, Liechtenstein) Group T. 2. Flow composite resin (IVOCLAR, Titric N-Flow, Liechtenstein) Group F. 3. Resin Reinforced Glass Ionomer Cement (3M ESPE, Vitermer, USA) Group G. The teeth were crowned with Nickel-Chrome crowns and then an oblique force was applied at an angle of 45 to the tooth axis using a general mechanical testing device at a speed of 1mm / min until failure occur. Results: It was found that group T premolars restored with composite resin had nine Cervical Fracture states and once in middle while the locations of fracture fore premolars restored with Flow resin had eight Cervical Fracture states and twice in Middle, and locations of fracture for premolars Restored with Glass ionomer cement had ten Cervical Fracture, and significant differences were observed between groups (P =1). Conclusion: As it turns out, there is no correlation to the core building-up material in the failure model.
The complete mitochondrial genome of Homatula berezowskii (Cypriniformes, Nemacheilidae, Nemachilinae)

Abstract Homatula berezowskii (Günther 1896), used to be recognized as a synonym of Homatula variegate, was now identified as a valid species. However, these morphological studies lack genetic evidence to support. In the present study, we determined the first complete mitochondrial genome of H. berezowskii by Sanger dideoxy sequencing. The genome size is 16,570 bp and it contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding control region (D-loop). Phylogenetic analyses based on the complete mitochondrial genome indicated the H. berezowskii was clustered with H. potanini first and then with the H. variegate. This work may be helpful to clarify the taxonomic status of H. berezowskii.
Bayesian Inference of Mantle Viscosity From Whole‐Mantle Density Models

The long‐wavelength geoid is sensitive to Earth's mantle density structure as well as radial variations in mantle viscosity. We present a suite of inversions for the radial viscosity profile using whole‐mantle models that jointly constrain the variations in density, shear‐ and compressional‐wavespeeds using full‐spectrum tomography. We use a Bayesian approach to identify a collection of viscosity profiles compatible with the geoid, while enabling uncertainties to be quantified. Depending on tomographic model parameterization and data weighting, it is possible to obtain models with either positive‐ or negative‐buoyancy in the large low shear velocity provinces. We demonstrate that whole‐mantle density models in which density and VS variations are correlated imply an increase in viscosity below the transition zone, often near 1,000 km. Many solutions also contain a low‐viscosity channel below 650 km. Alternatively, models in which density is less‐correlated with VS—which better fit normal mode data—require a reduced viscosity region in the lower mantle. This feature appears in solutions because it reduces the sensitivity of the geoid to buoyancy variations in the lowermost mantle. The variability among the viscosity profiles obtained using different density models is indicative of the strong nonlinearities in modeling the geoid and the limited resolving power of the geoid kernels. We demonstrate that linearized analyses of model resolution do not adequately capture the posterior uncertainty on viscosity. Joint and iterative inversions of viscosity, wavespeeds, and density using seismic and geodynamic observations are required to reduce bias from prior assumptions on viscosity variation and scalings between material properties.
Electroforming-free flexible organic resistive random access memory based on a nanocomposite of poly(3-hexylthiophene-2,5-diyl) and orange dye with a low threshold voltage

The charge trapping characteristics of an organic nanocomposite based on two polymers, poly(3-hexylthiophene-2,5-diyl) (P3HT) and orange dye (OD), were investigated by fabricating a sandwiched structure on a flexible polyethylene terephthalate substrate. The fabricated flexible organic device with a configuration of silver (Ag)/P3HT–OD/Ag displayed highly stable results consistent with a bipolar non-volatile resistive random access memory (RRAM) device using simple and controllable fabrication technology. It was observed that by the addition of OD, low threshold voltages (V th) of V set = 1.5 V and V reset = −1.5 V were achieved owing to the values of work function and energy bandgap of the materials used. Electrical rewritable effects of the fabricated memory device were tested for 102 voltage sweeps and 104s without any considerable degradation of its bistable resistive states. The switching mechanism was considered to be space charge limited current and this was verified by plotting the double logarithmic I–V curve. This is the first RRAM device based on P3HT polymer whose mechanical robustness has been tested for its mechanical robustness by bending it for 25 bending cycles at a bending diameter ranging from 15 cm to 5 cm without any considerable change in its properties. This finding offers important guidelines for reproducing next-generation flexible organic nanocomposite-based memory devices that are simple to fabricate and have low operating voltages and highly stable memory behavior.
One Cycle Control of a PWM Rectifier a New Approach

This paper analyzes a Digital Signal Processor (DSP) based One Cycle Control (OCC) strategy for a Power Factor Corrector (PFC) rectifier with Common-mode Voltage (CMV) immunity. It is proposed a strategy that utilizes an emulated-resistance-controller in closed-loop configuration to set the dc-link voltage to achieve unity power factor (UPF). It is shown that if the PFC can achieve UPF condition and if the phase voltage is only affected by CMV, then phase current is free from CMV, as well as a lead-lag compensator (LLC) to average phase current.
A Survey of Road Accident Reporting and Driver’s Behavior Awareness Systems: The Case of Tanzania

Road traffic accidents are a leading cause of death in developed and developing countries. It has been shown that road accident reporting systems could reduce their effects by minimizing response time and mapping road accident-prone areas. This paper provides an overview of the systems and applications for road accident reporting and drivers’ behavior awareness. A field survey, conducted in Dar es Salaam region in Tanzania, investigated the current state of road traffic accident reporting. Findings showed that the main means of reporting road accidents were physical reporting and police emergency phone calls. The absence of alternative means for reporting road accidents causes information delay and lack of precise accident location for the emergency first responders. This paper concludes by proposing a mobile application system for road accident reporting and drivers’ over-speed awareness, in order to improve road safety in developing countries.
Metformin rescues muscle function in BAG3 myofibrillar myopathy models

Dominant de novo mutations in the co-chaperone BAG3 cause a severe form of myofibrillar myopathy, exhibiting progressive muscle weakness, muscle structural failure, and protein aggregation. To identify therapies we generated two zebrafish models, one conditionally expressing BAG3P209L and one with a nonsense mutation in bag3. Whilst transgenic BAG3P209L expressing fish display protein aggregation, modelling the early phase of the disease, bag3−/− fish demonstrate impaired autophagic activity, exercise dependent fibre disintegration, and reduced swimming activity, consistent with later stages. We confirmed the presence of impaired autophagy in patient samples and screened autophagy promoting compounds for their effectiveness at removing protein aggregates, identifying nine including Metformin. Further evaluation demonstrated Metformin is not only able to remove the protein aggregates in zebrafish and human myoblasts but is also able to rescue the fibre disintegration and swimming deficit observed in the bag3−/− fish. Therefore, repurposing Metformin provides a promising therapy for BAG3 myopathy.
New In Situ Aerosol Hyperspectral Optical Measurements over 300–700 nm, Part 1: Spectral Aerosol Extinction (SpEx) Instrument Field Validation during the KORUS-OC cruise

1National Institute of Aerospace, Hampton, Virginia, United States of America 2NASA Langley Research Center, Hampton, Virginia, United States of America 3NASA Goddard Space Flight Center, Greenbelt, Maryland, United States of America 10 4City University of New York, New York, New York, United States of America 5Science Systems and Applications Inc., Hampton, Virginia, United States of America 6California State University, San Bernardino, California, United States of America 7Springfield College, Springfield, Massachusetts, United States of America
Comparative analysis of the Agrobacterium mediated transformation using primary and secondary callus of indica rice (Oryza sativa L.) using phosphinothricin as selecting medium

Inefficiency of the 'Agrobacterium'-mediated transformation in indica rice cultivar has been widely reported in the literature. Till date, mature seeds, primary and secondary calli have been the mostly used explants for transformation in indica rice. Therefore, the present investigation was undertaken to compare the Agrobacterium mediated transformation using primary and secondary callus as explants in the indica rice and testing a herbicide phosphinothricin (PPT) based bar gene selection system. Four different constructs containing the bar gene expression cassette were made. The constructs I and II were transformed with the secondary calli based protocol by three independent experiments. Similarly, constructs III and IV were transformed with the primary calli based protocol by 9 and 20 independent experiments, respectively. The transformation efficiency for the primary and secondary calli based transformation under PPT selection were calculated in the range of 0.13 - 0.26% and 2.0 - 2.66%, respectively. The transgenic escapes were detected by genomic DNA PCR amplification, Southern blot analysis and basta leaf painting assay. It was found that the primary calli based transformation has 46-50% transgenic escapes, whereas secondary calli based transformation have only 20-29% transgenic escapes. The present study reports that secondary calli as explants perform better than primary calli under PPT selection in the Agrobacterium-mediated indica rice transformation.
eTumorRisk, an algorithm predicts cancer risk based on comutated gene networks in an individual’s germline genome

Early cancer detection has potentials to reduce cancer burden. A prior identification of the high-risk population of cancer will facilitate cancer early detection. Traditionally, cancer predisposition genes such as BRCA1/2 have been used for identifying high-risk population of developing breast and ovarian cancers. However, such high-risk genes have only a few. Moreover, the complexity of cancer hints multiple genes involved but also prevents from identifying such predictors for predicting high-risk subpopulation. Therefore, we asked if the germline genomes could be used to identify high-risk cancer population. So far, none of such predictive models has been developed. Here, by analyzing of the germline genomes of 3,090 cancer patients representing 12 common cancer types and 25,701 non-cancer individuals, we discovered significantly differential co-mutated gene pairs between cancer and non-cancer groups, and even between cancer types. Based on these findings, we developed a network-based algorithm, eTumorRisk, which enables to predict individuals’ cancer risk of six genetic-dominant cancers including breast, colon, brain, leukemia, ovarian and endometrial cancers with the prediction accuracies of 74.1-91.7% and have 1-3 false-negatives out of the validating samples (n=14,701). The eTumorRisk which has a very low false-negative rate might be useful in screening of general population for identifying high-risk cancer population.
Optimized Shallow Neural Networks for Sum-Rate Maximization in Energy Harvesting Downlink Multiuser NOMA Systems

This article considers a power allocation problem in energy harvesting downlink non-orthogonal multiple access (NOMA) systems in which a transmitter sends desired messages to their respective receivers by using harvested energy. To tackle this problem, we make use of a reinforcement learning approach based on a shallow neural network structure. We prove that the optimal power allocation policy and the optimal action-value function depend monotonically on some of their input variables and the shallow neural network structure is designed based on properties revealed in the proof. Different from inefficient deep learning methods that tend to require tremendous computational resources, this structure is capable of fully capturing the characteristics of the desired function with a single hidden layer. The optimized structure also allows learning agents to be robust and highly reliable in learning about randomly occurring data. Furthermore, we provide comprehensive experimental results in harsh environments where various arbitrary factors are assumed in order to demonstrate the robustness of the proposed learning approach compared with deep neural networks without proper grounds. It is also shown that the proposed learning process converges to a policy that outperforms existing power allocation algorithms.
Development of a Manually Operated Hydraulic Cattle Feed Block Making Machine

Feed blocks, which are made by improving the nutritional status of agricultural by-products, are a proved solution to uplift the productivity of dairy animals in Sri Lanka. Though feed block making machines are locally available, their prices are unaffordable for small-scale rural farmers. Therefore, the objective of this study was to introduce an efficient and affordable feed block making machine for small-scale farmers. The newly fabricated machine consisted of hydraulically operated jack, mould and a piston fixed to an iron frame. The total cost of production was 43,000 LKR. Feed blocks were produced with the new machine using two separate mixtures of ingredients with four different compaction times. Mixture 1 contained 10% molasses apart from other ingredients and without cement, whereas mixture 2 replaced 5% of molasses with cement. The suitable compaction time for the mixture 1 and mixture 2 were 15 minutes and 10 minutes, respectively at 19265 kN m-2 maximum pressure. The actual capacity of the machine for mixture 1 prepared with 15 min compaction time was 3 blocks h-1, while it was 4 blocks h-1 for the mixture 2 prepared with 10 min compaction time irrespective to the gender. The post-compression expansion and durability of mixture 1 were 23.73% and 99.64%, respectively while the corresponding figures for mixture 2 were 18.64% and 99.82%. No change could be observed in appearance, colour and odour of the feed blocks within 30 days of storage. According to the results, this new machine is affordable to small-scale farmers and it can be successfully used to produce feed blocks for cattle.
Survival under conditions of variable food availability: Resource utilization and storage in the cold‐water coral Lophelia pertusa

Cold‐water coral (CWC) reefs are hotspots of biodiversity and productivity in the deep sea, but their distribution is limited by the availability of food, which undergoes complex local and temporal variability. We studied the resource utilization, metabolism, and tissue storage of CWC Lophelia pertusa during an experimentally simulated 3‐day food pulse, of 13C15N‐enriched phytodetritus, followed by a 4‐week food deprivation. Oxygen consumption (0.145 μmol O2 [mmol organic carbon {OC}]−1 h−1), release of particulate organic matter (0.029 μmol particulate organic carbon [POC] [mmol OC]−1 h−1 and 0.005 μmol particulate organic nitrogen [mmol OC]−1 h−1), ammonium excretion (0.004 μmol NH4+ [mmol OC]−1 h−1), tissue C and N content, and fatty acid (FA) and amino acid composition did not change significantly during the experiment. Metabolization of the labeled phytodetritus, however, underwent distinct temporal dynamics. Initially, L. pertusa preferentially used phytodetritus‐derived C for respiration (2.2 ± 0.36 nmol C [mmol OC]−1 h−1) and mucus production (0.94 ± 0.52 nmol C [mmol OC]−1 h−1), but those tracer fluxes declined exponentially to <20% within 2 weeks after feeding and then remained stable, indicating that the remainder of the incorporated phytodetritus had entered a tissue pool with lower turnover. Analysis of 13C in individual FAs revealed a mismatch between the FAs incorporated from phytodetritus and the FA requirements of the coral. We suggest that feeding on other resources, such as lipid‐rich zooplankton, could fill this deficiency. A release of 10% of their total OC as respired C and POC during the 4‐week food deprivation underlines the importance of regular food pulses for CWC reefs.