Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of PLCζ induced Ca²⁺ oscillations in mouse eggs at fertilisation

All the events of egg activation in mammalian eggs are triggered physiologically by transient increases in cytosolic free Ca²⁺ referred to as Ca²⁺ioscillations. These oscillations are initiated by the sperm derived PLC isoform, PLCζ. PLCζ releases Ca²⁺ by hydrolysing its substrate PI(4,5)P₂ to produce IP₃, however, many of the mechanisms by which PLCζ elicits Ca²⁺release in eggs are poorly understood. The results of this thesis confirm that whilstPLCζ cRNA and recombinant protein is able to cause Ca²⁺ioscillations in mouse eggs the sperm derived protein PAWP does not cause any Ca²⁺ release in any circumstances. It is shown that EF hand domain and XY linker of PLCζ are important in determining its Ca²⁺i releasing ability by enabling PLCζ binding to its substrate PI(4,5)P₂ through electrostatic interactions. The C2 domain of PLCζ was also found to play a crucial role in the Ca²⁺ releasing ability of PLCζ, possibly by binding to lipids or proteins in the target membrane. The Ca²⁺releasing ability of eggs is acquired during oocyte maturation and a dramatic increase in PLCζ sensitivity of oocytes occurs after germinal vesicle breakdown.A variety of markers for PLCζ’s substrate PI(4,5)P₂ including fluorescent PI(4,5)P₂ and gelsolin based fluorescent probes suggests that this PI(4,5)P₂ is localised to intracellular vesicles that could derive from Golgi apparatus. Attempts are made to measure PI turnover in these intracellular compartments of eggs during PLCζ induced Ca²⁺i oscillations using several probes. The results of this thesis suggest that PLCζ releases Ca²⁺ by a novel IP₃ based signalling pathway that involves an intracellular source of PI(4,5)P₂ .
A New Species of Bennini (Hemiptera, Cixiidae) from Granitic Subterranean Environment in Vietnam, an Under-Investigated Biotope

Abstract. A new species of the planthopper taxon Bennini (Hemiptera: Fulgoromorpha: Cixiidae) was discovered in the wide interstitial voids of a granitic blockfield in Vietnam. A key to the species of the Vietnam-endemic Bennini genus Sanghabenna is provided and Sanghabenna florenciana sp. nov. is described and illustrated. Molecular data including 18S in part and CO1 barcode sequences of the species, as well as for the first time a detailed description of nymphal morphology of a Bennini are provided. According to the ecological parameters of its habitat and its morphological configuration, Sanghabenna florenciana sp. nov. is classified as an exapted eutroglophile taxon.
Detailed simulation of regenerative braking of BLDC motor for electric vehicles

Reducing the use of fossil fuels is among the targets of the countries. Because they are likely to run out in the future and cause greenhouse gas emissions to the environment. One of the causes of greenhouse gas emissions is fossil fuel vehicles. The fossil-fueled vehicles can be replaced by electric vehicles. Electric vehicles have lower fuel costs due to the high efficiency of electric motors compared to internal combustion engines. The inadequacy in the batteries and the lack of charging stations require these vehicles to be used within certain distances. One of the ways to increase the distance is the regenerative braking of brushless direct current (BLDC) motors, which makes it re-usable when the vehicle is braking. This study presents a detailed simulation of the operation of a BLDC motor both as a motor and as a generator with regenerative braking by using Matlab/Simulink program. According to a simulation scenario, an energy recovery of 0.35% was achieved.
Phytoremediation of contaminated soils using ornamental plants

Phytoremediation has attracted increasing attention and is a promising technology for addressing soil contamination problems. Unlike other kinds of remediation plants, ornamental plants grown for decorative purposes in gardens and landscape design projects have been an important source of remediation plants in recent years. In addition to beautifying the environment, some ornamental plants can not only grow well but also accumulate or degrade contaminants when growing in soil contaminated with heavy metals or organic pollutants. Especially in contaminated urban areas, it is comparatively rare and commendable when remediation plants with ornamental value are applied. In this review, we summarized the current research on the phytoremediation of contaminated soils using ornamental plants, evaluated the phytoremediation capacity of ornamental plants in heavy-metal and organic pollutant-contaminated soils, and highlighted specific ornamental plants with a strong accumulation ability and tolerance to pollutants.
Improve Quality of Alfalfa Silage Ensiled with Orange Pulp and Bacterial Additive

This study evaluated the effects of Lactobacillus buchneri (LAB) and orange pulp (OP) supplementation on chemical composition, in vitro and in situ degradability, dry matter (DM), pH and aerobic stability of alfalfa silage. Treatments were 1) alfalfa without any additive (control), 2) alfalfa + OP (70% alfalfa mixed with 30% fresh OP, LAB0), 3) treatment 2 with 1.5 g LAB/ton (LAB1), 4) treatment 2 with 3 g LAB/ton (LAB2) and 5) treatment 2 with 4.5 g LAB/ton (LAB3). Treatments were replicated three times in laboratory mini silos for 90 d in a closed barn with a ambient temperature (15 to 18 oC). As a result of this study, the experimental treatments did not affect on DM of silage at the end of the ensiling period. Control treatment had the highest pH (4.5) among the experimental treatments ( P<0.05). Supplementation alfalfa with OP resulted in significant increase in water soluble carbohydrate (WSC) and total volatile fatty acids (VFAs) ( P<0.05). Treating alfalfa silage with OP and LAB improved aerobic stabilities of treatments significantly, as compared to LAB0. Supplementation of silage with OP and bacterial inoculant increased DM digestibility. These findings indicated that LAB can improve the aerobic stability and quality of silage in laboratory silos and also, OP and LAB might improve silage quality and cause better silage management in the farm.
Investigating Lateral Line Canal Morphogenesis as a Bone Remodeling Process in Lake Malawi Cichlids

The lateral line (LL) system is a key non-visual sensory modality founded in all fishes and larval and adult aquatic amphibians. In bony fishes, the LL system consists of series of superficial neuromasts (on the skin surface) and canal neuromasts (housed in bony canals). Differences in LL canal phenotype have consequences for LL sensory capabilities, and, as such, could contribute to speciation. The LL system develops with a process of neuromast patterning followed by the genesis of canals from dermal bone around a subset of neuromasts. This study used histochemical methods to describe canal morphogenesis by assessing osteoblast (OB, bone building cells) and osteoclast (OC, bone resorbing cells) activity through ontogeny. OB and OC activity was studied along the length and around the circumference of the mandibular LL canal in two species of Lake Malawi cichlids. Aulonocara stuartgranti (widened canals) and Tramitichromis sp. (narrow canals) are known to develop their different canal phenotypes as a result of dissociated heterochrony. In both species, OB activity is concentrated in the canal roof and floor (behind the neuromast), while OC activity is focused primarily in the canal walls. Further, both species demonstrate one pulse of bone deposition early in ontogeny and another pulse of bone resorption later in ontogeny, but in Aulonocara not Tramitichromis, the pulse of bone resorption is accompanied by high levels of OB activity. Thus, the second pulse of bone cell activity in Aulonocara is defined by bone resorption and bone deposition: active bone remodeling by the simultaneous action of OBs and OCs. These results corroborate the observation of dissociated heterochrony (Bird and Webb, 2014) at the cell level, suggesting that the nature of neuromast-centered canal morphogenesis may differ depending on LL canal phenotypes.
Myosin II activity is not required for Drosophila tracheal branching morphogenesis

The Drosophila tracheal system consists of an interconnected network of monolayered epithelial tubes that ensures oxygen transport in the larval and adult body. During tracheal dorsal branch (DB) development, individual DBs elongate as a cluster of cells, led by tip cells at the front and trailing cells in the rear. Branch elongation is accompanied by extensive cell intercalation and cell lengthening of the trailing stalk cells. While cell intercalation is governed by Myosin II (MyoII)-dependent forces during tissue elongation in the Drosophila embryo leading to germ-band extension, it remained unclear whether MyoII plays a similar active role during tracheal branch elongation and intercalation. Here, we use a nanobody-based approach to selectively knock-down MyoII in tracheal cells. Our data shows that despite the depletion of MyoII function, tip cells migration and stalk cell intercalation (SCI) proceeds at a normal rate. Therefore, our data confirms a model in which DB elongation and SCI in the trachea occurs as a consequence of tip cell migration, which produces the necessary forces for the branching process. Summary statement Branch elongation during Drosophila tracheal development mechanistically resembles MyoII-independent collective cell migration; tensile forces resulting from tip cell migration are reduced by cell elongation and passive stalk cell intercalation. Abbreviations DB Dorsal branch DC Dorsal closure E-Cad E-Cadherin GBE Germ-band extension MRLC Myosin regulatory light chain MyoII Myosin II SCI stalk cell intercalation Sqh Spaghetti squash Sxll Sex lethal TC Tip cell Tr Tracheomere
Improved Global Localization and Resampling Techniques for Monte Carlo Localization Algorithm

Global indoor localization algorithms enable the robot to estimate its pose in pre-mapped environments using sensor measurements when its initial pose is unknown. The conventional Adaptive Monte Carlo Localization (AMCL) is a highly efficient localization algorithm that can successfully cope with global uncertainty. Since the global localization problem is paramount in mobile robots, we propose a novel approach that can significantly reduce the amount of time it takes for the algorithm to converge to true pose. Given the map and initial scan data, the proposed algorithm detects regions with high likelihood based on the observation model. As a result, the suggested sample distribution will expedite the process of localization. In this study, we also present an effective resampling strategy to deal with the kidnapped robot problem that enables the robot to recover quickly when the sample weights drop-down due to unmapped dynamic obstacles within the sensor’s field of view. The proposed approach distributes the random samples within a circular region centered around the robot’s pose by taking into account the prior knowledge about the most recent successful pose estimation. Since the samples are distributed over the region with high probabilities, it will take less time for the samples to converge to the actual pose. The percentage of improvement for the small sample set (500 samples) exceeded 90% over the large maps and played a big role in reducing computational resources. In general, the results demonstrate the localization efficacy of the proposed scheme, even with small sample sets. Consequently, the proposed scheme significantly increases the real-time performance of the algorithm by 85.12% on average in terms of decreasing the computational cost.
Design of a Hybrid Competition-Cooperation Teacher-Students Model for Single Channel Based Sleep Staging

A competition-cooperation teacher-student model is proposed for knowledge transfer between channels for sleep staging. The teacher model was trained simultaneously with competitor and cooperator student models. One extra “competitor” student model was added to the traditional teacher-student model. The performance of the teacher model can be optimized during the competition with the competitor model. The over-fitting of the student model is greatly reduced in cooperation with the teacher model. A three-step competition-cooperation training process was proposed to optimize the performance of both the teacher model and the student models. The experimental results demonstrate a 2.7% and a 1.6% improvement of the accuracy for the teacher model and the student model, respectively. A state-of-the-art sleep staging accuracy of 83.7% with single-channel input and 85.9% with multi-channel inputs was achieved by the proposed algorithm.
Stability and magnetic behaviour of 19-, 23- and 26-atom trimetallic Pt–Ni–Ag nanoalloys

A systematic investigation of Pt2NinAg17-n, Pt3NinAg20-n and Pt4NinAg22-n trimetallic nanoalloy systems has been performed. We are particularly interested in learning the effect of systematic Ni atom addition on the stability, chemical ordering and magnetic behaviour of the nanoalloys. We have performed Gupta and Density Functional Theory (DFT) approaches on chosen systems. Our excess energy analysis showed that the most stable structure of the 19-, 23- and 26-atom nanoalloy systems found at Gupta level does not agree with those of DFT. However, DFT results confirm the Gupta level calculations for the lowest energy structures of the trimetallic systems with small shifts on bond lengths. We have computed the order parameter (R) and it was observed that Ag atoms prefer to locate on the surface and Pt atoms mostly prefer to locate in the inner site of the trimetallic nanoalloys. Besides, inner sites are heavily compressed with the substitution of Ni atoms for most compositions. It was also obtained that total magnetic moment of the nanoalloys follows an almost linear dependence on the Ni atom concentration. Thus, it can be said that total magnetic moment can be enhanced by ternary alloying with 3d magnetic element like Ni. GRAPHICAL ABSTRACT
Accuracy of programs for the determination of HLA alleles from NGS data

The human leukocyte antigen (HLA) genes code for proteins that play a central role in the function of the immune system by presenting peptide antigens to T cells. As HLA genes show extremely high genetic polymorphism, HLA typing on the allele level is demanding and is based on DNA sequencing. Determination of HLA alleles is warranted as many HLA alleles are major genetic factors that confer susceptibility to autoimmune diseases and is important for the matching of HLA alleles in transplantation. Here, we compared the accuracy of several published HLA-typing algorithms that are based on next generation sequencing (NGS) data. As genome screens are becoming increasingly routine in research, we wanted to test how well HLA alleles can be deduced from genome screens not designed for HLA typing. The accuracies were assessed using datasets consisting of NGS data produced using the ImmunoSEQ platform, including the full 4 Mbp HLA segment, from 94 stem cell transplantation patients and exome sequences from the 1000 Genomes collection. When used with the default settings none of the methods gave perfect results for all the genes and samples. However, we found that ensemble prediction of the results or modifications of the settings could be used to improve accuracy. Most of the algorithms did not perform very well for the exome-only data. The results indicate that the use of these algorithms for accurate HLA allele determination based on NGS data is not straightforward.
Compatibility between agents as a tool for coarse-grained descriptions of quantum systems

Shedding a new light in the coarse-graining scenario, in this contribution we came up with different necessary and sufficient conditions for the existence of a well-defined coarse-grained state. For doing so, we had to break apart with the usual quantum channels perspective and assume a more decision-theoretical posture. Broadly speaking, we reinterpret the coarse-graining problem in the language of quantum state pooling, and by making an extensive use of the conditional quantum states toolkit, we have been able to derive more tangible conditions for the emergence of a compatible effective coarse-grained state.
Post-fledging Golden-winged Warblers require forests with multiple stand developmental stages

ABSTRACT Our understanding of songbird habitat needs during the breeding season stems largely from studies of nest success. However, growing evidence shows that nesting habitat and post-fledging habitat often differ. Management guidelines for declining species need to be reevaluated and updated to account for habitat shifts that may occur across the full breeding cycle. The Golden-winged Warbler (Vermivora chrysoptera) is a declining songbird species for which best management practices (BMPs) are based overwhelmingly on nesting habitat. We studied stand-scale habitat selection by fledgling Golden-winged Warblers during May–July, 2014–2017, in 2 landscapes (2 yr of data for each landscape), 200 km apart in Pennsylvania. Across 4 yr, we radio-tagged and tracked 156 fledglings. We used discrete-choice models to evaluate habitat selection during 2 post-fledging time periods (days 1–5, days 6–28). Fledglings used a variety of cover types, but most telemetry relocations (i.e. 85%) occurred in forest in the stand initiation stage, stem exclusion stage, or mature forest upland. Fledglings primarily selected stand initiation forest during the first 5 days, but preferred habitats differed between regions during days 6–28 post-fledging. Fledglings in one landscape favored stands in the stem exclusion stage while fledglings in the other landscape continued to select stands in the initiation stage. Fledglings moved greater distances as they aged and dispersed ∼750 m by day 28 post-fledging. These findings suggest the need to update Golden-winged Warbler BMPs to account for the broader habitat needs of fledglings during the breeding season. In addition, these results indicate that regional studies of habitat requirements can help guide management of dynamic forest landscapes for birds. LAY SUMMARY Little is known about the post-fledging ecology and habitat requirements of many migratory songbirds. We used VHF radio-transmitters to track 156 fledgling Golden-winged Warblers (Vermivora chrysoptera) from two subpopulations in Pennsylvania, USA, and describe their movements, habitat use, and habitat selection. On average fledglings dispersed ∼750 m from nest sites by day 28 post-fledging with the maximum dispersal distance being 3.6 km. Fledglings used all cover types but 85% of relocations occurred in stand initiation, stem exclusion, or mature forest uplands. Habitat selection was directed primarily toward forest in the stand initiation stage, however fledglings in one landscape also selected for stem exclusion stands. Managers should consider promoting additional forest stand age class diversity (especially forest in the stem exclusion stage) in areas proximate to Golden-winged Warbler nesting habitat to provide the structure necessary for fledglings.
Harmonious interaction of kaolin and two insect predator species in plant protection

ABSTRACT Lacewings and lady beetles represent two important groups of natural enemies for pest control. Kaolin is used in various crop ecosystems to reduce abiotic plant stressors and pest colonization. Compatible methods aimed at reducing abiotic and biotic plant stressors are desired in crop management systems. Therefore, this work evaluated the development and survival of Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) and Eriopis connexa (Germar) (Coleoptera: Coccinellidae) larvae of different ages treated with kaolin at three different concentrations (ca. 60, 80, and 100 g/L) and prey consumption when treated with kaolin at a field rate of 60 g/L. The prey used were the whitefly Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) and the aphid Lipaphis erysimi (Kalt.) (Hemiptera: Aphididae). Survival rates and development durations for E. connexa larvae topically treated with kaolin at different ages were similar to those for untreated larvae. However, larvae of C. externa reduced survival and delayed development when treated with kaolin concentrations greater than the recommended field rate. Otherwise, kaolin treatments did not affect prey consumption by larvae and adults of both predator species.
Carpinus langaoensis (Betulaceae), a new hornbeam species from the Daba Mountains in Shaanxi, China

Carpinus langaoensis Z. Qiang Lu & J. Quan Liu, a new hornbeam species from the Daba Mountains in the Shanxi province of China, is described and illustrated in this study. Morphological comparisons show that this species is similar to C. tientaiensis W. C. Cheng and C. mianningensis Yi, with which it shares the presence of the long bract with lobes at bases of both inner and outer margins and large glabrescent nutlet. However, it is distinct from both in the dense pubescence on the abaxial leaf, and the long infructescence bract. Phylogenetic analyses of ITS sequence variation indicates that these three species form a well-supported monophyletic group, but all examined individuals of the new species are separated from all others by three fixed nucleotide mutations. The new species is also geographically isolated from these two closely related ones. Therefore, all available evidence suggests that a new species ( C. langaoensis ) should be established for this evolutionarily independent lineage. The new species is known from only a single small population, and so should be treated as a critically endangered species according to the IUCN categories and criteria.
Evaluation of the effectiveness of level soil bund and soil bund age on selected soil physicochemical properties in Somodo Watershed, Jimma Zone, SouthWestern Ethiopia

This study was conducted to investigate the effect of level soil bund stabilized with Vetiver grass and soil bund age on selected soil physicochemical properties on Somodo watershed, Jimma Zone, South-western, Ethiopia. A reconnaissance survey was conducted to identify a representative sampling site. From the selected sampling site croplands with level soil bund aged three years, six years and adjacent untreated cropland were identified. A total of 108 composite soil samples (3 treatments * 6 replications * 2 depths * 3 zones) were collected. Soil samples were analyzed following standard laboratory analysis. Ages of level soil bund (LSB) significantly affected SMC (soil moisture content) (p<0.01), BD (bulk density) (p<0.01), and SOC (soil organic carbon) (p<0.01). Zones showed significant difference in sand content (p<0.05), SMC (p<0.01), BD (p<0.05) and SOC (p<0.01). Moreover, the soil depths also significantly influenced silt content (p<.05), SMC (p<.01), BD (p<0.01), SOC (p<0.01), TN (total nitrogen) (p<0.01), Av. -P (available phosphorous) (p<0.01) and CEC (p<0.05). The interaction effect of the age of LSB with zone was significant for SOC (P<0.05). To sum up, the effect of the constructed level soil bund had a positive impact on selected soil physicochemical properties of the site. Therefore, the study suggests that it is essential to maintain the structure to sustain the effectiveness and scale up the technology to other watersheds with similar agroecology of the country. Further study is encouraged to understand more about the effect of the slope and Vetiver grass bund stabilization role independently on selected soil properties.