Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial pore-forming proteins induce non-monotonic dynamics due to lipid ejection and crowding

Developing alternate strategies against pore forming toxin (PFT) mediated bacterial virulence factors require an understanding of the target cellular response to combat rising antimicrobial resistance. Membrane-bound protein complexes involving PFTs, released by virulent bacteria are known to form pores leading to host cell lysis. However, membrane disruption and related lipid mediated active repair processes during attack by PFTs remain largely unexplored. We report counter intuitive and non-monotonic variations in lipid diffusion, measured using confocal fluorescence correlation spectroscopy, due to interplay of lipid ejection and crowding by membrane bound oligomers of a prototypical cholesterol dependent cytolysin, Listeriolysin O (LLO). The observed protein concentration dependent dynamical cross-over is correlated with transitions of LLO oligomeric state populations from rings to arc-like pore complexes, predicted using a proposed two-state free area based diffusion model. At low PFT concentrations, a hitherto unexplored regime of increased lipid diffusivity is attributed to lipid ejection events due to a preponderance of ring-like pore states. At higher protein concentrations where membrane inserted arc-like pores dominate, lipid ejection is less efficient and the ensuing crowding results in a lowering of lipid diffusion. These variations in lipid dynamics are corroborated by macroscopic rheological response measurements of PFT bound vesicles. Our study correlates PFT oligomeric state transitions, membrane remodelling and mechanical property variations, providing unique insights into developing strategies to combat virulent bacterial pathogens responsible for several infectious diseases. SIGNIFICANCE Developing alternate strategies against pore forming toxin (PFT) mediated bacterial virulence factors requires understanding target cellular responses and cellular defence strategies to combat rising antimicrobial resistant strains. While it is well understood that PFTs exist in a wide variety of oligomeric states, the underlying membrane response to these states is unexplored. Using confocal fluorescence correlation spectroscopy and a membrane free area based model we relate non-monotonic variations in the lipid diffusivity arising from an interplay of lipid ejection events and membrane crowding due to variations in concentration of membrane bound listeriolysin O. Our observations have a direct bearing on understanding cellular defense and repair mechanisms effective during initial stages of bacterial infection and intrinsically connected to the underlying membrane fluidity.
DNA methylation during development and regeneration of the annelid Platynereis dumerilii

Background Methylation of cytosines in DNA (5mC methylation) is a major epigenetic modification that modulates gene expression and is important for embryonic development and cell reprogramming in vertebrates. In mammals, 5mC methylation in promoter regions is linked to transcriptional repression. Transcription regulation by 5mC methylation notably involves the Nucleosome Remodeling and Deacetylase complex (NuRD complex) which bridges DNA methylation and histone modifications. Less is known about roles and mechanisms of 5mC methylation in non-vertebrate animals. In this paper, we study 5mC methylation in the marine annelid worm Platynereis dumerilii, an emerging evolutionary and developmental biology model capable of regenerating the posterior part of its body upon amputation. The regenerated region includes both differentiated structures and a growth zone consisting of stem cells required for the continuous growth of the worm. Results Using in silico and experimental approaches, we show that P. dumerilii displays a high level of DNA methylation comparable to that of mammalian somatic cells. 5mC methylation in P. dumerilii is dynamic along the life cycle of the animal and markedly decreases at the transition between larval to post-larval stages. We identify a full repertoire of mainly singlecopy genes encoding the machinery associated to 5mC methylation or members of the NuRD complex in P. dumerilii and show, through phylogenetic analyses, that this repertoire is close to the one inferred for the last common ancestor of bilaterians. These genes are dynamically expressed during P. dumerilii development, growth and regeneration. Treatment with the DNA hypomethylating agent Decitabine, impairs P. dumerilii larval development and regeneration, and has long-term effects on post-regenerative growth by affecting the functionality of stem cells of the growth zone. Conclusions Our data indicate high-level of 5mC methylation in the annelid P. dumerilii, highlighting that this feature is not specific to vertebrates in the bilaterian clade. Analysis of DNA methylation levels and machinery gene expression during development and regeneration, as well as the use of a chemical inhibitor of DNA methylation, suggest an involvement of 5mC methylation in P. dumerilii development, regeneration and stem cell-based post-regenerative growth. We also present data indicating that P. dumerilii constitutes a promising model to study biological roles and mechanisms of DNA methylation in non-vertebrate bilaterians and to provide new knowledge about evolution of the functions of this key epigenetic modification in bilaterian animals.
Experimental Verification of Phase Diagram Calculations of Zr-Based Alloys after High-Temperature Oxidation

Zirconium-based alloys are commonly used as a material for nuclear fuel claddings in the light water reactors. The cladding material must function to fix a huge number of pellets, while conducting heat into the coolant that flows turbulently around the fuel rods. Cladding tubes can contain gaseous fission products that escape the fuel. Thus, by functioning as a sealed unit, it prevents a contamination of the coolant water with high-radioactive fission products. The integrity of claddings is always a critical issue during reactor operation and wet or dry storage and transport of the spent fuel rods. Moreover, the role gains importance at Loss of Coolant Accidents (LOCA). After Fukushima accident, cladding materials are widely studied with the purpose to reduce the high-temperature oxidation rate and enhance accident tolerance. In our contribution, we introduce the studies on Zr-1Nb (E110) cladding tubes after high-temperature steam oxidation at 1350 °C. During the testing of claddings, microscopy analytical methods play an important role in experimental verification of pseudo-binary phase diagram Zr1Nb-O, i. e. particularly in oxygen content determination at phase transitions. Wave Dispersive Spectroscopy (WDS) with complementary nano-indentation method were used to characterize the Zr1Nb microstructure formed after LOCA. It includes the regions from an oxide and oxygen-stabilized α-Zr(O) to the acicular prior β-Zr phase. The decrease of hardness and Young's modulus corresponds with oxygen content measured in line-profiles by WDS. The oxygen level at transition points was partly determined from Fe, Nb β-stabilizers and significant change in mechanical properties in fine-grained prior β-Zr. The slight fluctuation of oxygen values in adjacent grains can be caused by preferential oxidation through the favorably oriented α-Zr(O) grains studied by WDS+EBSD. As well, the non-uniform oxygen-rich α-Zr(O) phase adjacent to the oxide was characterized by EBSD & WDS. Increasing hydrogen content in specimens, 10, 700 and 1000 ppm H, caused increasing solubility of oxygen in prior β-Zr phase upon high-temperature and the cladding material hardening.
Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748, Isolated from a Dragonfly

Spiroplasma platyhelix is a helical bacterium belonging to the class Mollicutes. First isolated from a Pachydiplax longipennis dragonfly, it has the smallest reported Spiroplasma genome size of 740 kbp. Here, we report the genome sequence of S. platyhelix ATCC 51748. ABSTRACT Spiroplasma platyhelix is a helical bacterium belonging to the class Mollicutes. First isolated from a Pachydiplax longipennis dragonfly, it has the smallest reported Spiroplasma genome size of 740 kbp. Here, we report the genome sequence of S. platyhelix ATCC 51748.
Synthesis of Silicon- and Carbonate-doped Biomimetic Hydroxyapatite in the Presence of Citrate Ions and its Physicochemical, Bioactivity Properties

The present study investigated the phase composition, the structural, morphological, and bioactivity properties of silicon- and carbonate-doped biomimetic hydroxyapatite synthesized by precipitation from aqueous solutions in the presence of different amounts of citrate ions. The X-ray diffraction and Fourier transform infrared spectroscopy analyses confirmed that all the samples exhibited single-phase. Base on the results of the morphological study, all the obtained samples consisted of porous agglomerated particles made up of tiny crystallites in the nanometer range. The change in structural order, as well as the decrease in particle size and degree of crystallinity result from the presence of citrate ions were revealed by X-ray diffraction, dynamic light scattering, and scanning electron microscopy analyses. Bioactivity properties of samples were studied by analyzing their bioresorbability in physiological saline (ω (NaCl) = 0.9%) and evaluating their solubility in SBF solution after a certain period of soaking time. The amount of the released Ca2+ ions was found to increase with the increasing concentration of citrate ions introduced in the synthesis process. The better solubility of material with the presence of citrate ions was beneficial in the growth of apatite on its surface that made produced material more biocompatible.
Structural Nature of ZnAl4Cu1 Alloy Plasticity Affected by Various Technological Treatments

The aim of this work was to analyse the microstructural nature of plasticity in ZnAl4Cu1 alloy and its dependence on the processing technology. The alloy condition was analysed after gravity casting, after forging and after ECAP processing. Two alloys with slightly different compositions were studied. For alloy A, the returnable material from a prominent Zn alloy producer was used. For B alloy input raw materials of relatively high purity were used. Tensile testing showed that in the as-cast alloy tensile strength had relatively low levels up to 211 MPa, and particularly low values of ductility only up to 2.5 % were found in B alloy, which was more polluted. By means of ECAP processing of the as-cast alloy, the tensile strength was improved by 50 % (Rm = 312 MPa). In the case of the purer A alloy the majority of samples improved to level A = 27.9 %. Forging of the as-cast alloy preserved strength on a level similar to the ECAP result, but ductility was improved to the level of 34.4 %, although alloy B had lower purity. Further significant ductility improvement was obtained through ECAP processing to A = 147 % of the as-forged alloy. The microstructure of ZnAl4Cu1 consists primarily of segregated η phase (rich in Zn) and fine eutectoid composed of η and alpha phases segregated mostly in dispersive state, but in places also in lamellar form. Close correlation between microstructure and processing method resulted from our fractographic study. In the case of ECAP processing of the forged state the finest microstructure was achieved, which was accompanied by higher plasticity and also by fine dimples of transcrystalline ductile fracture (DTDF).
Draft Genome Sequences of Four Bacterial Species as Part of an Experiential Microbiology Project at SUNY Geneseo

Here, we report four draft genome sequences related to the genera Bacillus and Escherichia, recovered from surfaces associated with human interaction, and Sediminibacterium, recovered from an aquatic environment. This study was part of an undergraduate microbial bioinformatics course at the State University of New York at Geneseo. ABSTRACT We report four draft genome sequences related to the genera Bacillus and Escherichia, recovered from surfaces associated with human interaction, and Sediminibacterium, recovered from an aquatic environment. This study was part of an undergraduate microbial bioinformatics course at the State University of New York at Geneseo.
Evaluation method for the corona discharge of insulator based on convolution neural network with the dual-spectra camera

Abstract. As insulators play an important role in power transmission lines, we propose an intelligent method based on the convolution neural network (CNN) to evaluate the corona discharge of an insulator. In this method, the imaging device is a dual-spectra camera with a visible channel and an ultraviolet (UV) channel. The CNN is adopted to identify the detection distance of the insulator with the visible channel. To train the network, the dataset of the insulator is obtained by the experimental setup and deep convolutional generative adversarial networks. Through adjusting the training parameters and optimizing the network structure, an optimal trained model is achieved. Then the image pixel ratio method is adopted to measure the UV signal strength of the images captured by the UV channel. Meanwhile, the relationship between the detection distance and the UV signal strength is discussed. The critical value for the corona discharge of the insulator is obtained via experiments at the standard detection distance. Finally, the corona discharge of the insulator is evaluated by combining the detection distance with the UV signal strength. The experimental results show the method has the advantages of high accuracy and robustness and can effectively evaluate the corona discharge of the insulator.
Lepidoptera Diversity Based on Continuous Surveys 2009–2011 and 2017–2019 at a Transition Zone Site in the Central Cascade Range, Washington, USA

ABSTRACT. Lepidoptera at a single mid-elevation site in the central Cascade Range in Washington state were surveyed for six full seasons spanning 11 years (2009–2011, 2017–2019). Sampling was performed continuously with a blacklight trap, and was supplemented with pheromone traps, searches for immature stages, day collecting, observation, photography, and sugar bait traps. The habitat is forested transition zone, including old growth forest, slightly east of the Cascade divide in the southern part of the North Cascades ecoregion. The fauna of 822 species is categorized by the number of seasons each species was found over the span of the study. The higher-order distribution of the fauna within Lepidoptera, impact of sampling methods, annual and multi-year fluctuations in abundance, and local climate effects on flight period are presented. Taxonomic challenges and noteworthy records are discussed. Representative species and genitalia are illustrated.
A Study of the High-K Enhanced Depletion-JTE for Ultra-High Voltage SiC Power Device with Improved JTE-Dose Window

In this paper, a High-K dielectric permittivity Enhanced Depletion-JTE(HKED-JTE) for 10 kV ultra-high voltage is studied. The HKED-JTE improves the terminal protection efficiency by the self-charge balance of High-K dielectric polarization charges. The tolerance of the implantation dose window of HKED-JTE reaches 9 times as large as that of normal TZ-JTE with the same terminal area, and the corresponding BV holding theoretical breakdown voltage is over 80%. The thicker High-K layer accomplishes the modulation of the surface electric flux and decreases the electric field up to 51% and 47% at the abrupt junction J2 and J3 along the device interface between the SiC and High-K materials.
Pulse shapings employed in an underwater visible-light communication system based on carrierless amplitude and phase modulation utilizing a complex deep neural network equalizer

Abstract. We experimentally demonstrate the performance of a complex deep neural network (CDNN) equalizer in multi-band super-Nyquist carrier-less amplitude and phase (m-SCAP) modulation for underwater visible-light communications (UVLC). The in-phase and quadrature of the complex data after the match filter and down-sampling are combined as real number pairs and input to the CDNN, which outputs the real part and the imaginary part of the equalized complex data. We compare the different performances of three pulse shapings [better-than-Nyquist pulse shaping (BTN), square-root raised cosine (SRRC), and Xia] utilized in the m-SCAP UVLC system based on the CDNN. We demonstrate that the CDNN equalizer can outperform the traditional equalizer based on the Volterra series and least-mean-square algorithm. The experiments show that the low-roll-off BTN performs best, and the high-roll-off SRRC performs best in the m-SCAP system. In our experiment, the bit-error rate (BER) of the BTN system is 2.6 × 10 − 4, the BER of the SRRC is 3.6 × 10 − 4, and the BER of the Xia system is 7.3 × 10 − 4 when the spectral efficiency is 3.76 bit / s / Hz and the signal peak-to-peak voltage (Vpp) is 0.9 V.
Boronizing of AISI 316L Stainless Steel Using Spark Plasma Sintering Technique

Austenitic stainless-steel has been widely used. Although it offers excellent corrosion resistance, processability, and nonmagnetic properties, it is inferior in terms of wear resistance and hardness. Therefore, the purpose of this study is to form iron boride on an austenitic stainless-steel surface using the spark plasma sintering (SPS) method and to evaluate its properties. The SPS method was utilized because the rapid heating involved in the process reduces the processing time. AISI 316L as a sample material was boronized for 3.6 ks at 1073 – 1273 K at applied pressures of 4 MPa and 8 MPa with a powder mixture of B4C and KBF4. The Vickers hardness profile results showed that the hardness of the untreated sample was ~ 200 HV whereas that of the boronized sample was ~ 2300 HV. The wear test profile showed that the wear resistance of the boronized sample was significantly improved. Moreover, according to elemental analyses, boron diffused from the sample surface to 200 μm and 60 μm when the applied pressure was 8 MPa and 4 MPa, respectively. This indicated that boron diffused to a greater depth when the applied pressure was increased.
EEG-Based Prediction of Cognitive Load in Intelligence Tests

Measuring and assessing the cognitive load associated with different tasks is crucial for many applications, from the design of instructional materials to monitoring the mental wellbeing of aircraft pilots. The goal of this paper is to utilize EEG to infer the cognitive workload of subjects during intelligence tests. We chose the well established advanced progressive matrices test, an ideal work-frame because it presents problems at increasing levels of difficulty, and has been rigorously validated in past experiments. We train classic machine learning models using basic EEG measures as well as measures of network connectivity and signal complexity. Our findings demonstrate that cognitive load can be well predicted using these features, even for a low number of channels. We show that by creating an individually tuned neural network for each subject, we can improve prediction compared to a general model and that such models are robust to decreasing the number of available channels as well.
Spatiotemporal feature extraction and classification of Alzheimer’s disease using deep learning 3D-CNN for fMRI data

Abstract. Purpose: Through the last three decades, functional magnetic resonance imaging (fMRI) has provided immense quantities of information about the dynamics of the brain, functional brain mapping, and resting-state brain networks. Despite providing such rich functional information, fMRI is still not a commonly used clinical technique due to inaccuracy involved in analysis of extremely noisy data. However, ongoing developments in deep learning techniques suggest potential improvements and better performance in many different domains. Our main purpose is to utilize the potentials of deep learning techniques for fMRI data for clinical use. Approach: We present one such synergy of fMRI and deep learning, where we apply a simplified yet accurate method using a modified 3D convolutional neural networks (CNN) to resting-state fMRI data for feature extraction and classification of Alzheimer’s disease (AD). The CNN is designed in such a way that it uses the fMRI data with much less preprocessing, preserving both spatial and temporal information. Results: Once trained, the network is successfully able to classify between fMRI data from healthy controls and AD subjects, including subjects in the mild cognitive impairment (MCI) stage. We have also extracted spatiotemporal features useful for classification. Conclusion: This CNN can detect and differentiate between the earlier and later stages of MCI and AD and hence, it may have potential clinical applications in both early detection and better diagnosis of Alzheimer’s disease.
Draft Genome Sequence of Bifidobacterium longum subsp. infantis BI-G201, a Commercialization Strain

Bifidobacterium longum subsp. infantis has been widely used in many food products, such as solid beverages or dietary supplements. Here, a draft genome sequence of a commercialization strain, Bifidobacterium longum subsp. infantis BI-G201, was reported. ABSTRACT Bifidobacterium longum subsp. infantis has been widely used in many food products such as solid beverages and dietary supplements. Here, a draft genome sequence of a commercialization strain, Bifidobacterium longum subsp. infantis BI-G201, is reported.
EARLY FLOWERING 3 controls temperature responsiveness of the circadian clock

Predictable changes in light and temperature during a diurnal cycle are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue, especially in light of climate change scenarios. In Arabidopsis, the clock component EARLY FLOWERING 3 (ELF3) not only serves as an essential light Zeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role of ELF3 in temperature entrainment of the circadian clock is not fully understood. Here, we report that ELF3 is essential for delivering temperature input to the clock. We demonstrate that in the absence of ELF3, the oscillator was unable to properly respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Together, our results reveal that ELF3 is an essential Zeitnehmer for temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.