Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta) from the east and gulf coast of the United States based on molecular data

Ulva (Ulvophyceae, Chlorophyta) is common in intertidal environments and can also be found in freshwater ecosystems. The difficulty to morphologically identify Ulva species due to cryptic diversity and morphological plasticity has caused a taxonomic conundrum. Fortunately, molecular data have begun to unravel a better understanding of its diversity. Here, we present a molecular analysis with 247 samples of Ulva from the Gulf of Mexico and Atlantic USA based on chloroplast (rbcL and tufA) and nuclear (ITS1‐5.8S‐ITS2) molecular markers. Twenty‐four Ulva taxa had previously been reported for this area based on morphology and earlier molecular studies mostly from Northeastern USA and Canada. In this study, sixteen Ulva clades were identified representing 13 named clades and putatively three undescribed species. Only nine of the 24 taxa previously reported for the Western Atlantic were confirmed. Four species were identified for the first time in the U.S. East and Gulf Coast (U. aragoënsis, U. californica, U. meridionalis, and U. tepida). This study provides a foundation for future research on Ulva in this area and reiterates the necessity of using molecular‐assisted identifications for this group.
Spectroscopic investigations of corona discharge in high pressure helium at 300 K

Gaseous Helium at 300 K and pressure (0.1–3) MPa was excited using a corona discharge both for negative and positive high voltages. The light emitted from the ionization zone of the discharge was analyzed. Asymmetric shape of atomic lines 706 nm and 728 nm was recorded. Blue wings of the lines are more intensive than their red wings. The line shape is described as a convolution of Lorentz profile of the line center and a quasi-statistical profile of a blue wing of the line. Such analysis predicts no heating of the gas in the ionization zone for positive corona and considerable heating for negative corona.
DeepACSON: Automated Segmentation of White Matter in 3D Electron Microscopy

To trace the entirety of ultrastructures in large-scale three-dimensional electron microscopy (3D-EM) images of brain tissue, automated segmentation techniques are essential. The current automated techniques use deep convolutional neural networks (DCNNs), approaching human-level segmentation, but designed for tracing small numbers of neurites and for high-resolution datasets. Therefore, we developed DeepACSON to segment 3D-EM datasets of white matter at low-resolutions and for tens of thousands of myelinated axons. DeepACSON performs DCNN-based semantic-segmentation and shape decomposition-based instance-segmentation: a top-down design to account for severe membrane discontinuities inherited with low-resolution imaging. We applied DeepACSON to ten serial block-face scanning electron microscopy datasets of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of mitochondria with excellent evaluation scores. DeepACSON quantified the morphological and spatial aspects of white matter ultrastructures.
On the Convergence of Quantized Parallel Restarted SGD for Central Server Free Distributed Training.

Communication is a crucial phase in the context of distributed training. Because parameter server (PS) frequently experiences network congestion, recent studies have found that training paradigms without a centralized server outperform the traditional server-based paradigms in terms of communication efficiency. However, with the increasing growth of model sizes, these server-free paradigms are also confronted with substantial communication overhead that seriously deteriorates the performance of distributed training. In this paper, we focus on communication efficiency of two serverless paradigms, i.e., Ring All-Reduce (RAR) and gossip, by proposing the Quantized Parallel Restarted Stochastic Gradient Descent (QPRSGD), an algorithm that allows multiple local SGD updates before a global synchronization, in synergy with the quantization to significantly reduce the communication overhead. We establish the bound of accumulative errors according to the synchronization mode and the network topology, which is essential to ensure the convergence property. Under both aggregation paradigms, the algorithm achieves the linear speedup property with respect to the number of local updates as well as the number of workers. Remarkably, the proposed algorithm achieves a convergence rate $O(1/\sqrt{NK^2M})$ under the gossip paradigm and outperforms all existing compression methods, where $N$ is the times of global synchronizations, and $K$ is the number of local updates, while $M$ is the number of nodes. An empirical study on various machine learning models demonstrates that the communication overhead is reduced by 90\%, and the convergence speed is boosted by up to 18.6 times, in a low bandwidth network, in comparison with Parallel SGD.
Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease

Introduction A coeliac disease (CD) diagnosis is likely in children with levels of tissue transglutaminase autoantibodies (anti-TG2) >10 times the upper reference value, whereas children with lower anti-TG2 levels need an intestinal biopsy to confirm or rule out CD. A blood sample is easier to obtain than an intestinal biopsy sample, and stabilised blood is suitable for routine diagnostics because transcript levels are preserved at sampling. Therefore, we investigated gene expression in stabilised whole blood to explore the possibility of gene expression-based diagnostics for the diagnosis and follow-up of CD. Design We performed RNA sequencing of stabilised whole blood from active CD cases (n=10), non-CD cases (n=10), and treated CD cases on a gluten-free diet (n=10) to identify diagnostic CD biomarkers and pathways involved in CD pathogenesis. Results No single gene was differentially expressed between the sample groups. However, by using gene set enrichment analysis (GSEA), significantly differentially expressed pathways were identified in active CD, and these pathways involved the inflammatory response, negative regulation of viral replication, translation, as well as cell proliferation, differentiation, migration, and survival. The results indicate that there are differences in pathway regulation in CD, which could be used for diagnostic purposes. Comparison between GSEA results based on stabilised blood with GSEA results based on small intestinal biopsies revealed that type I interferon response, defence response to virus, and negative regulation of viral replication were identified as pathways common to both tissues. Conclusions Stabilised whole blood is not a suitable sample for clinical diagnostics of CD based on single genes. However, diagnostics based on a pathway-focused gene expression panel may be feasible, but requires further investigation.
Properties of vibrational energy spectra of the molecular crystal-acetanilide

The quantum vibrational energy spectra of the amides in the molecular crystal acetanilide have been calculated by using the discrete nonlinear Schrodinger equation. Numerical results of energy levels including higher excited states have been calculated which are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. Using the energy spectra we have well explained the Raman spectrum obtained by Careri et al.
High-fidelity musculoskeletal modeling reveals that motor planning variability contributes to the speed-accuracy tradeoff

A long-standing challenge in motor neuroscience is to understand the relationship between movement speed and accuracy, known as the speed-accuracy tradeoff. Here, we introduce a biomechanically realistic computational model of three-dimensional upper extremity movements that reproduces well-known features of reaching movements. This model revealed that the speed-accuracy tradeoff, as described by Fitts’ law, emerges even without the presence of motor noise, which is commonly believed to underlie the speed-accuracy tradeoff. Next, we analyzed motor cortical neural activity from monkeys reaching to targets of different sizes. We found that the contribution of preparatory neural activity to movement duration (MD) variability is greater for smaller targets than larger targets, and that movements to smaller targets exhibit less variability in population-level preparatory activity, but greater MD variability. These results propose a new theory underlying the speed-accuracy tradeoff: Fitts’ law emerges from greater task demands constraining the optimization landscape in a fashion that reduces the number of ‘good’ control solutions (i.e., faster reaches). Thus, contrary to current beliefs, the speed-accuracy tradeoff could be a consequence of motor planning variability and not exclusively signal-dependent noise.
Lymphatic Vessels and Their Surroundings: How Local Physical Factors Affect Lymph Flow

Simple Summary Lymphatic vessels are responsible for the drainage of liquids, solutes, and cells from interstitial spaces and serosal cavities. Their task is fundamental in order to avoid fluid accumulation leading to tissue swelling and edema. The lymphatic system does not possess a central pump, instead lymph is propelled against an overall hydraulic pressure gradient from interstitial spaces to central veins thanks to two pumping mechanisms, which rely on extrinsic forces or the intrinsic rhythmic contractility of lymphatic muscle cells embedded in vessel walls. This latter mechanism can very rapidly adapt to subtle changes in the microenvironment due to hydraulic pressure, lymph flow-induced wall shear stress, liquid osmolarity, and local tissue temperature. Thus, endothelial and lymphatic muscle cells possess mechanosensors that sense these stimuli and promote a change in contraction frequency and amplitude to modulate lymph flow accordingly. In this review, we will focus on the known physical parameters that can modulate lymph flow and on their putative cellular and molecular mechanisms of transduction. Abstract Lymphatic vessels drain and propel lymph by exploiting external forces that surrounding tissues exert upon vessel walls (extrinsic mechanism) and by using active, rhythmic contractions of lymphatic muscle cells embedded in the vessel wall of collecting lymphatics (intrinsic mechanism). The latter mechanism is the major source of the hydraulic pressure gradient where scant extrinsic forces are generated in the microenvironment surrounding lymphatic vessels. It is mainly involved in generating pressure gradients between the interstitial spaces and the vessel lumen and between adjacent lymphatic vessels segments. Intrinsic pumping can very rapidly adapt to ambient physical stimuli such as hydraulic pressure, lymph flow-derived shear stress, fluid osmolarity, and temperature. This adaptation induces a variable lymph flow, which can precisely follow the local tissue state in terms of fluid and solutes removal. Several cellular systems are known to be sensitive to osmolarity, temperature, stretch, and shear stress, and some of them have been found either in lymphatic endothelial cells or lymphatic muscle. In this review, we will focus on how known physical stimuli affect intrinsic contractility and thus lymph flow and describe the most likely cellular mechanisms that mediate this phenomenon.
Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network

Covalently closed circular RNAs were recently described in the human DNA tumor viruses Epstein-Barr virus (EBV), Kaposi’s sarcoma-associated herpesvirus (KSHV), and human papillomavirus (HPV). Here, we show that MCV, another DNA tumor virus, generates circRNAs from its early regulatory region in concert with T antigen linear transcripts. ABSTRACT Viral noncoding RNAs have acquired increasing prominence as important regulators of infection and mediators of pathogenesis. Circular RNAs (circRNAs) generated by backsplicing events have been identified in several oncogenic human DNA viruses. Here, we show that Merkel cell polyomavirus (MCV), the etiologic cause of ∼80% of Merkel cell carcinomas (MCCs), also expresses circular RNAs. By RNase R-resistant RNA sequencing, four putative circRNA backsplice junctions (BSJs) were identified from the MCV early region (ER). The most abundantly expressed MCV circRNA, designated circMCV-T, is generated through backsplicing of all of ER exon II to form a 762-nucleotide (nt) circular RNA molecule. Curiously, circMCV-T, as well as two other less abundantly expressed putative MCV circRNAs, overlaps in a complementary fashion with the MCV microRNA (miRNA) locus that encodes MCV-miR-M1. circMCV-T is consistently detected in concert with linear T antigen transcripts throughout infection, suggesting a crucial role for this RNA molecule in the regulatory functions of the early region, known to be vital for viral replication. Knocking out the hairpin structure of MCV-miR-M1 in genomic early region expression constructs and using a new high-efficiency, recombinase-mediated, recircularized MCV molecular clone demonstrates that circMCV-T levels decrease in the presence of MCV-miR-M1, underscoring the interplay between MCV circRNA and miRNA. Furthermore, circMCV-T partially reverses the known inhibitory effect of MCV-miR-M1 on early gene expression. RNase R-resistant RNA sequencing of lytic rat polyomavirus 2 (RatPyV2) identified an analogously located circRNA, stipulating a crucial, conserved regulatory function of this class of RNA molecules in the family of polyomaviruses. IMPORTANCE Covalently closed circular RNAs were recently described in the human DNA tumor viruses Epstein-Barr virus (EBV), Kaposi’s sarcoma-associated herpesvirus (KSHV), and human papillomavirus (HPV). Here, we show that MCV, another DNA tumor virus, generates circRNAs from its early regulatory region in concert with T antigen linear transcripts. MCV circMCV-T interacts with another MCV noncoding RNA, miR-M1, to functionally modulate early region transcript expression important for viral replication and long-term episomal persistence. This work describes a dynamic regulatory network integrating circRNA/miRNA/mRNA biomolecules and underscores the intricate functional modulation between several classes of polyomavirus-encoded RNAs in the control of viral replication.
Feed Intake, Methane Emissions, Milk Production and Rumen Methanogen Populations of Grazing Dairy Cows Supplemented with Various C 18 Fatty Acid Sources

Simple Summary Reducing methane emissions from dairy cows is environmentally important. In this experiment, pasture fed dairy cows offered concentrates containing linseed oil emitted 18% less methane per kg of milk solids produced than those offered concentrates containing either stearic acid or soy oil. Additionally, cows fed linseed oil or soy oil produced more milk than those fed stearic acid. These results may contribute to the development of strategies to reduce methane emissions from pasture-based livestock whilst maintaining or improving animal productivity. Abstract Emissions of methane (CH4) from dairy production systems are environmentally detrimental and represent an energy cost to the cow. This study evaluated the effect of varying C18 fatty acid sources on CH4 emissions, milk production and rumen methanogen populations in grazing lactating dairy cows. Forty-five Holstein Friesian cows were randomly allocated to one of three treatments (n = 15). Cows were offered 15 kg dry matter (DM)/d of grazed pasture plus supplementary concentrates (4 kg DM/d) containing either stearic acid (SA), linseed oil (LO), or soy oil (SO). Cows offered LO and SO had lower pasture DM intake (DMI) than those offered SA (11.3, 11.5 vs. 12.6 kg/d). Cows offered LO and SO had higher milk yield (21.0, 21.3 vs. 19.7 kg/d) and milk protein yield (0.74, 0.73 vs. 0.67 kg/d) than those offered SA. Emissions of CH4 (245 vs. 293, 289 g/d, 12.4 vs. 15.7, 14.8 g/kg of milk and 165 vs. 207, 195 g/kg of milk solids) were lower for cows offered LO than those offered SA or SO. Methanobrevibacter ruminantium abundance was reduced in cows offered LO compared to SA. Offering supplementary concentrates containing LO can reduce enteric CH4 emissions from pasture fed dairy cows.
Two-dimensional simulation of fast gas heating in an atmospheric pressure streamer discharge and humidity effects

Gas heating in an atmospheric-pressure streamer discharge was analysed by a two-dimensional streamer discharge simulation model describing internal molecular energy transfer. Our two-dimensional streamer simulation model incorporates concepts from the fast gas heating mechanism proposed by Popov (2011 J. Phys. D: Appl. Phys. 44 285201) and our self-developed state-to-state vibrational kinetics. In dry air, gas heating occurs mainly from electron-impact dissociation reactions of O2 molecules and from quenching processes of electronically excited N2(B 3Πg, C 3Πu) molecules and O(1D) atoms. In humid air, rapid vibration-to-translation transitions of H2O and the exothermicity of the OH formation reactions additionally increase the gas temperature. It is shown that gas heating during the discharge pulse increases with humidity.
Effects of Titanium Dioxide Nanoparticles on Photosynthetic and Antioxidative Processes of Scenedesmus obliquus

The effects of the photocatalytic toxicity of titanium dioxide nanoparticle (nano-TiO2) on phytoplankton are well understood. However, as UV light intensity decreases sharply with the depth of the water column, the effects of nano-TiO2 itself on deeper water phytoplankton, such as green algae, need further research. In this research, we investigated the effects of three sizes of TiO2 (10, 50 and 200 nm) on the photosynthetic and antioxidative processes of Scenedesmus obliquus in the absence of UV light. We found that 50 nm and 10 nm TiO2 (10 mg/L) inhibited growth rates and the maximal photosystem II quantum yield compared to the control in Scenedesmus obliquus. The minimal and maximal fluorescence yields, and the contents of reactive oxygen species and lipid peroxidation, increased, indicating that photosynthetic energy/electrons transferred to oxygen and induced oxidative stress in nano-TiO2-treated samples. In addition, we found that aggregations of algae and 10 nm TiO2 were present, which could induce cell membrane disruption, and vacuoles were induced to cope with nano-TiO2 stress in Scenedesmus obliquus. These results enhance our understanding of the effects of nano-TiO2 on the photosynthetic and antioxidative processes of green algae, and provide basic information for evaluating the ecotoxicity of nano-TiO2 in freshwater ecosystems.
Difference between Selenite and Selenate in the Regulation of Growth and Physiological Parameters of Nickel-Exposed Lettuce

Simple Summary Nickel is a trace metal that can cause toxicity in plants. In contrast, selenium, as a beneficial element, can have a favorable effect on plants grown under metal stress. However, the biological activity of selenium largely depends on its chemical form. Therefore, we assessed the effect of two chemical forms of Se (selenite and selenate) on the toxicity and accumulation of Ni in lettuce. We found that Ni phytotoxicity severely increased in the presence of higher doses of selenite. On the other hand, a low dose of selenate stimulated the growth of roots of Ni-exposed plants. We found that selenium can modify Ni activity in lettuce, but this depends not only on the concentration but also on the form of selenium. The strong intensification of Ni toxicity in the presence of selenite was most likely related to the very high selenium accumulation in root tissues. The obtained results indicate that depending on the conditions in the root environment, Se in a given concentration and chemical form can be either beneficial or toxic for plants. Therefore, the use of selenium in metal-stressed plants requires consideration of not only the concentration but also the chemical form of this element. Abstract Nickel is an essential plant micronutrient; however, even at low concentrations, it may be phytotoxic. Selenium is a beneficial element with an alleviating effect that has been confirmed in the case of many abiotic stresses, including metal toxicity. The aim of this study is to assess the effect of two forms of Se (Se(IV) or Se(VI)) on the phytotoxicity, accumulation, and translocation of Ni in lettuce. Nickel causes a reduction in lettuce growth and vitality of roots, probably through increased lipid peroxidation. The application of Se(IV) to a Ni-contaminated medium resulted in a further reduction of growth, especially in the presence of 6 µM Se(IV). The growth-promoting effect of Se was found only in the 2 µM Se(VI)/10 µM Ni treatment. The application of 6 µM Se, regardless of the Se form, to the Ni-containing substrate caused an increase in shoot Ni concentration. In turn, a decrease in root Ni content was found for all Se treatments. The strong aggravation of Ni phytotoxicity in the presence of 6 µM Se(IV) was most likely related to the accumulation of high Se concentration in the roots, and the combination of high root Ni accumulation caused irreversible dysregulation of cell metabolism.
Comparison of dry deposition predicted from models and measured with a water surface sampler

Atmospheric deposition, which is commonly classified as either dry or wet, has received a great deal of study over the past decade due to concerns about the effect of deposited material on the environment. Atmospheric deposi tion is an important mechanism controlling the fate of airborne toxics and their transfer from the atmosphere to natural surfaces. In this study, a circular water surface sampler was developed to measure the dry deposition flux of atmospheric gases and particles. The sampler consists of a sharp-edged, acrylic plate, filled with water (37 cm diameter and 0.5 cm deep) that is continuously replenished from a reservoir by a pump that maintains a constant water depth. To evaluate the water surface sampler, the sulfate flux was measured in Chicago, IL. Sulfate was selected as the test compound because it is deposited to water as both a particulate (SO42-) and a gas (SO2) (SO2 is quickly hydrolyzed and oxidized to SO42- in water). The SO2 fluxes measured directly with a water surface sampler.