Miracle-dz/UniFAR-FTUs huggingface dataset:
A LysM Domain-Containing Protein LtLysM1 Is Important for Vegetative Growth and Pathogenesis in Woody Plant Pathogen Lasiodiplodia theobromae

Lysin motif (LysM) proteins are reported to be necessary for the virulence and immune response suppression in many herbaceous plant pathogens, while far less is documented in woody plant pathogens. In this study, we preliminarily characterized the molecular function of a LysM protein LtLysM1 in woody plant pathogen Lasiodiplodia theobromae. Transcriptional profiles revealed that LtLysM1 is highly expressed at infectious stages, especially at 36 and 48 hours post inoculation. Amino acid sequence analyses revealed that LtLysM1 was a putative glycoprotein with 10 predicted N-glycosylation sites and one LysM domain. Pathogenicity tests showed that overexpressed transformants of LtLysM1 displayed increased virulence on grapevine shoots in comparison with that of wild type CSS-01s, and RNAi transformants of LtLysM1 exhibited significantly decreased lesion length when compared with that of wild type CSS-01s. Moreover, LtLysM1 was confirmed to be a secreted protein by a yeast signal peptide trap assay. Transient expression in Nicotiana benthamiana together with protein immunoblotting confirmed that LtLysM1 was an N-glycosylated protein. In contrast to previously reported LysM protein Slp1 and OsCEBiP, LtLysM1 molecule did not interact with itself based on yeast two hybrid and co-immunoprecipitation assays. These results indicate that LtLysM1 is a secreted protein and functions as a critical virulence factor during the disease symptom development in woody plants.
EPAC in Vascular Smooth Muscle Cells

Vascular smooth muscle cells (VSMCs) are major components of blood vessels. They regulate physiological functions, such as vascular tone and blood flow. Under pathological conditions, VSMCs undergo a remodeling process known as phenotypic switching. During this process, VSMCs lose their contractility and acquire a synthetic phenotype, where they over-proliferate and migrate from the tunica media to the tunica interna, contributing to the occlusion of blood vessels. Since their discovery as effector proteins of cyclic adenosine 3′,5′-monophosphate (cAMP), exchange proteins activated by cAMP (EPACs) have been shown to play vital roles in a plethora of pathways in different cell systems. While extensive research to identify the role of EPAC in the vasculature has been conducted, much remains to be explored to resolve the reported discordance in EPAC’s effects. In this paper, we review the role of EPAC in VSMCs, namely its regulation of the vascular tone and phenotypic switching, with the likely involvement of reactive oxygen species (ROS) in the interplay between EPAC and its targets/effectors.
Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land

Abstract Plants provide resources and shape the habitat of soil organisms thereby affecting the composition and functioning of soil communities. Effects of plants on soil communities are largely taxon‐dependent, but how different functional groups of herbaceous plants affect trophic niches of individual animal species in soil needs further investigation. Here, we studied the use of basal resources and trophic levels of dominating soil meso‐ and macrofauna using stable isotope ratios of carbon and nitrogen in arable fallow systems 3 and 14–16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a nonlegume herb (Taraxacum officinale), and a grass (Bromus sterilis). We found virtually no consistent effects of plant identity on stable isotope composition of soil animals and on thirteen isotopic metrics that reflect general food‐web structure. However, in old fallows, the carbon isotope composition of some predatory macrofauna taxa had shifted closer to that of co‐occurring plants, which was particularly evident for Lasius, an aphid‐associated ant genus. Trophic levels and trophic‐chain lengths in food webs were similar across plant species and fallow ages. Overall, the results suggest that variations in local plant diversity of grassland communities may little affect the basal resources and the trophic level of prey consumed by individual species of meso‐ and macrofauna belowground. By contrast, successional changes in grassland communities are associated with shifts in the trophic niches of certain species, reflecting establishment of trophic interactions with time, which shapes the functioning and stability of soil food webs.
Novel Decomposition Technique on Rational-Based Neuro-Transfer Function for Modeling of Microwave Components

The rational-based neuro-transfer function (neuro-TF) method is a popular method for parametric modeling of electromagnetic (EM) behavior of microwave components. However, when the order in the neuro-TF becomes high, the sensitivities of the model response with respect to the coefficients of the transfer function become high. Due to this high-sensitivity issue, small training errors in the coefficients of the transfer function will result in large errors in the model output, leading to the difficulty in training of the neuro-TF model. This paper proposes a new decomposition technique to address this high-sensitivity issue. In the proposed technique, we decompose the original neuro-TF model with high order of transfer function into multiple sub-neuro-TF models with much lower order of transfer function. We then reformulate the overall model as the combination of the sub-neuro-TF models. New formulations are derived to determine the number of sub-models and the order of transfer function for each sub-model. Using the proposed decomposition technique, we can decrease the sensitivities of the overall model response with respect to the coefficients of the transfer function in each sub-model. Therefore, the modeling approach using the proposed decomposition technique can increase the modeling accuracy. Two EM parametric modeling examples are used to demonstrate the proposed decomposition technique.
Complete mitochondrial genome and assembled DNA barcoding analysis of Lutjanus fulgens (Valenciennes, 1830) and its comparison with other Lutjanus species

Abstract Lutjanus fulgens (Valenciennes, 1830) is a teleost species classified under the family Lutjanidae which is a native of the Eastern Atlantic Ocean. Though highly commercialized due to its abundance and good taste, the production output has declined in recent years. This is an indication of the need for effective management and conservation measures. However, accurate species identification will ensure strategic management and conservation measure. DNA‐based species identification has proven its reliability in this regard via precise species identification. Several researchers have confirmed the accuracy of DNAbarcode as a species identification tool as well as species phylogeny analysis based on both the complete mitogenome and COI gene. Currently, nine specimens of L. fulgens were sampled from Ghana and subjected to DNA‐based analysis, namely, complete mitochondrial DNAand COI gene (DNA barcoding) analyses. The mitogenomic result revealed that L. fulgens is made up of a 16,500 base pairs (bp) mtDNA which consists of 22 transfer RNAs, 13 protein‐coding genes, and two ribosomal RNAs (GenBank Accession Number: MN398650). Furthermore, a sequence polymorphism analysis of the COIgene (MN986442–MN986450) detected two haplotypes. These haplotypes were both collected from the same fish landing site which suggests a possible cryptic linage diversity in the L. fulgens population at Vodza. According to the phylogeny examination, a close taxonomic relationship exists between L. fulgens and Lutjanus buccanella caused by a recent evolution termed as sympatric speciation. This study serves as a novel study for this species, building the foundation for future molecular‐based study for this species and as a DNA barcode reference data.
The Role of Herpes Simplex Virus Type 1 Infection in Demyelination of the Central Nervous System

Herpes simplex type 1 (HSV-1) is a neurotropic virus that infects the peripheral and central nervous systems. After primary infection in epithelial cells, HSV-1 spreads retrogradely to the peripheral nervous system (PNS), where it establishes a latent infection in the trigeminal ganglia (TG). The virus can reactivate from the latent state, traveling anterogradely along the axon and replicating in the local surrounding tissue. Occasionally, HSV-1 may spread trans-synaptically from the TG to the brainstem, from where it may disseminate to higher areas of the central nervous system (CNS). It is not completely understood how HSV-1 reaches the CNS, although the most accepted idea is retrograde transport through the trigeminal or olfactory tracts. Once in the CNS, HSV-1 may induce demyelination, either as a direct trigger or as a risk factor, modulating processes such as remyelination, regulation of endogenous retroviruses, or molecular mimicry. In this review, we describe the current knowledge about the involvement of HSV-1 in demyelination, describing the pathways used by this herpesvirus to spread throughout the CNS and discussing the data that suggest its implication in demyelinating processes.
Sleep in Isolated, Confined, and Extreme (ICE): A Review on the Different Factors Affecting Human Sleep in ICE

The recently renewed focus on the human exploration of outer space has boosted the interest toward a variety of questions regarding health of astronauts and cosmonauts. Among the others, sleep has traditionally been considered a central issue. To extend the research chances, human sleep alterations have been investigated in several analog environments, called ICEs (Isolated, Confined, and Extreme). ICEs share different features with the spaceflight itself and have been implemented in natural facilities and artificial simulations. The current paper presents a systematic review of research findings on sleep disturbances in ICEs. We looked for evidence from studies run in polar settings (mostly Antarctica) during space missions, Head-Down Bed-Rest protocols, simulations, and in a few ICE-resembling settings such as caves and submarines. Even though research has shown that sleep can be widely affected in ICEs, mostly evidencing general and non-specific changes in REM and SWS sleep, results show a very blurred picture, often with contradictory findings. The variable coexistence of the many factors characterizing the ICE environments (such as isolation and confinement, microgravity, circadian disentrainment, hypoxia, noise levels, and radiations) does not provide a clear indication of what role is played by each factor per se or in association one with each other in determining the pattern observed, and how. Most importantly, a number of methodological limitations contribute immensely to the unclear pattern of results reported in the literature. Among them, small sample sizes, small effect sizes, and large variability among experimental conditions, protocols, and measurements make it difficult to draw hints about whether sleep alterations in ICEs do exist due to the specific environmental characteristics, and which of them plays a major role. More systematic and cross-settings research is needed to address the mechanisms underlying the sleep alterations in ICE environments and possibly develop appropriate countermeasures to be used during long-term space missions.
Meditation-Relaxation (MR Therapy) for Sleep Paralysis: A Pilot Study in Patients With Narcolepsy

Sleep paralysis (SP) is a condition where a person is paralyzed upon waking or falling asleep. SP afflicts ~20% of people, and is also one of the typical symptoms in narcolepsy. During SP the sleeper may experience hallucinations. Unsurprisingly, SP is associated with great fear globally. To date, there are no published clinical trials or outcome data for treating this condition. However, few non-pharmacological interventions have been proposed, including cognitive behavioral approaches, and case studies showing clinical amelioration with auto-hypnosis and Meditation-Relaxation (MR) therapy. The latter for instance showed positive preliminary results; when applied for 8 weeks it reduced SP frequency and anxiety/worry symptoms. With this paper we aimed to evaluate, with a small-scale pilot study, the efficacy of MR therapy for SP in patients with narcolepsy. Ten patients with narcolepsy and SP were enrolled in the study. Notably, MR therapy (n = 6), applied for 8 weeks, resulted in a dramatic decrease in the number of days SP occurred (50% reduction); and the total number of SP episodes (54% reduction) in the last month of the study (demonstrated by large within-group effect sizes); unlike the control intervention (deep breathing) (n = 4). These findings are preliminary and exploratory given the small sample. Nonetheless, they represent the first proof of concept at providing empirically-guided insights into the possible efficacy of a novel treatment for frequently occurring SP. Although the study was conducted in patients with narcolepsy we cautiously suggest that the findings may generalize to individuals with isolated SP.
Mechanical Cell-to-Cell Interactions as a Regulator of Topological Defects in Planar Cell Polarity Patterns in Epithelial Tissues

A precise structural organization of epithelial cells is needed for the proper functioning and development of different tissues. The epithelial cell packing mechanism is associated with mechanical interactions between cells that place the tissue in a state with the lowest free energy. In addition, planar cell polarity has been recognized as another important mechanism for the epithelial organization that ensures the orientational ordering of the cells. Planar cell polarity is a consequence of an asymmetric distribution of certain transmembrane proteins, which is driven by specific intracellular signaling pathways. Mutations and other disruptions of these pathways were found to cause an impaired cytoarchitecture of the epithelium layer. Mutant cells with disrupted activities of signaling proteins basically represent topological defects in the polarization patterns of adjacent cells, which can lead to dysfunctions in tissue operation. Motivated by the fact that regional variations of bond tensions were found in the vicinity of mutant cells, we implement a computational model that combines the tissue development processes following the concept of free energy minimization and the cellular polarization. Our results reveal that a decrease in mechanical interactions between normal and mutant epithelium cells represents a conceivable regulatory mechanism that diminishes the impact of topological defects caused by mutant cells.
The H+-Translocating Inorganic Pyrophosphatase From Arabidopsis thaliana Is More Sensitive to Sodium Than Its Na+-Translocating Counterpart From Methanosarcina mazei

Overexpression of membrane-bound K+-dependent H+-translocating inorganic pyrophosphatases (H+-PPases) from higher plants has been widely used to alleviate the sensitivity toward NaCl in these organisms, a strategy that had been previously tested in Saccharomyces cerevisiae. On the other hand, H+-PPases have been reported to functionally complement the yeast cytosolic soluble pyrophosphatase (IPP1). Here, the efficiency of the K+-dependent Na+-PPase from the archaeon Methanosarcina mazei (MVP) to functionally complement IPP1 has been compared to that of its H+-pumping counterpart from Arabidopsis thaliana (AVP1). Both membrane-bound integral PPases (mPPases) supported yeast growth equally well under normal conditions, however, cells expressing MVP grew significantly better than those expressing AVP1 under salt stress. The subcellular distribution of the heterologously-expressed mPPases was crucial in order to observe the phenotypes associated with the complementation. In vitro studies showed that the PPase activity of MVP was less sensitive to Na+ than that of AVP1. Consistently, when yeast cells expressing MVP were grown in the presence of NaCl only a marginal increase in their internal PPi levels was observed with respect to control cells. By contrast, yeast cells that expressed AVP1 had significantly higher levels of this metabolite under the same conditions. The H+-pumping activity of AVP1 was also markedly inhibited by Na+. Our results suggest that mPPases primarily act by hydrolysing the PPi generated in the cytosol when expressed in yeast, and that AVP1 is more susceptible to Na+ inhibition than MVP both in vivo and in vitro. Based on this experimental evidence, we propose Na+-PPases as biotechnological tools to generate salt-tolerant plants.
Novel Muscle Imaging in Inflammatory Rheumatic Diseases—A Focus on Ultrasound Shear Wave Elastography and Quantitative MRI

In recent years, imaging has played an increasing role in the clinical management of patients with rheumatic diseases with respect to aiding diagnosis, guiding therapy and monitoring disease progression. These roles have been underpinned by research which has enhanced our understanding of disease pathogenesis and pathophysiology of rheumatology conditions, in addition to their key role in outcome measurement in clinical trials. However, compared to joints, imaging research of muscles is less established, despite the fact that muscle symptoms are very common and debilitating in many rheumatic diseases. Recently, it has been shown that even though patients with rheumatoid arthritis may achieve clinical remission, defined by asymptomatic joints, many remain affected by lingering constitutional systemic symptoms like fatigue, tiredness, weakness and myalgia, which may be attributed to changes in the muscles. Recent improvements in imaging technology, coupled with an increasing clinical interest, has started to ignite new interest in the area. This perspective discusses the rationale for using imaging, particularly ultrasound and MRI, for investigating muscle pathology involved in common inflammatory rheumatic diseases. The muscles associated with rheumatic diseases can be affected in many ways, including myositis—an inflammatory muscle condition, and myopathy secondary to medications, such as glucocorticoids. In addition to non-invasive visual assessment of muscles in these conditions, novel imaging techniques like shear wave elastography and quantitative MRI can provide further useful information regarding the physiological and biomechanical status of the muscle.
Heteromeric Channels Formed From Alternating Kv7.4 and Kv7.5 α-Subunits Display Biophysical, Regulatory, and Pharmacological Characteristics of Smooth Muscle M-Currents

Smooth muscle cells of the vasculature, viscera, and lungs generally express multiple α-subunits of the Kv7 voltage-gated potassium channel family, with increasing evidence that both Kv7.4 and Kv7.5 can conduct “M-currents” that are functionally important for the regulation of smooth muscle contractility. Although expression systems demonstrate that functional channels can form as homomeric tetramers of either Kv7.4 or Kv7.5 α-subunits, there is evidence that heteromeric channel complexes, containing some combination of Kv7.4 and Kv7.5 α-subunits, may represent the predominant configuration natively expressed in some arterial myocytes, such as rat mesenteric artery smooth muscle cells (MASMCs). Our previous work has suggested that Kv7.4/Kv7.5 heteromers can be distinguished from Kv7.4 or Kv7.5 homomers based on their biophysical, regulatory, and pharmacological characteristics, but it remains to be determined how Kv7.4 and Kv7.5 α-subunits combine to produce these distinct characteristics. In the present study, we constructed concatenated dimers or tetramers of Kv7.4 and Kv7.5 α-subunits and expressed them in a smooth muscle cell line to determine if a particular α-subunit configuration can exhibit the features previously reported for natively expressed Kv7 currents in MASMCs. Several unique characteristics of native smooth muscle M-currents were reproduced under conditions that constrain channel formation to a Kv7.4:Kv7.5 stoichiometry of 2:2, with alternating Kv7.4 and Kv7.5 α-subunits within a tetrameric structure. Although other subunit arrangements/combinations are not ruled out, the findings provide new insights into the oligomerization of α-subunits and the ways in which Kv7.4/Kv7.5 subunit assembly can affect smooth muscle signal transduction and pharmacological responses to Kv7 channel modulating drugs.
Large-Scale Variability of Physical and Biological Sea-Ice Properties in Polar Oceans

In this study, we present unique data collected with a Surface and Under-Ice Trawl (SUIT) during five campaigns between 2012 and 2017, covering the spring to summer and autumn transition in the Arctic Ocean, and the seasons of winter and summer in the Southern Ocean. The SUIT was equipped with a sensor array from which we retrieved: sea-ice thickness, the light field at the underside of sea ice, chlorophyll a concentration in the ice (in-ice chl a), and the salinity, temperature, and chl a concentration of the under-ice water. With an average trawl distance of about 2 km, and a global transect length of more than 117 km in both polar regions, the present work represents the first multi-seasonal habitat characterization based on kilometer-scale profiles. The present data highlight regional and seasonal patterns in sea-ice properties in the Polar Ocean. Light transmittance through Arctic sea ice reached almost 100% in summer, when the ice was thinner and melt ponds spread over the ice surface. However, the daily integrated amount of light under sea ice was maximum in spring. Compared to the Arctic, Antarctic sea-ice was thinner, snow depth was thicker, and sea-ice properties were more uniform between seasons. Light transmittance was low in winter with maximum transmittance of 73%. Despite thicker snow depth, the overall under-ice light was considerably higher during Antarctic summer than during Arctic summer. Spatial autocorrelation analysis shows that Arctic sea ice was characterized by larger floes compared to the Antarctic. In both Polar regions, the patch size of the transmittance followed the spatial variability of sea-ice thickness. In-ice chl a in the Arctic Ocean remained below 0.39 mg chl a m−2, whereas it exceeded 7 mg chl a m−2 during Antarctic winter, when water chl a concentrations remained below 1.5 mg chl a m−2, thus highlighting its potential as an important carbon source for overwintering organisms. The data analyzed in this study can improve large-scale physical and ecosystem models, habitat mapping studies and time series analyzed in the context of climate change effects and marine management.
LBM modeling and analysis on microchannel slip flow and heat transfer under different heating conditions

Abstract This article aims to explore the effects of buoyancy force and thermal boundary condition on the mixed convection heat transfer performance of air in a horizontal microchannel. Three different heat flux models, including bottom wall heated, top wall heated (single wall heating – a novel heating approach compared to recent studies) and both walls heated, are analyzed at four different values of the Grashof number (Gr = 0, 100, 300, 600) using a lattice Boltzmann method (LBM). The slip velocity boundary condition is also applied to the bottom and top walls. It can be found that the buoyancy force changes the velocity distribution structure near the bottom wall and top wall, particularly at the inlet regions in all models, and a negative slip velocity is generated due to the backflow formed at a relatively large Grashof number and it strictly determines the local wall friction coefficient. Either the bottom wall or the top wall is heated. A vortex is found close to the top wall because the mixing position of the hot and cold fluids is in the vicinity of the top wall. This feature facilitates the heat transfer near the top wall and core flow zone. The thermal performance is most positive for the case when the top wall is heated due to the generation of an induced vortex and no influence of the vortex near the bottom wall.