Miracle-dz/UniFAR-FTUs huggingface dataset:
Absence of miRNA-146a Differentially Alters Microglia Function and Proteome

Background: MiR-146a is an important regulator of innate inflammatory responses and is also implicated in cell death and survival. Methods: By sorting CNS resident cells, microglia were the main cellular source of miR-146a. Therefore, we investigated microglia function and phenotype in miR-146a knock-out (KO) mice, analyzed the proteome of KO and wild-type (WT) microglia by LC-MS/MS, and examined miR-146a expression in different brain lesions of patients with multiple sclerosis (MS). Results: When stimulated with LPS or myelin in vitro, microglia from KO mice expressed higher levels of IL-1β, TNF, IL-6, IL-10, CCL3, and CCL2 compared to WT. Stimulation increased migration and phagocytosis of WT but not KO microglia. CD11c+ microglia were induced by cuprizone (CPZ) in the WT mice but less in the KO. The proteome of ex vivo microglia was not different in miR-146a KO compared to WT mice, but CPZ treatment induced differential and reduced protein responses in the KO: GOT1, COX5b, CRYL1, and cystatin-C were specifically changed in KO microglia. We explored discriminative features of microglia proteomes: sparse Partial Least Squares-Discriminant Analysis showed the best discrimination when control and CPZ-treated conditions were compared. Cluster of ten proteins separated WT and miR-146a KO microglia after CPZ: among them were sensomes allowing to perceive the environment, Atp1a3 that belongs to the signature of CD11c+ microglia, and proteins related to inflammatory responses (S100A9, Ppm1g). Finally, we examined the expression of miR-146a and its validated target genes in different brain lesions of MS patients. MiR-146 was upregulated in all lesion types, and the highest expression was in active lesions. Nineteen of 88 validated target genes were significantly changed in active lesions, while none were changed in NAWM. Conclusion: Our data indicated that microglia is the major source of miR-146a in the CNS. The absence of miR-146a differentially affected microglia function and proteome, and miR-146a may play an important role in gene regulation of active MS lesions.
3D model retrieval based on deep learning approach with weighted three-view deep features

With the development of computer graphics and three-dimensional (3D) modeling technology, 3D model retrieval has been widely used in different applications, such as industrial design, virtual reality, medical diagnosis, etc. Massive data brings new opportunities and challenges to the development of the 3D model retrieval technology. However, with the emergence of complex models, traditional retrieval algorithms are not applicable to some extent. One important reason for this is that the traditional content-based retrieval methods do not take the spatial information of 3D models into account during feature extraction. Therefore, how to use the spatial information of a 3D model to obtain a more extensive feature has become a significant issue. In our proposed algorithm, we first normalize and voxelize the model, and then extract features from different views of the voxelized model. Secondly, deep features are extracted by using our proposed feature learning network. Then, a new feature weighting algorithm is applied to our 3D-view-based features, which can emphasize the more important views of the 3D models, so the retrieval performance can be improved. The experimental results on the standard 3D model dataset, Princeton ModelNet10, show that our model can achieve promising performance.
Super-resolution image generation for improvement of orbital thin bone segmentation

We generate super-resolution orbital bone CT images using 3D SRGAN network to improve the accuracy of segmentation of thin bones with large slice thickness. Our method consists of data preparation and super-resolution thin bone image generation. Experimental results show that the generated super-resolution images using 3D SRGAN are clearly observed in thin bone areas and are more similar to the original high resolution images than other images using bilinear and bicubic interpolations.
Free-breathing contrast-enhanced upper abdominal MRI in children: comparison between Cartesian acquisition and stack-of-stars acquisition with two different fat-suppression techniques

Background Respiratory artifacts impair image quality of magnetic resonance imaging (MRI) in children who cannot hold breath during MRI examination. Purpose To compare the quality of free-breathing contrast-enhanced 3D T1-weighted (T1W) images of the upper abdomen in children using Cartesian acquisition (Cartesian eTHRIVE), stack-of-stars acquisition with spectral fat suppression (3D VANE eTHRIVE), and stack-of-stars acquisition with fat suppression using modified Dixon (3D VANE mDixon). Material and Methods Pediatric patients (aged <19 years) who underwent whole-body MRI with free-breathing contrast-enhanced T1W axial scans of upper abdomen using Cartesian eTHRIVE, 3D VANE eTHRIVE, and 3D VANE mDixon were enrolled. Image quality parameters were assessed including overall image quality, hepatic edge sharpness, hepatic vessel clarity, respiratory artifacts, radial artifacts, lesion conspicuity, and lesion edge sharpness using the Likert scale, where a lower score indicated poorer image quality. The coefficients of variation of signal intensity of liver and spleen were analyzed. Results In 41 patients, 3D VANE eTHRIVE showed the highest scores for all image quality parameters (P ≤ 0.001). 3D VANE eTHRIVE also showed higher scores for respiratory (P ≤ 0.001) and radial artefacts than 3D VANE mDixon (P = 0.001). There were no significant differences in coefficients of variation of signal intensity of the liver and spleen between 3D VANE eTHRIVE and 3D VANE mDixon. Acquisition time was longer for 3D VANE eTHRIVE (81.26 ± 16 s) than for Cartesian eTHRIVE (7.87 ± 0.95 s) and 3D VANE mDixon (76.66 ± 12.4 s, P < 0.001). Conclusion The application of stack-of-stars acquisition to 3D T1W abdominal MRI resulted in better image quality than Cartesian acquisition in free-breathing children. In stack-of-stars acquisition, spectral fat suppression resulted in better image quality and fewer artifacts than mDixon.
Synthesis of Amide Linked Nucleosides at the 6 Position of Deoxy Inosine and Their application to DNA synthesis, Hybridization Studies.

Abstract Synthesis of amide linked nucleosides at the 6 position of the purine base to recognize “G:C” base pair in a DNA duplex is described. Here we describe the synthesis of amide linked nucleosides containing heteroatoms N, O and C and their application to DNA synthesis and hybridization studies.
Field measurements of air-sea CO2 exchange

The direction and magnitude of air-sea exchanges depend on the difference of gas partial pressure (ΔP) between phases and on a gas exchange coefficient (K). In this work, field air-sea CO2 exchange and ΔPco2 have been measured simultaneously to study the in situ relations between parameters. Experiments have been carried out at three sites: the Bay of Calvi (Corsica), the Ligurian Sea, and the North Sea. Flux measurements were made with a direct chamber method to detect invasion or evasion of gas. Due to its bed of seagrass (P(Posidonia), the Bay of Calvi is the site of regular, daily, and yearly variations of surface CO2 content. Daily variations are often too small to overcome the variation of K and to find a correlation between hourly measured fluxes and daily changes of ΔP. The yearly variation of Pco2 in surface water (from 300 ppm in winter to 900 ppm in summer) has however permitted derivation of a linear relationship between mean fluxes and ΔP that fits well with fluxes measured at the two other sites under similar meteorological conditions and thus with nearly the same K. Calculated coefficients range between 10−5 and 4 × 10−5 m s−1 and so agree well with those determined with radiotracers or in wind tunnels. Measurements in the North Sea under different meteorological conditions show the influence of wind speed and sea state on exchanges measured by the in situ methodology used and allow the results to be compared with those obtained by others in wind tunnels.
Visual analysis of fish feeding intensity for smart feeding in aquaculture using deep learning

This paper presents a novel deep-learning approach to analyze the fish feeding intensity based on the images of fish tanks during the fish feeding process. The grade of the fish feeding intensity is an important indicator of fish appetite. On the design of a smart feeding system in aquaculture, this information is of great significance for guiding feeding and optimizing the fish production. However, conventional fish appetite assessment methods are inefficient and subjective. To solve these problems, in this study, based on a space-time two-stream 3D CNN, a deep learning approach for grading fish feeding intensity is proposed to evaluate fish appetite. The flow of the approach is implemented as follows. First, a fixed RGB camera is setup to capture the videos from the fish tanks during the feeding processes. This also constructs a dataset for training the two-stream neural network, and the fish appetite levels are graded using the trained neural network model. Finally, the performance of the method is evaluated and compared with other CNN-based deep learning approaches. The results show that the grading accuracy reached 91.18%, which outperforms the compared CNN-based approaches. Thus, the model can be used to detect and evaluate fish appetite to guide production practices.
Trends in Land Use, Irrigation, and Streamflow Alteration in the Mississippi River Alluvial Plain

The Mississippi River Alluvial Plain is a critical region for agricultural production in the United States, providing the majority of the nation's rice, catfish, and cotton. Although it is a humid region, high agricultural yields are maintained through irrigation from groundwater and surface water sources. Heavy groundwater extraction has led to cones of depression in the alluvial aquifer in both Arkansas and Mississippi. This study explores the link between increasing irrigation and streamflow alteration within the alluvial plain. Changing land use patterns were evaluated utilizing the USDA Census of Agriculture datasets to determine changes in land-use, irrigation, and crop yield from 1969 to 2017. Temporal land use patterns set the background for the analysis of sixteen long-term streamflow records from the USGS, which were assessed using the Indicators of Hydrologic Alteration (IHA) software to determine changes in low flow patterns in rivers overlying the Mississippi River Valley alluvial aquifer. Most streamflow records had significant hydrologic alteration with respect to low flow conditions, including higher frequency of low flow events, lower annual minima, or a declining base flow index. Changes in streamflow coincide with areas of massive increases in irrigated cropland area. This study provides further context for the tradeoffs between intensive agricultural production and agroecosystem sustainability.
Coherent oscillations of a levitated birefringent microsphere in vacuum driven by nonconservative rotation-translation coupling

Coupling between the rotational and translational motions of an optically levitated microsphere leads to coherent oscillations. We demonstrate an effect whereby stochastic, thermal fluctuations combine with nonconservative optical forces to break detailed balance and produce increasingly coherent, apparently deterministic motion for a vacuum-trapped particle. The particle is birefringent and held in a linearly polarized Gaussian optical trap. It undergoes oscillations that grow rapidly in amplitude as the air pressure is reduced, seemingly in contradiction to the equipartition of energy. This behavior is reproduced in direct simulations and captured in a simplified analytical model, showing that the underlying mechanism involves nonsymmetric coupling between rotational and translational degrees of freedom. When parametrically driven, these self-sustained oscillators exhibit an ultranarrow linewidth of 2.2 μHz and an ultrahigh mechanical quality factor in excess of 2 × 108 at room temperature. Last, nonequilibrium motion is seen to be a generic feature of optical vacuum traps, arising for any system with symmetry lower than that of a perfect isotropic microsphere in a Gaussian trap.
Efficient Energy Management of IoT-Enabled Smart Homes Under Price-Based Demand Response Program in Smart Grid

There will be a dearth of electrical energy in the prospective world due to exponential increase in electrical energy demand of rapidly growing world population. With the development of internet-of-things (IoT), more smart devices will be integrated into residential buildings in smart cities that actively participate in electricity market via demand response (DR) programs to efficiently manage energy in order to meet this increasing energy demand. Thus, with this incitement, an energy management strategy using price-based DR program is developed for IoT-enabled residential buildings. We propose a wind-driven bacterial foraging algorithm (WBFA), which is a hybrid of wind-driven optimization (WDO) and bacterial foraging optimization (BFO) algorithms. Subsequently, we devised a strategy based on our proposed WBFA to systematically manage the power usage of IoT-enabled residential building smart appliances by scheduling to alleviate peak-to-average ratio (PAR), minimize cost of electricity, and maximize user comfort (UC). This increases effective energy utilization, which in turn increases the sustainability of IoT-enabled residential buildings in smart cities. The WBFA-based strategy automatically responds to price-based DR programs to combat the major problem of the DR programs, which is the limitation of consumer’s knowledge to respond upon receiving DR signals. To endorse productiveness and effectiveness of the proposed WBFA-based strategy, substantial simulations are carried out. Furthermore, the proposed WBFA-based strategy is compared with benchmark strategies including binary particle swarm optimization (BPSO) algorithm, genetic algorithm (GA), genetic wind driven optimization (GWDO) algorithm, and genetic binary particle swarm optimization (GBPSO) algorithm in terms of energy consumption, cost of electricity, PAR, and UC. Simulation results show that the proposed WBFA-based strategy outperforms the benchmark strategies in terms of performance metrics.
“Slowed Down but Not Stopped”: A Spiritual Life Review Intervention in Patients with Neurodegenerative Disease

Spiritual health is important in managing and coping with chronic and debilitating illnesses, such as neurodegenerative diseases. However, few spiritual interventions have addressed this population. This article quantitatively and qualitatively evaluates outcomes of a spiritual life review in neurodegenerative diseases patients. The majority of participants improved or maintained quality of life and spiritual/emotional well-being following the intervention. Spiritual life review may be an important intervention in the comprehensive care of patients with neurodegenerative diseases.
Eukaryotic Microbial Communities in Japanese Arable Andisols Investigated by Amplicon Sequencing of 18S rRNA Genes

Compared with the well-studied soil prokaryotic communities, little is known about soil eukaryotic communities. Here, we investigated the eukaryotic community structures in 43 arable soils using amplicon sequencing of 18S rRNA genes. Major taxonomic groups, such as Fungi, Holozoa, and Stramenopiles, were detected in all samples. ABSTRACT Compared with the well-studied soil prokaryotic communities, little is known about soil eukaryotic communities. Here, we investigated the eukaryotic community structures in 43 arable soils using amplicon sequencing of 18S rRNA genes. Major taxonomic groups, such as Fungi, Holozoa, and Stramenopiles, were detected in all samples.
Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers.

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers revealed robust amplification profiles and were able to differentiate the 41 genotypes of sweet sorghum evaluated. Analysis of the frequency and distribution of polymorphic fragments allowed for the detection of unique (AFLP) and rare (SSR) alleles in several genotypes (RBSS‑8, RBSS‑9, RBSS‑25, RBSS‑32, and RBSS‑37), indicating that these markers may be associated with a feature that has not yet been determined or may be useful for the identification of these genotypes. The genetic relationships indicated the presence of at least two types of sweet sorghum: a group of modern genotypes used for sugar and biofuel production, and another group consisting of historic and modern genotypes used for the production of syrups. Sweet sorghum genotypes may be used to develop new varieties with higher sugar and juice contents.
Navigational Distances between UX Information and User Stories in Agile Virtual Environments

: User stories (US) are valuable artifacts to agile teams, being a succinct requirement description with its details complemented by other artifacts. User eXperience (UX) is an important cross-cutting quality requirement that has gained spotlight over the past years. Many approaches on merging agile and UX are presented in the literature, but few have analysed how UX information and US are related in agile virtual environments. This paper presents a case study which investigates the navigational distances between UX information and USs. The goal was to understand how agile practitioners linked UX information to USs. To do this, we conducted a qualitative analysis in 13 requirement documents of three different industry projects and also we explored the USs derived from such documents. We propose a classiﬁcation of navigational distances found among UX information and USs, discussing the pros and cons of each distance type. Our work contributes to motivate agile teams in rethinking about different forms to organize the information, artifacts and documents in virtual environments.
Dynamic imaging reveals surface exposure of virulent Leishmania amastigotes during pyroptosis of infected macrophages.

Leishmania spp are obligate intracellular parasites that infect phagocytes, notably macrophages. No information is available on how Leishmania parasites respond to pyroptosis of their host cell, known to limit microbial infection. Here, we analyzed the pyroptotic process and the fate of intracellular amastigotes at the single cell level using high-content, real-time imaging. Bone marrow-derived macrophages were infected with virulent L. amazonensis amastigotes and sequentially treated with lipopolysaccharide and adenosine triphosphate for pyroptosis induction. Real-time monitoring identified distinct pyroptotic phases, including rapid decay of the parasitophorous vacuole (PV), progressive cell death, and translocation of the luminal PV membrane to the cell surface in 40% of macrophages, resulting in the extracellular exposure of amastigotes that remained anchored to PV membranes. Electron microscopy analyses revealed an exclusive polarized orientation of parasites, with the anterior pole exposed toward the extracellular milieu, and the parasite posterior pole attached to the PV membrane. Exposed parasites retain their full infectivity towards naïve macrophages suggesting that host cell pyroptosis may contribute to parasite dissemination.
INTRAGUILD PREY SUFFER FROM ENRICHMENT OF THEIR RESOURCES: A MICROCOSM EXPERIMENT WITH CILIATES

Predation among species that compete for resources is widespread. Theory suggests a counterintuitive consequence of such intraguild predation: enrichment of the shared resource, for which the intraguild prey must be the superior competitor, reduces the population size of the intraguild prey and may even cause its extinction. Experiments with bacteria (shared resource) and the ciliates Tetrahymena (intraguild prey) and Blepharisma (intraguild predator) confirmed these expectations. Tetrahymena was the better resource competitor. Grown separately, it persisted at lower levels of enrichment and drove bacterial densities to lower levels than did Blepharisma. When grown together with Blepharisma, Tetrahymena declined in density with increasing enrichment, whereas bacteria and Blepharisma increased. The data thus support the theoretically suggested mechanism as the cause of this pattern: with enrichment, increasing densities of bacteria sustained an increasing predation pressure from Blepharisma on Tetrahymena, which overrode the direct positive effect of bacteria as a food source of Tetrahymena. Generalizing from these results, we speculate that staggered invasions of omnivores followed by extinctions of intermediate prey should contribute to the frequently observed unimodal or neutral responses of species richness and food chain length to increasing productivity.
Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area

Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.