Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of the Couple Stress Convective Micropolar Fluid Flow in a Hall MHD Generator System

The steady non-isothermal convective heat transfer in magnetohydrodynamic micropolar fluid flow over a non-linear extending wall is examined. The fluid flow is treated with strong magnetic field. The influence of magnetic field, Hall current, viscous dissipation, and couple stress are mainly focused in this work. The fluid flow problem is solved by analytical method. The impact of developing dimensionless parameters on primary, secondary, and angular velocity components and temperature profile are determined through graphs. The greater magnetic parameter, local Grashof number, Hall parameter, power-law index, Prandtl number, nonlinear wall geometric parameter, and couples stress parameter reduce the primary velocity component while the material parameter, and Eckert number escalates the primary velocity component. The greater local Grashof number, material parameter, power-law index, Prandtl number, and wall geometric parameter reduces the secondary velocity component while the greater magnetic parameter, Hall parameter, Eckert number, and couple stress parameter escalates the secondary velocity component.
On Alternative Uses of Structural Compliance for the Development of Adaptive Robot Grippers and Hands

Adaptive robot hands are typically created by introducing structural compliance either in their joints (e.g., implementation of flexures joints) or in their finger-pads. In this paper, we present a series of alternative uses of structural compliance for the development of simple, adaptive, compliant and/or under-actuated robot grippers and hands that can efficiently and robustly execute a variety of grasping and dexterous, in-hand manipulation tasks. The proposed designs utilize only one actuator per finger to control multiple degrees of freedom and they retain the superior grasping capabilities of the adaptive grasping mechanisms even under significant object pose or other environmental uncertainties. More specifically, in this work, we introduce, discuss, and evaluate: (a) a design of pre-shaped, compliant robot fingers that adapts/conforms to the object geometry, (b) a hyper-adaptive finger-pad design that maximizes the area of the contact patches between the hand and the object, maximizing also grasp stability, and (c) a design that executes compliance adjustable manipulation tasks that can be predetermined by tuning the in-series compliance of the tendon routing system and by appropriately selecting the imposed tendon loads. The grippers are experimentally tested and their efficiency is validated using three different types of tests: (i) grasping tests that involve different everyday objects, (ii) grasp quality tests that estimate the contact area between the grippers and the objects grasped, and (iii) dexterous, in-hand manipulation experiments to evaluate the manipulation capabilities of the Compliance Adjustable Manipulation (CAM) hand. The devices employ mechanical adaptability to facilitate and simplify the efficient execution of robust grasping and dexterous, in-hand manipulation tasks.
Green Fluorescent Protein- and Discosoma sp. Red Fluorescent Protein-Tagged Organelle Marker Lines for Protein Subcellular Localization in Rice

The subcellular localization of proteins is a fundamental aspect of protein functions. Determining the subcellular localization is important for understanding the biological functions of proteins. Here, we developed a set of rice organelle marker lines, in which the expressing fluorescent organelle markers could be used as comparative standards in determining the subcellular localization of the protein of interest. We constructed green fluorescent protein (GFP)- and/or Discosoma sp. red fluorescent protein (DsRed)-tagged organelle markers targeted to the endoplasmic reticulum (ER), mitochondria, Golgi apparatus, peroxisome, actin cytoskeleton, plastid, tonoplast, plasma membrane, and nucleus, respectively. The utility of the rice marker lines for protein subcellular localization studies was demonstrated by detecting a nucleus-localized OsWRKY45 and a mitochondria-associated NbHxk1 in protoplasts of the GFP-OsH2B and the ScCOX4-DsRed lines, respectively. Using a sheath-inoculation method, followed by a live-cell imaging, we detected co-localization of a Magnaporthe oryzae PWL2:mCherry : NLS fusion with the nucleus marker in the GFP-OsH2B rice epidermal cells, confirming the translocation of the M. oryzae effector PWL2 into host cells, and further demonstrating the feasibility of using the organelle marker lines for studying dynamics of proteins in rice cells in the interactions between rice and pathogens. The set of organelle marker lines developed in the present study, provides a valuable resource for protein subcellular localization studies in rice.
Structured Channel Covariance Estimation from Limited Samples in Massive MIMO

Obtaining channel covariance knowledge is of great importance in various Multiple-Input Multiple-Output MIMO communication applications, including channel estimation and user grouping. Considering recently proposed massive MIMO systems, covariance estimation proves to be challenging due to the large number of antennas (M >> 1) employed in the base station. In this case, the number of pilot transmissions N becomes comparable to the number of antennas and standard estimators, such as the sample covariance, yield a poor estimate of the true covariance and are hence undesirable. In this paper, we propose a Maximum-Likelihood (ML) massive MIMO covariance estimator, based on a parametric representation of the channel angular spread function (ASF). The parametric representation emerges from super-resolving discrete ASF components plus approximating its continuous components using carefully chosen limited-support density function. We maximize the likelihood function using a Concave-Convex procedure, which is initialized via a non-negative least-squares optimization problem. Our simulation results show that the proposed method outperforms the state of the art in various estimation quality metrics.
Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool

Homoacetogens are efficient CO2 fixing bacteria using H2 as electron donor to produce acetate. These organisms can be enriched at the biocathode of microbial electrosynthesis (MES) for electricity-driven CO2 reduction to acetate. Studies exploring homoacetogens in MES are mainly conducted using pure or mix-culture anaerobic inocula from samples with standard environmental conditions. Extreme marine environments host unique microbial communities including homoacetogens that may have unique capabilities due to their adaptation to harsh environmental conditions. Anaerobic deep-sea brine pools are hypersaline and metalliferous environments and homoacetogens can be expected to live in these environments due to their remarkable metabolic flexibility and energy-efficient biosynthesis. However, brine pools have never been explored as inocula for the enrichment of homacetogens in MES. Here we used the saline water from a Red Sea brine pool as inoculum for the enrichment of halophilic homoacetogens at the biocathode (−1 V vs. Ag/AgCl) of MES. Volatile fatty acids, especially acetate, along with hydrogen gas were produced in MES systems operated at 25 and 10% salinity. Acetate concentration increased when MES was operated at a lower salinity ∼3.5%, representing typical seawater salinity. Amplicon sequencing and genome-centric metagenomics of matured cathodic biofilm showed dominance of the genus Marinobacter and phylum Firmicutes at all tested salinities. Seventeen high-quality draft metagenome-assembled genomes (MAGs) were extracted from the biocathode samples. The recovered MAGs accounted for 87 ± 4% of the quality filtered sequence reads. Genome analysis of the MAGs suggested CO2 fixation via Wood–Ljundahl pathway by members of the phylum Firmicutes and the fixed CO2 was possibly utilized by Marinobacter sp. for growth by consuming O2 escaping from the anode to the cathode for respiration. The enrichment of Marinobacter sp. with homoacetogens was only possible because of the specific cathodic environment in MES. These findings suggest that in organic carbon-limited saline environments, Marinobacter spp. can live in consortia with CO2 fixing bacteria such as homoacetogens, which can provide them with fixed carbon as a source of carbon and energy.
Muscle Contributions to Upper-Extremity Movement and Work From a Musculoskeletal Model of the Human Shoulder

Musculoskeletal models enable movement scientists to examine muscle function by computing the mechanical work done by muscles during motor tasks. To estimate muscle work accurately requires a model that is physiologically plausible. Previous models of the human shoulder have coupled scapula movement to humeral movement. While coupled movement produces a stereotypical scapulohumeral rhythm, it cannot model shrugging or independent movement of the scapula and humerus. The artificial coupling of humeral elevation to scapular rotation permits muscles that cross the glenohumeral joint, such as the rotator-cuff muscles and deltoids, to do implausible work to elevate and rotate the scapula. In reality, the motion of the scapula is controlled by thoracoscapular muscles, yet the roles of these muscles in shoulder function remains unclear. To elucidate the roles of the thoracoscapular muscles, we developed a shoulder model with an accurate scapulothoracic joint and includes scapular muscles to drive its motion. We used the model to compute the work done by the thoracoscapular muscles during shrugging and arm elevation. We found that the bulk of the work done in upper-extremity tasks is performed by the largest muscles of the shoulder: trapezius, deltoids, pectoralis major, and serratus-anterior. Trapezius and serratus anterior prove to be important synergists in performing upward-rotation of the scapula. We show that the large thoracoscapular muscles do more work than glenohumeral muscles during arm-elevation tasks. The model, experimental data and simulation results are freely available on SimTK.org to enable anyone to explore our results and to perform further studies in OpenSim 4.0.
Soil Aggregates as a Source of Dissolved Organic Carbon to Streams: An Experimental Study on the Effect of Solution Chemistry on Water Extractable Carbon

Over the past two decades, headwater streams of the northern hemisphere have shown increased amounts of dissolved organic carbon (DOC), coinciding with decreased acid deposition. The exact nature of the mechanistic link between precipitation composition and stream water DOC is still widely debated in the literature. We hypothesize that soil aggregates are the main source of stream water DOC and that DOC release is greater in organic rich, riparian soils versus hillslope soils. To test these hypotheses, we collected soils from two main landscape positions (hillslope and riparian zones) from the acid-impacted Sleepers River Research Watershed in northeastern Vermont. We performed aqueous soil extracts with solutions of different ionic strength (IS) and composition to simulate changes in soil solution. We monitored dynamic changes in soil particle size, aggregate architecture and composition, leachate DOC concentrations, dissolved organic matter (DOM) characteristics with fluorescence spectroscopy and trends in bioavailability. In low IS solutions, extractable DOC concentrations were significantly higher, particle size (by laser diffraction) was significantly smaller and organic material was separated from mineral particles in scanning electron microscope observations. Furthermore, higher DOC concentrations were found in Na+ compared to Ca2+ solutions of the same IS. These effects are attributed to aggregate dispersion due to expanding diffuse double layers in decreased IS solutions and to decreased bridging by divalent cations. Landscape position impacted quality but not quantity of released DOC. Overall, these results indicate that soil aggregates might be one important link between Critical Zone inputs (i.e. precipitation) and exports in streams.
Helicobacter pylori Infection Aggravates Dysbiosis of Gut Microbiome in Children With Gastritis

Introduction: Helicobacter pylori infection consistently leads to chronic and low degree of inflammatory response in gastric mucosa and is closely related with gastrointestinal and extra-gastric diseases. Effects of local microbiome in the stomach have been studied in adults and children with H. pylori infection. It is, however, not known whether the intestinal microbial community differs in children with varying H. pylori infection. The aim of this study is to characterize the altered composition of microbiome induced by H. pylori infection and in gastritis. Materials and Methods: This study involved 154 individuals, including 50 children affected by H. pylori-induced gastritis, 42 children with H. pylori-negative gastritis, and 62 healthy controls. Gut microbiome composition was analyzed using 16S rRNA gene-based pyrosequencing. Fecal bacterial diversity and composition were then compared. Results: On the basis of an analysis of similarities and differences, we found that children with H. pylori-induced gastritis exhibited gut bacteria dysbiosis. The ratio of Firmicutes/Bacteroidetes (F:B) at the phylum level had dramatically decreased in H. pylori-positive gastritis group (HPG) and H. pylori-negative gastritis group (HNG), compared with the healthy control group (HCG). At the family and genus levels, relative abundance of Bacteroidaceae and Enterobacteriaceae was prevalent in HPG and HNG, whereas relative abundance of Lachnospiraceae, Bifidobacteriaceae, and Lactobacillaceae was seen in HCG. Prevalence of different taxa of gut microbiome at the class, order, family, and genus levels was also observed among the three groups. Conclusions: Gastritis can cause changes in composition of fecal microbiome, which is exacerbated by H. pylori infection. These changes in gut microbiome may be related to drug resistance and development of chronic gastrointestinal diseases.
Three ORF-Containing Group I Introns in Chloroplast SSU of Caulerpa sertularioides (Ulvophyceae) and Their Evolutionary Implications

Except for a group I intron in trnL-uaa occuring in eubacteria and plastids, group I introns are rarely documented in plastid genomes. Here, we report that a green alga, Caulerpa sertularioides, contains three group IA3 introns in the 16S gene (cpSSU), CS-cpSSU.i1, CS-cpSSU.i2 and CS-cpSSU.i3. Each intron has an open reading frame with LAGLIDADG motifs. CS-cpSSU.i1orf and CS-cpSSU.i3orf occur at Loop 6 in the intron secondary structure and CScpSSU. i2orf at Loop 8. CS-cpSSU.i1orf and CS-cpSSU.i2orf contain both LAGLI-DADG motifs but CS-cpSSU.i3orf has only one. CS-cpSSU.i1 and CS-cpSSU.i2 share the insetion sites and the ORFs at Loop 6 and 8 with CpSSU·1 and CpSSU·2 introns of Chlamydomonas pallidostigmatica (Chlorophyceae). In contrast, CS-cpSSU.i3, containing 28 copies of GAAATAT at Loop 6, is a novel intron found only in Caulerpa sertularioides. Possible scenarios of the evolution of the three introns and their possible use in systematic research are discussed.
Escherichia coli Culture Filtrate Enhances the Growth of Gemmata spp.

Background Planctomycetes bacteria are known to be difficult to isolate, we hypothesized this may be due to missing iron compounds known to be important for other bacteria. We tested the growth-enhancement effect of complementing two standard media with Escherichia coli culture filtrate on two cultured strains of Gemmata spp. Also, the acquisition of iron by Gemmata spp. was evaluated by measuring various molecules involved in iron metabolism. Materials and Methods Gemmata obscuriglobus and Gemmata massiliana were cultured in Caulobacter and Staley’s medium supplemented or not with E. coli culture filtrate, likely containing siderophores and extracellular ferrireductases. We performed iron metabolism studies with FeSO4, FeCl3 and deferoxamine in the cultures with the E. coli filtrate and the controls. Results and Discussion The numbers of G. obscuriglobus and G. massiliana colonies on Caulobacter medium or Staley’s medium supplemented with E. coli culture filtrate were significantly higher than those on the standard medium (p < 0.0001). Agar plate assays revealed that the Gemmata colonies near E. coli colonies were larger than the more distant colonies, suggesting the diffusion of unknown growth promoting molecules. The inclusion of 10–4 to 10–3 M FeSO4 resulted in rapid Gemmata spp. growth (4–5 days compared with 8–9 days for the controls), suggesting that both species can utilize FeSO4 to boost their growth. In contrast, deferoxamine slowed down and prevented Gemmata spp. growth. Further studies revealed that the complementation of Caulobacter medium with E. coli culture filtrate and 10–4 M FeSO4 exerted a significant growth-enhancement effect compared with that obtained with Caulobacter medium supplemented with E. coli culture filtrate alone (p < 0.0122). Moreover, the intracellular iron concentrations in G. obscuriglobus and G. massiliana cultures in iron-depleted broth supplemented with the E. coli filtrate were 0.63 ± 0.16 and 0.78 ± 0.12 μmol/L, respectively, whereas concentrations of 1.72 ± 0.13 and 1.56± 0.11 μmol/L were found in the G. obscuriglobus and G. massiliana cultures grown in broth supplemented with the E. coli filtrate and FeSO4. The data reported here indicated that both E. coli culture filtrate and FeSO4 act as growth factors for Gemmata spp. via a potentiation mechanism.
Inhibition of Aminotransferases by Aminoethoxyvinylglycine Triggers a Nitrogen Limitation Condition and Deregulation of Histidine Homeostasis That Impact Root and Shoot Development and Nitrate Uptake

Background and Aims: Although AVG (aminoethoxyvinylglycine) is intensely used to decipher signaling in ethylene/indol-3-acetic acid (IAA) interactions on root morphogenesis, AVG is not a specific inhibitor of aminocyclopropane-1-carboxylate synthase (ACS) and tryptophan aminotransferase (TAA) and tryptophan aminotransferase related (TAR) activities since it is able to inhibit several aminotransferases involved in N metabolism. Indeed, 1 mM glutamate (Glu) supply to the roots in plants treated with 10 μM AVG partially restores the root growth. Here, we highlight the changes induced by AVG and AVG + Glu treatments on the N metabolism impairment and root morphogenetic program. Methods: Root nitrate uptake induced by AVG and AVG + Glu treatments was measured by a differential labeling with 15NO3 - and 15Nglutamate. In parallel a profiling of amino acids (AA) was performed to decipher the impairment of AA metabolism. Key Results: 10 μM AVG treatment increases K15NO3 uptake and 15N translocation during root growth inhibition whereas 10 μM AVG + 1 mM 15Nglutamate treatment inhibits K15NO3 uptake and increases 15Nglutamate uptake during partial root growth restoration. This is explained by a nitrogen (N) limitation condition induced by AVG treatment and a N excess condition induced by AVG + Glu treatment. AA levels were mainly impaired by AVG treatment in roots, where levels of Ser, Thr, α-Ala, β-Ala, Val, Asn and His were significantly increased. His was the only amino acid for which no restoration was observed in roots and shoots after glutamate treatment suggesting important control of His homeostasis on aminotransferase network. Results were discussed in light of recent findings on the interconnection between His homeostasis and the general amino acid control system (GAAC) in eukaryotes. Conclusions: These results demonstrate that AVG concentration above 5 μM is a powerful pharmacological tool for unraveling the involvement of GAAC system or new N sensory system in morphological and metabolic changes of the roots in leguminous and non-leguminous plants.
Influence of Awe on Green Consumption: The Mediating Effect of Psychological Ownership

The increasing demand for environmental protection has given rise to burgeoning research on green consumption. The present research adds to this expanding literature by investigating a novel predictor of consumer green consumption: awe. As a self-transcendent emotion, awe arises when people encounter perceptually vast stimuli that overwhelm their existing knowledge and mental structures, and, meanwhile, this also elicits a need for accommodation. This research proposes and demonstrates that, compared with happiness and a neutral affective state, experience of awe promotes green consumption via an enhanced psychological ownership of nature. Moreover, this research identifies a condition by showing that, while awe promotes green consumption when interdependent self-construal is activated, this effect diminishes when independent self-construal is activated.
Altered Cerebro-Cerebellar Limbic Network in AD Spectrum: A Resting-State fMRI Study

Recent evidence suggests that the cerebellum is related to motor and non-motor cognitive functions, and that several coupled cerebro-cerebellar networks exist, including links with the limbic network. Since several limbic structures are affected by Alzheimer pathology, even in the preclinical stages of Alzheimer’s disease (AD), we aimed to investigate the cerebral limbic network activity from the perspective of the cerebellum. Twenty patients with mild cognitive impairment (MCI), 18 patients with AD, and 26 healthy controls (HC) were recruited to acquire Resting-state functional MRI (rs-fMRI). We used seed-based approach to construct the cerebro-cerebellar limbic network. Two-sample t-tests were carried out to explore the differences of the cerebellar limbic network connectivity. The first result, a sub-scale network including the bilateral posterior part of the orbitofrontal cortex (POFC) extending to the anterior insular cortex (AIC) and left inferior parietal lobule (L-IPL), showed greater functional connectivity in MCI than in HC and less functional connectivity in AD than in MCI. The location of this sub-scale network was in accordance with components of the ventral attention network. Second, there was decreased functional connectivity to the right mid-cingulate cortex (MCC) in the AD and MCI patient groups relative to the HC group. As the cerebellum is not compromised by Alzheimer pathology in the prodromal stage of AD, this pattern indicates that the sub-scale ventral attention network may play a pivotal role in functional compensation through the coupled cerebro-cerebellar limbic network in MCI, and the cerebellum may be a key node in the modulation of social cognition.