Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of associative N2-fixation by streptomycin-resistant mutants of Azospirillum brasilense with genotypes of chick pea Rhizobium strains

SUMMARY Azospirillum brasilense was treated with nitrosoguanidine and two mutants isolated which were resistant to 500 μg streptomycin/ml. Ultraviolet sensitivity, photoreactivation and effect of acriflavin on pre- and post-irradiation were studied. Chick pea showed an increase in grain yield, nodule dry weight, N2ase activity and active iron content of nodules when inoculated with A. brasilense or its mutants together with Rhizobium. The interaction between Rhizobium strains and genotypes of chick pea was significant.
Analysis of Current Patterns to Determine the Bladder Volume by Electrical Impedance Tomography (EIT)

A non-invasive method based on Electrical Impedance Tomography (EIT) is represented here to determine the bladder volume which indicates the volume of urine. Two different current patterns using with EIT i.e. opposite pattern and adjacent pattern (which is more popular) were investigated by simulation on six 3D-realistic models including bone, rectum, and bladder. Sixteen electrodes were attached by two-plane configuration. Five geometries of the bladder having different volumes were used to determine the boundary voltage response to the conductivity change. A case of the bladder volumes was used to determine the performance of image reconstruction of these patterns. The simulation result shows a strong correlation between the voltage responses and the volume changes, in inverse manner. Using the opposite pattern conducted larger amplitude voltage response than using the adjacent pattern, and resulted in higher sensitivity in the upper mid-region between the electrode planes. The reconstruction image of both patterns can clearly locate the bladder. The reconstructed bladder in the case of using the opposite pattern is larger in amplitude than using the adjacent pattern. However, the image of the opposite pattern has more artifacts at the boundary. This is probably due to the incomparable number of current patterns and measurements of each pattern, and the insufficiency of the current flow patterns of the opposite pattern designed in this study. The higher sensitivity to noise and error of the opposite pattern is probably another cause as well.
DAE-GP: denoising autoencoder LSTM networks as probabilistic models in estimation of distribution genetic programming

Estimation of distribution genetic programming (EDA-GP) algorithms are metaheuristics where sampling new solutions from a learned probabilistic model replaces the standard mutation and recombination operators of genetic programming (GP). This paper presents DAE-GP, a new EDA-GP which uses denoising autoencoder long short-term memory networks (DAE-LSTMs) as probabilistic model. DAE-LSTMs are artificial neural networks that first learn the properties of a parent population by mapping promising candidate solutions to a latent space and reconstructing the candidate solutions from the latent space. The trained model is then used to sample new offspring solutions. We show on a generalization of the royal tree problem that DAE-GP outperforms standard GP and that performance differences increase with higher problem complexity. Furthermore, DAE-GP is able to create offspring with higher fitness from a learned model in comparison to standard GP. We believe that the key reason for the high performance of DAE-GP is that we do not impose any assumptions about the relationships between learned variables which is different to previous EDA-GP models. Instead, DAE-GP flexibly identifies and models relevant dependencies of promising candidate solutions.
Associations Between Plasma Immunomodulatory and Inflammatory Mediators With VACS Index Scores Among Older HIV-Infected Adults on Antiretroviral Therapy

The prevalence of age-related comorbidities is increased in people living with HIV, even in those well-controlled on combination antiretroviral therapy (ART). Persistent immune activation and inflammation may play pivotal roles in the pathogenesis; however, the burden of morbidities in the older HIV infected population may be exacerbated and driven by distinct mechanisms. In a cross sectional study of 45 HIV-infected participants 60 years or older, we examined the relationships between 14 immunomodulatory and inflammatory factors and the Veterans Aging Cohort Study (VACS) Index, a metric of multimorbidity and mortality comprised of age, CD4 count, hemoglobin, Fibrosis-4 [FIB-4], and estimated glomerular filtration rate [eGFR], by linear regression analysis. All participants were virally suppressed (<50 HIV RNA copies/mL), on ART, and primarily Caucasian (86.7%), and male (91.1%). Plasma levels of monocyte/macrophage-associated (neopterin, IP-10, sCD163, sCD14, and MCP-1) and glycan-binding immunomodulatory factors (galectin (Gal)-1, Gal-3, and Gal-9) were assessed, as well as inflammatory biomarkers previously linked to the VACS Index (i.e., CRP, cystatin C, TNF-α, TNFRI, IL-6, and D-dimer) for comparison. In regression analysis, higher VACS index scores were associated with higher levels of neopterin, cystatin C, TNFRI, and Gal-9 (all p < 0.05), potentially driven by correlations found with individual VACS components, including age, CD4 count, FIB-4, and eGFR. Gal-9, cystatin C, and TNFRI directly correlated with the extent of multimorbidity. Multiple correlations among markers were observed, suggesting an interplay of overlapping, but distinct, pathways. Collectively, in addition to cystatin C and TNFRI, both galectin-9 and neopterin, independently emerged as novel fluid markers of the VACS Index and burden of comorbidity and may further guide in understanding pathogenic mechanisms of age-related disorders in older HIV-infected individuals on suppressive ART.
Generation of Powerful Human Tolerogenic Dendritic Cells by Lentiviral-Mediated IL-10 Gene Transfer

The prominent role of dendritic cells (DC) in promoting tolerance and the development of methods to generate clinical grade products allowed the clinical application of tolerogenic DC (tolDC)-based therapies for controlling unwanted immune responses. We established an efficient method to generate tolerogenic human DC, producing supra-physiological levels of IL-10, by genetically engineering monocyte-derived DC with a bidirectional Lentiviral Vector (bdLV) encoding for IL-10 and a marker gene. DCIL−10 are mature DC, modulate T cell responses, promote T regulatory cells, and are phenotypically and functionally stable upon stimulation. Adoptive transfer of human DCIL−10 in a humanized mouse model dampens allogeneic T cell recall responses, while murine DCIL−10 delays acute graft-vs.-host disease in mice. Our report outlines an efficient method to transduce human myeloid cells with large-size LV and shows that stable over-expression of IL-10 generates an effective cell product for future clinical applications in the contest of allogeneic transplantation.
Role of the Functional Food (Pomegranate-Yoghourt) as Hepatoprotective Effect on Liver Injured Rats

The challenge is, however, choosing the right functional nutrients and formulating a message that works. Yoghurt is a fermented dairy product, having several health benefits, so is healthier for consumption (lourens-Hattingh and Viljoen 2001). Yoghurt is beneficial to our digestive system, especially stomach and colon; it enhances the immune response which will be in turn increase resistance to immunerelated diseases (Meydani et al 2000). Yoghurt can be developed with fruit juice which can be part of a healthy diet (Aswal et al 2012), which increases the aesthetic value of the new product as a functional pigment (Ghadge et al 2008; Coisson et al 2005). ISSN: 2319-7706 Volume 3 Number 8 (2014) pp. 185-196 http://www.ijcmas. com
An experimental demonstration of exploitation competition in an ongoing invasion

A native asexual gecko, Lepidodactylus lugubris, declines numerically when the sexual gecko Hemidactylus frenatus invades urban/suburban habitats throughout the Pacific. Previous studies showed that the competitive displacement occurs rapidly and is facilitated by clumped insect resources. Five lines of evidence suggest that the mechanism of displacement is primarily due to differences in the ability of each species to exploit insect resources. (1) These species show nearly complete diet overlap. (2) Insects are a limiting resource for both geckos as evidenced by positive demographic effects with in- creased insect abundance. (3) Hemidactylus frenatus depletes insect resources to lower levels than L. lugubris, which results in reduced rates of resource acquisition in L. lugubris. (4) This reduced resource acquisition translates into significant reductions in the body condition, fecundity, and survivorship of L. lugubris individuals. (5) Evidence for inter- ference (and other) mechanisms does not account for these negative demographic effects on L. lugubris. Interspecific competition is stronger than intraspecific competition for L. lugubris, with increasing L. lugubris density having negligible effect on H. frenatus, mirroring the asym- metry of the large-scale displacement. The superior harvesting ability of H. frenatus is most pronounced when insects are clumped spatially and temporally, and is attributable to a variety of species-specific traits such as their larger body size, faster running speed, and reduced intraspecific interference while foraging. We conclude that clumped resources can increase interspecific exploitation competition, and this mechanism may contribute to spe- cies turnover when human environmental alterations redistribute resources.
Corruption and the agricultural production efficiency of the European countries during the recent economic crisis

This paper examines the association between controls of corruption and the agricultural production efficiency of 23 European Union Member States during the recent economic crisis. Production efficiency, measured in terms of technical efficiency, is the effectiveness of a given set of inputs that is used to produce an output. Owing to climate and geographical location agriculture in European countries is diverse. The economic downturn led by the financial crisis which started in mid-2007, is still prevailing across European countries. Control of corruption along with the existing economic crisis of the member states are affecting agriculture production efficiency. This study used the national level production data for the period of 2003-2009. It shows that the technical efficiency of most Member States have declined over the years and that it was significantly lower in austere economic crisis time 2007-09 than 2003-06 for all countries. It is also found that the declining trend of technical efficiency is significantly lower for central and eastern European countries than for the western European countries. Study finds that the control of corruption in the presence of high government effectiveness, decreases the technical efficiency of agricultural production in the Member States. Res. Agric. , Livest. Fish.2(3): 427-437, December 2015
Digital approaches for mental health in the age of covid-19

Gold’s editorial on psychological first aid interventions recognises the major psychological consequences arising in the covid-19 pandemic.1 In this current climate, mounting effective mental health responses faces challenges, including the widespread reduction of available in-person mental health services and broad limitations in mobility as a result of the public health measures enacted. Covid-19 is occurring in an age of unprecedented adoption of digital technology, creating opportunities for data driven testing and dissemination …
Identification of the critical replication targets of CDK reveals direct regulation of replication initiation factors by the embryo polarity machinery in C. elegans

During metazoan development, the cell cycle is remodelled to coordinate proliferation with differentiation. Developmental cues cause dramatic changes in the number and timing of replication initiation events, but the mechanisms and physiological importance of such changes are poorly understood. Cyclin-dependent kinase (CDK) is important for regulating S-phase length in many metazoa, and here we show in the nematode Caenorhabditis elegans that an essential function of CDK during early embryogenesis is to regulate the interactions between three replication initiation factors SLD-3, SLD-2 and MUS-101 (Dpb11/TopBP1). Mutations that bypass the requirement for CDK to generate interactions between these factors is sufficient for viability in the absence of CyclinE/Cdk2, demonstrating that this is a critical embryonic function of this cyclin/CDK complex. Both SLD-2 and SLD-3 are asymmetrically localised in the early embryo and the levels of these proteins inversely correlate with S-phase length. We also show that SLD-2 asymmetry is determined by direct interaction with the polarity protein PKC-3. This study explains the essential function of CDK for replication initiation in a metazoan and provides the first direct molecular mechanism through which polarization of the embryo is coordinated with DNA replication initiation. Author Summary How and when a cell divides changes as the cell assumes different fates. How these changes in cell division are brought about are poorly understood, but are critical to ensure that cells do not over-proliferate leading to cancer. The nematode C. elegans is an excellent system to study the role of cell cycle changes during animal development. Here we show that two factors SLD-2 and SLD-3 are critical to control the decision to begin genome duplication. We show that these factors are differently distributed to different cell lineages in the early embryo, which may be a key event in determining the cell cycle rate in these cells. For the first time we show that, PKC-3, a key component of the machinery that determines the front (anterior) from the back (posterior) of the embryo directly controls SLD-2 distribution, which might explain how the polarisation of the embryo causes changes in the proliferation of different cell lineages. As PKC-3 is frequently mutated in human cancers, how this factor controls cell proliferation may be important to understand tumour progression.
Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion

Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess genetic toolkit necessary for sexual reproduction. However, the mechanism of sexual development in a majority of microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in studying sex in microbial eukaryotes is lack of observational evidence, primarily due to its cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investigate sexual development using stage specific Differential Gene Expression (DGE) and cytological analyses. Both DGE and cytological results showed that most of the meiosis and sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Relative gene ontology (GO) category representations in unfused (single) and fused cells revealed functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. While single cells GO categories were dominated by metabolic pathways and other processes indicative of vegetative phase. Our study provides strong evidence that the fused cells represent a sexual stage in Cochliopodium. Our findings have further implications in understanding the evolution and mechanism of inheritance involving multiparents in other eukaryotes with similar reproductive strategy.
The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters into the cells through its spike proteins binding to human angiotensin-converting enzyme 2 (ACE2) protein and causes virus infection in host cells. Until now, there are no available antiviral drugs have been reported that can effectively block virus infection. The study aimed to discover the potential compounds to prevent viral spike proteins to bind to the human ACE2 proteins from Taiwan Database of Extracts and Compounds (TDEC) by structure-based virtual screening. In this study, to rapidly discover potential inhibitors against SARS-CoV-2 spike proteins, the molecular docking calculation was performed by AutoDock Vina program. Herein, we found that 39 potential compounds may have good binding affinities and can respectively bind to the viral receptor-binding domain (RBD) of spike protein in the prefusion conformation and spike-ACE2 complex protein in silico. Among those compounds, especially natural products thioflexibilolide A and candidine that were respectively isolated from the soft corals Sinularia flexibilis and Phaius mishmensis may have better binding affinity than others. This study provided the predictions that these compounds may have the potential to prevent SARS-CoV-2 spike protein from entry into cells.
The influence of temperature during the development of conidia on the germination of Uncinula necator

Research Note Conidia of the obligate parasite Uncinula necator (conidial stage Oidium tuckeri ) were cultured at various temperatures and subsequently observed during germination. Spores that produced at low temperatures had a higher germination rate at low temperatures compared to spores that developed at high temperatures. However, the latter still germinated at very high temperatures.
Distribution, Abundance and Habitat Use of American White Pelicans in the Delta Region of Mississippi and Along the Western Gulf of Mexico Coast

Abstract Aerial surveys of American White Pelicans (Pelecanus erythrorhynchos) were conducted over coastal Louisiana and the delta region of Mississippi on 1-2 days during December, February, and April each year from 1997 to 1999. Additional surveys were conducted in coastal Texas and Mexico during January 1998 and 1999. The numbers, location, and habitat of all pelicans observed were recorded. The coastal zone of Louisiana consistently had higher numbers of pelicans (18,000 to 35,000 birds) than other areas surveyed (3,000 to 8,000 birds), indicating that Louisiana may be the most important wintering area for American White Pelicans east of the Rocky Mountains. Among the four regions surveyed, the average size of pelican flocks was largest in Mississippi during January-February, particularly in 1999 (x̄ = 245 birds/flock). Pelican numbers in Mississippi peaked in February but in Louisiana they were more variable. Pelicans in the delta region of Mississippi were found most often in fresh water and sand bar habitats during December, flooded field habitats during February, and catfish ponds in April. In Louisiana, pelicans used fresh, intermediate, and brackish marshes during December, but showed a preference for brackish and saline marshes in February and April.
Characterization of the novel mitochondrial genome segregation factor TAP110 in Trypanosoma brucei

Proper mitochondrial genome inheritance is key for eukaryotic cell survival, however little is known about the molecular mechanism controlling this process. Trypanosoma brucei, a protozoan parasite, contains a singular mitochondrial genome aka kinetoplast DNA (kDNA). kDNA segregation requires anchoring of the genome to the basal body via the tripartite attachment complex (TAC). Several components of the TAC as well as their assembly have been described, it however remains elusive how the TAC connects to the kDNA. Here, we characterize the TAC associated protein TAP110 and for the first time use ultrastructure expansion microscopy in trypanosomes to reveal that TAP110 is the currently most proximal kDNA segregation factor. The kDNA proximal positioning is also supported by RNAi depletion of TAC102, which leads to loss of TAP110 at the TAC. Overexpression of TAP110 leads to expression level changes of several mitochondrial proteins and a delay in the separation of the replicated kDNA networks. In contrast to other kDNA segregation factors TAP110 remains only partially attached to the flagellum after DNAse and detergent treatment and can only be solubilized in dyskinetoplastic cells, suggesting that interaction with the kDNA might be important for stability of the TAC association. Furthermore, we demonstrate that the TAC, but not the kDNA, is required for correct TAP110 localization in vivo and suggest that TAP110 might interact with other proteins to form a >669 kDa complex. Summary Statement TAP110 is a novel mitochondrial genome segregation factor in Trypanosoma brucei that associates with the previously described TAC component TAC102. Ultrastructure expansion microscopy reveals its proximal position to the kDNA.
Temporal genetic structuring of a specialist parasitoid, Lysiphlebus hirticornis Mackauer (Hymenoptera: Braconidae) attacking a specialist aphid on tansy

In insect species characterized by inbreeding, limited dispersal, and a metapopulation structure, high genetic differentiation and reduced genetic diversity within local populations are expected. Using the model system Lysiphlebus hirticornis Mackauer, a specialist parasitoid of the tansy aphid, Metopeurum fuscoviride Stroyan (Hemiptera: Aphididae), we examined within-site temporal population dynamics and genetics, including molecular variation at the tansy plant level. Aphid-parasitoid dynamics were surveyed and parasitoids sampled from 72 tansy plants at 11 sites in and around Jena, Germany, over one growing season. Thereafter, parasitoid samples were genotyped at 11 polymorphic microsatellite loci. Colonization, extinction, and recolonization events occurred during the season. Allele numbers and identities were highly variable over time. When samples from all sites were pooled, allele number over all loci showed a decreasing trend with time. At the level of sites, temporal changes in genetic diversity were more variable. Analysis of molecular variance revealed that samples at the plant level explained the highest variance compared to at site level. We conclude that the genetic structuring of this insect is very fine grained (i.e. at the tansy plant level) and the temporal genetic diversity is explained by a combination of extinction and recolonization events, as well as inbreeding. (Less)
Food Production and Water Conservation in a Recirculating Aquaponic System in Saudi Arabia at Different Ratios of Fish Feed to Plants

An indoor aquaponic system (i.e., the integration of fish culture with hydroponic plant production in a recirculating setup) was operated for maximizing water reuse and year-round intensive food production (Nile tilapia, Oreochromis niloticus, and leaf lettuce) at different fish feed to plants ratios. The system consisted of a fish culture component, solid removal component, and hydroponic component comprising six long channels with floating styrofoam rafts for holding plants. Fish culture effluents flowed by gravity from the fish culture component to the solid removal component and then to the hydroponic component. Effluents were collected in a sump from which a 1-horsepower in-line pump recirculated the water back to the fish culture tanks at a rate of about 250 L/min. The hydroponic component performed as biofilter and effectively managed the water quality. Fish production was staggered to harvest one of the four fish tanks at regular intervals when fish attained a minimum weight of 250 g. Out of the total eight harvests in 13 mo, net fish production per harvest averaged 33.5 kg/m3 of water with an overall water consumption of 320 L/kg of fish produced along with the production of leaf lettuce at 42 heads/m2 of hydroponic surface area. Only 1.4% of the total system water was added daily to compensate the evaporation and transpiration losses. A ratio of 56 g fish feed/m2 of hydroponic surface effectively controlled nutrient buildup in the effluents. However, plant density could be decreased from 42 to 25–30 plants/m2 to produce a better quality lettuce.