Miracle-dz/UniFAR-FTUs huggingface dataset:
An interolog-based barley interactome as an integration framework for immune signaling

The barley MLA nucleotide-binding, leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many cereal diseases, including powdery mildew, stem and stripe rust, Victoria blight, and rice blast. We used interolog inference to construct a barley protein interactome (HvInt) comprising 66133 edges and 7181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared to the experimentally validated Arabidopsis interactome of 11253 proteins and 73960 interactions, verifying that the two networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific ‘omics’ datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and an infection-time-course transcriptome, we assembled resistant (R) and susceptible (S) subnetworks. The resulting differentially co-expressed (R-S) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to Mla through trans eQTL associations. Lastly, next-generation, yeast-two-hybrid screens identified fifteen novel MLA interactors, which were incorporated into HvInt, to predict receptor localization, and signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity. AUTHOR SUMMARY Powdery mildew fungi infect more than 9,500 agronomic and horticultural plant species. In order to prevent economic loss due to diseases caused by pathogens, plant breeders incorporate resistance genes into varieties that are grown for food, feed, fuel and fiber. One of these resistance genes encodes the barley MLA immune receptor, an ancestral cereal protein that confers recognition to powdery mildew, stem and stripe rust, rice blast and Victoria blight. However, in order to function properly, these immune receptors must interact with additional proteins and protein complexes during the different stages of fungal infection and plant defense. We used a combination of computational- and laboratory-based methods to predict over 66,000 possible protein-protein interactions in barley. This network of proteins was then integrated with various defense-specific datasets to assemble the molecular building blocks associated with resistance to the powdery mildew pathogen, in addition to those proteins that interact with the MLA immune receptor. Our application of genome-scale, protein-protein interaction data provides a foundation to decipher the complex molecular components that control immune responses in crops.
Operon formation by insertion sequence IS3 in Escherichia coli

Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion-deletion-excision reactions. This mechanism barely leaves traces of insertion sequences and is difficult to detect in evolution in nature. We performed, to the best of our knowledge, the first experimental demonstration of operon formation, as a proof of concept. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kilobase pair gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.
Steady as she goes : visual autocorrelators and antenna-mediated airspeed feedback in the control of flight dynamics in fruit flies and robotics

Achieving agile autonomous flight by an insect-sized micro aerial vehicle (MAV) will require improved technology that is radically smaller, lighter, and more power-efficient. One animal that has solved the problem is the fly, a virtuoso among insect flyers whose nervous system can perform sophisticated aerial maneuvers under severe computational constraints. This thesis is concerned with understanding and emulating the dynamics of the fly's feedback control system. Because vision is noisy and information rich, processing time may a problem for a fast-moving MAV or fly. By tracking the fruit fly Drosophila melanogaster in free flight in gusts of wind, I found that they incorporate feedback from wind-sensing antennae in a fast feedback loop that dampens the forward-flight dynamics. The slower dynamics are easier to control for long-delay visual feedback, making the fly more robust to the limitations of its visual system. Using the fly as inspiration, I designed a minimal, visual autocorrelation based controller that used a small array of visual sensors to stabilize a fan-actuated hovercraft robot in a narrow corridor. Using a model for correlators developed for the robot, I showed that a uniform array of visual correlators was sufficient to explain the free-flight velocity regulation behavior of flies, rather than a different model. In addition to illustrating the benefits of concurrent scientific analysis and engineering synthesis, the results give new insight into how to control small biological and man-made flying vehicles using limited, noisy sensors.
THE HUMAN BEHAVIOR: A TRACKING SYSTEM TO FOLLOW THE HUMAN OCCUPANCY

Various control strategies have been adopted to improve energy efficiency in commercial office buildings, particularly the alignment of energy consumption for space conditioning and lighting patterns with human occupancy. Considerable uncertainty however exists in these patterns but advancement in information and communication technology (ICT) has made it possible to reduce these uncertainties. More fine-grained building occupants information can now be gotten in real-time for dynamic demand-driven space lighting and conditioning controls. In this paper the performance of one of such technologies; radio frequency identification (RFID) system is accessed in the determination of human occupancy and location from experiments carried out in a typical office building in the Netherlands. The correlation between energy use by office appliance and human occupancy was also investigated. Furthermore, steps that could be taken to improve energy consumption for comfort through a demand-driven process control strategy are identified.
Simulation characteristics of ferroelectric liquid crystal by electronic model in PSPICE

This paper proposed electrical model is based on the elastic continuum theory applied to the ferroelectric liquid crystal (FELC), which gives a good description for the simulated switching and memory behavior by the different time order and driving waveforms. Optical transmission dependence onthe complex voltage waveforms and the rotational viscosity and spontaneous polarization of cell is obtained as a function of director profile. The model agree to 10 percent experimental results, over an applied voltage of 1.0 to 20 volt. The electrical model of real FELC displays may contribute to the design and development of optimized devices.
The Urine Biomarker PUR-4 Is Positively Associated with the Amount of Gleason 4 in Human Prostate Cancers

The Prostate Urine Risk (PUR) biomarker is a four-group classifier for predicting outcome in patients prior to biopsy and for men on active surveillance. The four categories correspond to the probabilities of the presence of normal tissue (PUR-1), D’Amico low-risk (PUR-2), intermediate-risk (PUR-3), and high-risk (PUR-4) prostate cancer. In the current study we investigate how the PUR-4 status is linked to Gleason grade, prostate volume, and tumor volume as assessed from biopsy (n = 215) and prostatectomy (n = 9) samples. For biopsy data PUR-4 status alone was linked to Gleason Grade group (GG) (Spearman’s, ρ = 0.58, p < 0.001 trend). To assess the impact of tumor volume each GG was dichotomized into Small and Large volume cancers relative to median volume. For GG1 (Gleason Pattern 3 + 3) cancers volume had no impact on PUR-4 status. In contrast for GG2 (3 + 4) and GG3 (4 + 3) cancers PUR-4 levels increased in large volume cancers with statistical significance observed for GG2 (p = 0.005; Games-Howell). These data indicated that PUR-4 status is linked to the presence of Gleason Pattern 4. To test this observation tumor burden and Gleason Pattern were assessed in nine surgically removed and sectioned prostates allowing reconstruction of 3D maps. PUR-4 was not correlated with Gleason Pattern 3 amount, total tumor volume or prostate size. A strong correlation was observed between amount of Gleason Pattern 4 tumor and PUR-4 signature (r = 0.71, p = 0.034, Pearson’s). These observations shed light on the biological significance of the PUR biomarker and support its use as a non-invasive means of assessing the presence of clinically significant prostate cancer.
Virtual vectors based predictive control of torque and flux of induction motor and speed sensorless drives

In this paper, a simple scheme of predictive control of torque and flux is proposed to decrease the torque ripple and improve the flux locus distortion at low speed range in the direct torque control (DTC) of an induction motor. The concept of virtual vectors is also introduced to generate a fixed and higher switching frequency for the PWM invertor. Also, a MRAS (model reference adaptive control system) method using the modified rotor flux model is implemented to identify the rotor speed of induction motor, which can achieve wider bandwidth speed control. The simulation results show that very good dynamic response and steady state precision can be obtained with the proposed schemes, and this is confirmed by the experiments realized with a digital control structure using signal processor TMS320C32.
The Response of Mitochondrial Respiration and Quantity in Skeletal Muscle and Adipose Tissue to Exercise in Humans with Prediabetes

Background: Mitochondrial dysfunction has been implicated in the pathogenesis of type 2 diabetes, but its contribution to the early stages of dysglycemia remains poorly understood. By collecting a high-resolution stage-based spectrum of dysglycemia, our study fills this gap by evaluating derangement in both the function and quantity of mitochondria. We sampled mitochondria in skeletal muscle and subcutaneous adipose tissues of subjects with progressive advancement of dysglycemia under a three-month exercise intervention. Methods: We measured clinical metabolic parameters and gathered skeletal muscle and adipose tissue biopsies before and after the three-month exercise intervention. We then assayed the number of mitochondria via citrate synthase (CS) activity and functional parameters with high-resolution respirometry. Results: In muscle, there were no differences in mitochondrial quantity or function at baseline between normoglycemics and prediabetics. However, the intervention caused improvement in CS activity, implying an increase in mitochondrial quantity. By contrast in adipose tissue, baseline differences in CS activity were present, with the lowest CS activity coincident with impaired fasting glucose and impaired glucose tolerance (IFG + IGT). Finally, CS activity, but few of the functional metrics, improved under the intervention. Conclusions: We show that in prediabetes, no differences in the function or amount of mitochondria (measured by CS activity) in skeletal muscle are apparent, but in adipose tissue of subjects with IFG + IGT, a significantly reduced activity of CS was observed. Finally, metabolic improvements under the exercise correlate to improvements in the amount, rather than function, of mitochondria in both tissues.
Statistical Optimization of Fermentation Process Parameters by Taguchi Orthogonal Array Design for Improved Bioethanol Production

The statistical optimization of different fermentation process parameters in SSF of mixed MAA and organosolv pretreated 1% (w v−1) wild grass, namely, recombinant Clostridium thermocellum hydrolytic enzymes’ volume (GH5 cellulase, GH43 hemicellulase), fermentative microbes’ inoculum volume (Saccharomyces cerevisiae, Candida shehatae), pH, and temperature, was accomplished by Taguchi orthogonal array design. The optimized parameters in 100 mL of fermentation medium were (%, v v−1) as follows: 1.0, recombinant GH5 cellulase (5.7 mg−1, 0.45 mg mL−1); 2.0, recombinant GH43 hemicellulase (3.7 U mg−1, 0.32 mg mL−1); 1.5, S. cerevisiae (3.9 × 108 cells mL−1); 0.25, C. shehatae (2.7 × 107 cells mL−1); pH, 4.3; and temperature, 35∘C. pH with p-value 0.001 was found to be the most significant factor affecting SSF. The ethanol titre obtained in Taguchi optimized shake flask SSF was 2.0 g L−1 implying a 1.3-fold increase as compared to ethanol titre of 1.5 g L−1 in unoptimized shake flask SSF. A 1.5-fold gain in ethanol titre (3.1 g L−1) was obtained with the same substrate concentration in lab scale bioreactor on scaling up the shake flask SSF with Taguchi optimized process parameters.
Thermal effects on the dielectric and electrical properties of relaxor ferroelectric ceramic-based MLCs

The effects of different thermal shock treatments on dielectric and electrical properties of relaxor based and BaTiO/sub 3/ based "0805" Y5V multilayer ceramic chip capacitors (MLCs) were investigated. It was found that thermal shock generally resulted in larger leakage currents and lower breakdown voltages. It is also confirmed that the thermal shock resistance of relaxer MLCs is in disadvantage to that of the barium titanate MLCs. Nevertheless, no obvious failure was found when the relaxor-based MLCs were subjected to the thermal effects in the normal infrared solder reflow process. Besides the relatively lower mechanical strength, low insulation resistivity and breakdown strength were also proposed to be important contributors to the undesirable reliability of relaxor MLCs.
Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs

Abstract Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human‐induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non‐adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade‐offs between defense/growth rate for prey and selectivity/half‐saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context‐dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non‐desirable alternative state. The basal‐intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.
Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction

The phenotypic efficacy of somatic copy number alterations (SCNAs) stems from their incidence per base pair of the genome, which is orders of magnitudes greater than that of point mutations. One mitotic event stands out in its potential to significantly change a cell’s SCNA burden–a chromosome missegregation. We present a general deterministic framework for modeling chromosome missegregations and use it to evaluate the possibility of missegregation-induced population extinction (MIE). The model predicts critical curves that separate viable from non-viable populations as a function of their turnover- and missegregation rates. Missegregation- and turnover rates estimated from a PAN-cancer scRNA-seq dataset of 15,464 cells are then compared to predictions. The majority of tumors across all cancer types had missegregation- and turnover rates that were within viable regions of the parameter space. When a dependency of missegregation rate on karyotype was introduced, karyotypes associated with low missegregation rates acted as a stabilizing refuge, rendering MIE impossible unless turnover rates are exceedingly high. Intra-tumor heterogeneity, including heterogeneity in missegregation rates, increases as tumors progress, rendering MIE unlikely. Author Summary When a cell missegregates a chromosome while dividing, the chance is high that its two daughter cells will behave drastically different from each other and from their parental cell. Chromosome missegregations are therefore one of the most powerful forces of phenotypic diversity. We developed a mathematical model of chromosome missegregations that allows for this cell-to-cell diversity to be accounted for. The model serves to help understand how selection acts upon cells with versatile chromosome contents, as a tool for genotype-to-phenotype mapping in various microenvironments. As a first application example we used the model to address whether there exists an upper limit on missegregation rate, beyond which cancer populations collapse. Chromosome missegregations are common. They occur in 1.2-2.3% per mitosis in normal cells [1] and in cancer cells their rate is between one and two orders of magnitudes higher [2]. The model revealed that the upper limit of missegregation rate is a function of the tumor’s turnover rate (i.e. how fast the tumor renews itself). In heterogenous populations however, cells with low missegregation rates protect the population from collapse. Intra-tumor heterogeneity, including heterogeneity in missegregation rates, increases as tumors progress, rendering missegregation-induced extinction unlikely.
The light switch in buildings

The paper reviews recent work at the UK Building Research Establishment aimed at deciding if there is a significant potential for saving energy used for lighting in buildings. This necessarily involves examining the ways in which building occupants use their switching facilities and hence their lighting. The savings which might accrue from automating lighting controls are discussed, with particular reference to daylight linking, and suggestions made for more sophisticated methods of manual switching.
Green Synthesis of Gold Nanoparticles Using Polianthes tuberosa L. Floral Extract

The developments of green-based metallic nanoparticles (gold) are gaining tremendous interest, having potential applications in health care and diagnosis. Therefore, in the present study, Polianthes tuberosa flower filtered extract was used as a reducing and stabilizing agent to synthesize gold nanoparticles (PtubAuNPs). The PtubAuNPs were extensively characterized by UV–visible spectroscopy, Fourier transform infrared spectroscopy, transmission electron microscopy, and X-ray diffraction. The antibacterial activity of PtubAuNPs was determined by the agar well diffusion method; the PtubAuNPs performed extreme antagonistic activity against the tested pathogens. Furthermore, the cytotoxicity of the PtubAuNPs was evaluated in MCF 7 cells by MTT assay. The PtubAuNPs induced toxicity in MCF 7 cells with the least concentration of 100 µg/mL in a dose-dependent method by inducing apoptosis. Overall, the study manifested that PtubAuNPs are a potent nanomaterial that can be employed as an antimicrobial and anticancer agent.
The migration of social workers to and from the United Kingdom: a comparative perspective

ABSTRACT This article reports findings from a large mixed-method study exploring the migration to the United Kingdom (UK) of social workers trained in Australia, Canada, India, Romania, South Africa, the US, and Zimbabwe, and the migration of British trained social workers to Australia. The project aimed at exploring the motivations for migration, the experiences of integration, and the impact of culture on these. This article focuses on the quantitative findings and will use some of the qualitative data to further explain and interrogate the differences between these groups based on their country of origin. The findings show the greater challenges migrants from developing countries have experienced, including lack of recognition of their qualifications and experience, and discrimination. The findings also show that contrary to common assumptions, the migration experiences of social workers coming from Australia, Canada and the US are not as easy as expected. American social workers who migrated to the UK turned out to be the group least professionally satisfied. The British in Australia on the other hand, were the most satisfied. Implications for practice and future research are explored.
Reflectivity calculation of a periodical-patch-loaded absorber by the FD-TD method

An objective of this paper is to show low reflectivity of a lossy material with periodical metal patches on the surface by FD-TD computations in addition to experiments. Symmetry conditions based on image theory have been introduced to reduce the computational volume. A uniaxial perfectly-matched-layer (UPML) is used as an absorbing boundary condition, which also reduces computer memory and calculation time. By the computations and experiments, the absorber of this kind is proved to have low reflectivity as a viable microwave absorber. It features potential versatility of design.
The Russian-American high magnetic field collaboration

The authors report here on a joint experimental shot series with teams from Russia and the United States. The program was based largely upon the MC-1 generator, a high magnetic field explosive flux compressor, developed by the Pavlovskii group at Arzamas-16. The series was of historical interest in that it was carried out in a Los Alamos security area, the first time for such a collaboration. They discuss a number of technical issues involved in matching Russian hardware with Los Alamos explosives, initiation systems and the seed field energy source, as well as comparison of field measuring diagnostics furnished by the two teams. They conclude with a discussion of an investigation of the high temperature superconductor YBa/sub 2/Cu/sub 3/O/sub 7/ (YBCO), employing these generators. The low temperature critical magnetic field of this material was found to be 340/spl plusmn/40 T, as determined from a 94 GHz microwave interferometer developed for this purpose.