Miracle-dz/UniFAR-FTUs huggingface dataset:
A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia

ABSTRACT The last few years have seen the advancement of high-throughput experimental techniques that have produced an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from, e.g., sequencing data and often motivate further targeted experiments. The broad discipline of “computational biology” extends far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods such as the use of mathematical models are not yet as well integrated into the research studying microbial interactions. The empirical complexity of microbial communities presents challenges that are difficult to address with in vivo/in vitro approaches alone, and with microbiology developing from a qualitative to a quantitative science, we see stronger opportunities arising for interdisciplinary projects integrating theoretical approaches with experiments. Indeed, the addition of in silico experiments, i.e., computational simulations, has a discovery potential that is, unfortunately, still largely underutilized and unrecognized by the scientific community. This minireview provides an overview of mathematical models of natural ecosystems and emphasizes that one critical point in the development of a theoretical description of a microbial community is the choice of problem scale. Since this choice is mostly dictated by the biological question to be addressed, in order to employ theoretical models fully and successfully it is vital to implement an interdisciplinary view at the conceptual stages of the experimental design.
Asymptotically Optimal Scheduling for Compute-and-Forward

Consider a Compute and Forward (CF) relay network with L users and a single relay. The relay tries to decode a linear function of the transmitted signals. For such a network, letting all L users transmit simultaneously, especially when L is large, causes a significant degradation in the rate in which the relay is able to decode. In fact, the rate goes to zero very fast with L. Therefore, in each transmission phase only a fixed number of users should transmit, i.e., users should be scheduled.In this work, we examine the problem of scheduling for CF and lay the foundations for identifying the optimal schedule which, to date, lacks a clear understanding. Specifically, we start with insights why when the number of users is large, good scheduling opportunities can be found. Then, we provide an asymptotically optimal, polynomial time scheduling algorithm and analyze it’s performance. We conclude that scheduling under CF provides a gain in the system sum-rate, up to the optimal scaling law of O(log log L).
FORMULATION AND STABILITY EVALUATION OF BAUHINIA VARIEGATA EXTRACT TOPICAL EMULSION.

This study presents the results for the development of water in oil (W/O) emulsion containing 2 % Bauhinia variegata (BV) extract with good antioxidant potential for cosmetic application. Different ratios of surfactant, oil and water were investigated to optimize the ratio of ingredients. It was found that emulsifier and oil4ratio were important in improving the stability of emulsion. The formulation having 2.5% Abil EM90, 12% liquid paraffin, 83.5% distilled water and 2% BV extract was found to be most stable. Stability of the formulation was further evaluated by characterizing for organoleptic, sedimentation, microscopic and rheological properties at a range of storage conditions for a period of 12 weeks. Experimental findings showed stable formulation behavior with respect to color change, liquefaction and phase separation. Centrifugation test was carried out to predict the long term stability.The rheological parameters were evaluated from Power Law and the flow index value less than 1 suggested non-Newtonian behavior of the W/O emulsion. The mean droplet size of the internal phase of freshly prepared formulation was 4.06 ? 1.99 pm that did not change significantly (p > 0.05) during the storage. The newly developed formulation exhibited promising attributes over long term storage and open opportunities for the topical delivery of natural antioxidants for cosmetic and pharmaceutical objectives.
The neuroprotective effects of an ethanolic turmeric (Curcuma longa L.) extract against trimethyltin-induced oxidative stress in rats

Introduction: Oxidative stress is known to contribute to the pathogenesis of neurodegenerative disorders. An ethanolic turmeric (Curcuma longa L.) extract containing curcumin has been reported to produce antioxidant effects. Objective: The present study aims to investigate the possible neuroprotective effects of the ethanolic turmeric extract against trimethyltin (TMT)-induced oxidative stress in Sprague Dawley rats. Methods: The ethanolic turmeric extract and citicoline were administered to the TMT exposed rats from day 1 to day 28 of the experiment. The TMT injection was administered on day 8 of the experiment. The plasma and brain malondialdehyde (MDA) and reduced glutathione (GSH) levels, and the activities of the superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) enzymes in the brain were examined at the end of the experiment. Results: The administration of 200 mg/kg bw of the ethanolic turmeric extract prevented oxidative stress by decreasing the plasma and brain MDA levels and increasing the SOD, CAT, and GPx enzyme activities and GSH levels in the brain. These effects seem to be comparable to those of citicoline. Discussion: The ethanolic turmeric extract at a dose of 200 mg/kg bw may exert neuroprotective effects on TMT-exposed Sprague Dawley rats by preventing them from oxidative stress. GRAPHICAL ABSTRACT
Human-in-the-loop optimization of hip assistance with a soft exosuit during walking

Human-in-the-loop optimization achieved a substantial metabolic reduction and demonstrated the value of individualization. Wearable robotic devices have been shown to substantially reduce the energy expenditure of human walking. However, response variance between participants for fixed control strategies can be high, leading to the hypothesis that individualized controllers could further improve walking economy. Recent studies on human-in-the-loop (HIL) control optimization have elucidated several practical challenges, such as long experimental protocols and low signal-to-noise ratios. Here, we used Bayesian optimization—an algorithm well suited to optimizing noisy performance signals with very limited data—to identify the peak and offset timing of hip extension assistance that minimizes the energy expenditure of walking with a textile-based wearable device. Optimal peak and offset timing were found over an average of 21.4 ± 1.0 min and reduced metabolic cost by 17.4 ± 3.2% compared with walking without the device (mean ± SEM), which represents an improvement of more than 60% on metabolic reduction compared with state-of-the-art devices that only assist hip extension. In addition, our results provide evidence for participant-specific metabolic distributions with respect to peak and offset timing and metabolic landscapes, lending support to the hypothesis that individualized control strategies can offer substantial benefits over fixed control strategies. These results also suggest that this method could have practical impact on improving the performance of wearable robotic devices.
Extracorporal Shock Wave Therapy Enhances Receptor for Advanced Glycated End-Product–Dependent Flap Survival and Angiogenesis

Background/Objectives Loss of skin flaps due to deteriorated wound healing is a crucial clinical issue. Extracorporal shock wave therapy (ESWT) promotes flap healing by inducing angiogenesis and suppressing inflammation. The receptor for advanced glycation end-products (RAGEs) was identified to play a pivotal role in wound healing. However, to date, the role of RAGE in skin flaps and its interference with ESWT are unknown. Methods Caudally pedicled musculocutanous skin flaps in RAGE−/− and wt mice were treated with low-dose extracorporal shock waves (s-RAGE−/−, s-wt) and analyzed for flap survival, histomorphologic studies, and immunohistochemistry during a 10-day period. Animals without ESWT served in each genotype as a control group (c-RAGE−/−, c-wt). Statistical analysis was carried out by repeated-measures analysis of variance. Results Flap necrosis was significantly reduced after ESWT in wt animals but increased in RAGE-deficient animals. Morphometric differences between the 4 groups were identified and showed a delayed wound healing with dysregulated inflammatory cells and deteriorated angiogenesis in RAGE−/− animals. Furthermore, spatial and temporal differences were observed. Conclusions The RAGE controls inflammation and angiogenesis in flap healing. The protective effects of ESWT are dependent on intact RAGE signaling, which enables temporary targeted infiltration of immune cells and neoangiogenesis.
Performance Analysis of a Master/Slave Switched Ethernet for Military Embedded Applications

Current military communication network is a generation old and is no longer effective in meeting the emerging requirements imposed by the next-generation military embedded applications. A new communication network based upon Full Duplex Switched Ethernet is proposed in this paper to overcome these limitations. To allow existing military subsystems to be easily supported by a Switched Ethernet network, our proposal consists in keeping their current centralized communication scheme by using an optimized master/slave transmission control on Switched Ethernet thanks to the Flexible Time Triggered (FTT) paradigm. Our main objective is to assess the performance of such a proposal and estimate the quality-of-service we can expect in terms of latency. Using the Network Calculus formalism, schedulability analysis are determined. These analysis are illustrated in the case of a realistic military embedded application extracted from a real military aircraft network, to highlight the proposal's ability to support the required time constrained communications.
Pattern of change in silica, ash, crude fibre, whiteness and bran pigmentation with progressive polish in rice varieties.

The pattern of changes in silica, ash, crude fibre, whiteness and residual bran pigments with progessive polish were studied in seven varieties of paddy. The constituents studied decreased or increased in a characteristic manner as the degree of polish was increased from 1 to 6 per cent. Silica and crude fibre content reached low and constant residual values at 6 per cent degree of polish and could serve as useful indicators of the degree of milling. For checking underpolishing below 3-4 per cent and over polishing above 3-4 per cent silica content and whiteness or reflectance value of the rice may serve as useful parameters with least varietal variations.
RJSplot: Interactive Graphs with R

Data visualization techniques provide new methods for the generation of interactive graphs. These graphs allow a better exploration and interpretation of data but their creation requires advanced knowledge of graphical libraries. Recent packages have enabled the integration of interactive graphs in R. However, R provides limited graphical packages that allow the generation of interactive graphs for computational biology applications. The present project has joined the analytical power of R with the interactive graphical features of JavaScript in a new R package (RJSplot). It enables the easy generation of interactive graphs in R, provides new visualization capabilities, and contributes to the advance of computational biology analytical methods. At present, 16 interactive graphics are available in RJSplot, such as the genome viewer, Manhattan plots, 3D plots, heatmaps, dendrograms, networks, and so on. The RJSplot package is freely available online at http://rjsplot.net.
Factors Associated With Greater Severity of Depression in Chilean Primary Care Patients.

Objective To determine clinical and psychosocial variables associated with increased depression severity in patients who consult public primary health care clinics (PHCs) in Chile. Methods The study included 394 patients diagnosed with major depressive disorder (MDD) according to ICD-10 criteria who were evaluated between February and September 2014 using a sociodemographic interview, the Mini-International Neuropsychiatric Interview (MINI), a screening for childhood trauma, a scale for partner violence, the Life Events Survey (LES), and the Hamilton Rating Scale for Depression (HRSD). Results Positive correlations were determined between greater severity of depression and more frequency of depressive episodes (r = 0.2, P < .01), psychiatric comorbidities (r = 0.36, P < .01), number of childhood traumatic events (r = 0.19, P < .01), intimate partner violence events (r = 0.155, P < .01), and stressful life events (r = 0.13, P < .05). Inverse correlation was determined with the age at first episode (r = -0.16, P < .01). The psychiatric comorbidities explained most of the variability of depressive symptoms (11.7%); addition of child abuse to the comorbidities increased the correlation to 12.7%. Conclusions The different covariates considered in this sample showed that psychiatric comorbidity played the principal role in explaining the severity of depression.
Conceptual Design of a Vertical Takeoff and Landing Unmanned Aerial Vehicle with 24-HR Endurance

This paper describes a conceptual design study for a vertical takeoff and landing (VTOL) unmanned aerial vehicle (UAV) that is able to carry a 25-lb science payload for 24 hr and is able to land and take off at elevations as high as 15,000 ft without human intervention. In addition to the science payload, this vehicle must be able to carry a satellite communication system, and the vehicle must be able to be transported in a standard full-size pickup truck and assembled by only two operators. This project started with a brainstorming phase to devise possible vehicle configurations that might satisfy the requirements. A down select was performed to select a near-term solution and two advanced vehicle concepts that are better suited to the intent of the mission. Sensitivity analyses were also performed on the requirements and the technology levels to obtain a better understanding of the design space. This study found that within the study assumptions the mission is feasible; the selected concepts are recommended for further development.
Detection, Alignment, and Recognition of Partially Occluded Human Face Based on Statistical Learning of Local Features

This paper proposes an integrated method to detect, align, and recognize human face focusing on maintaining its stability under partial occlusions. The proposed framework is based on the combination of three probabilistic models: face model, variation model, and background model. These probabilistic models are estimated by analyzing statistical distribution of local features from human face images and natural scene images. By combining three models, it is expected to achieve robustness to various local variations including partial occlusions. Through comparison with well-known face detection algorithm and a recent deep learning architecture, we confirm the robustness of proposed method in detection and recognition of occluded faces.
Effect of lithocholic acid on biologically active α,β-unsaturated aldehydes induced by H2O2 in glioma mitochondria for use in glioma treatment

Lithocholic acid (LCA) is known to kill glioma cells while sparing normal neuronal cells. However, the anti-glioma mechanism of LCA is unclear at present. Although malondialdehyde (MDA) is not specific to detect tumors, biologically active α,β-unsaturated aldehydes can be used to detect the outcome of gliomas, especially the mitochondria, as a research tool. The purpose of this research was to determine the optimum conditions for a lipid peroxidation model, according to changes in the aldehydes formed from the reaction between 2-thiobarbituric acid and biologically active α,β-unsaturated aldehydes. Experimental methods and procedures were successfully established for a model of lipid peroxidation induced by H2O2 in glioma mitochondria for glioma treatment and optimum conditions for LCA treatment were determined. The optimal conditions for the model were a glioma mitochondrial concentration of 1.5 mg/ml, H2O2 concentration of 0.3 mg/ml, duration of action of 30 min, and addition of 4.0 ml of 46 mM thiobarbituric acid. The effect of LCA, as determined by changes in the UV peaks at 450, 495, and 532 nm, was optimal at a concentration of 100 µM, a duration of action of 15 min, and in an acidic microenvironment. The study concluded that a suitable concentration of LCA has anti-glioma effects as determined by the effect on changes in the UV peaks at 450, 495 and 532 nm and the mitochondrial model developed should be conducive to further in-depth research.
Impaired action knowledge in amyotrophic lateral sclerosis

Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative condition affecting the motor system, but recent work also shows more widespread cognitive impairment. This study examined performance on measures requiring knowledge of actions, and related performance to MRI cortical atrophy in ALS. Methods: A total of 34 patients with ALS performed measures requiring word-description matching and associativity judgments with actions and objects. Voxel-based morphometry was used to relate these measures to cortical atrophy using high resolution structural MRI. Results: Patients with ALS were significantly more impaired on measures requiring knowledge of actions than measures requiring knowledge of objects. Difficulty on measures requiring action knowledge correlated with cortical atrophy in motor cortex, implicating degraded knowledge of action features represented in motor cortex of patients with ALS. Performance on measures requiring object knowledge did not correlate with motor cortex atrophy. Several areas correlated with difficulty for both actions and objects, implicating these brain areas in components of semantic memory that are not dedicated to a specific category of knowledge. Conclusion: Patients with amyotrophic lateral sclerosis are impaired on measures involving action knowledge, and this appears to be due to at least two sources of impairment: degradation of knowledge about action features represented in motor cortex and impairment on multicategory cognitive components contributing more generally to semantic memory.
Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway

In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. Our work reveals an evolutionary mechanism for rapidly expanding the targets of a transcription factor by changing its dependence on a co-activator, potentially refining the physiological response it regulates.
Several Similarity Measures of Neutrosophic Sets

Smarandache (1995) defined the notion of neutrosophic sets, which is a generalization of Zadeh's fuzzy set and Atanassov's intuitionistic fuzzy set. In this paper, we first develop some similarity measures of neutrosophic sets. We will present a method to calculate the distance between neutrosophic sets (NS) on the basis of the Hausdorff distance. Then we will use this distance to generate a new similarity measure to calculate the degree of similarity between NS. Finally we will prove some properties of the proposed similarity measures.
High-density polyethylene reinforced with titania nanoparticles

Titania nanoparticles were prepared by both hydrolysis of tetraethoxy titanium and hydrothermal crystallisation. Nanoparticles were also surface modified with alkylsilanes in order to improve the compatibility with organic polymers. HDPE/TiO2 composites were prepared by melt mixing and were mechanically characterized. The presence of titania nanoparticles (1%vol) led to a significant increase of elastic modulus together with a slight increase of yield stress and a decrease of ultimate elongation. An interesting decrease of creep compliance for both elastic and viscoelastic components was also evidenced.
Bordetella pertussis Adenylate Cyclase Toxin Disrupts Functional Integrity of Bronchial Epithelial Layers

ABSTRACT The airway epithelium restricts the penetration of inhaled pathogens into the underlying tissue and plays a crucial role in the innate immune defense against respiratory infections. The whooping cough agent, Bordetella pertussis, adheres to ciliated cells of the human airway epithelium and subverts its defense functions through the action of secreted toxins and other virulence factors. We examined the impact of B. pertussis infection and of adenylate cyclase toxin-hemolysin (CyaA) action on the functional integrity of human bronchial epithelial cells cultured at the air-liquid interface (ALI). B. pertussis adhesion to the apical surface of polarized pseudostratified VA10 cell layers provoked a disruption of tight junctions and caused a drop in transepithelial electrical resistance (TEER). The reduction of TEER depended on the capacity of the secreted CyaA toxin to elicit cAMP signaling in epithelial cells through its adenylyl cyclase enzyme activity. Both purified CyaA and cAMP-signaling drugs triggered a decrease in the TEER of VA10 cell layers. Toxin-produced cAMP signaling caused actin cytoskeleton rearrangement and induced mucin 5AC production and interleukin-6 (IL-6) secretion, while it inhibited the IL-17A-induced secretion of the IL-8 chemokine and of the antimicrobial peptide beta-defensin 2. These results indicate that CyaA toxin activity compromises the barrier and innate immune functions of Bordetella-infected airway epithelia.
Coeliac disease: further evidence that biopsy is not always necessary for diagnosis

Objectives Growing evidence supports the view that the diagnosis of coeliac disease (CD) can be made by serological tests alone, although this approach is still not widely accepted. We previously showed in retrospective and prospective studies that in adults an IgA-tissue transglutaminase antibody cut-off can be defined above which the positive predictive value for CD is 100%. Following a change in the analytical method for measuring the antibody, our objectives were to re-examine this finding in a larger series of adults to ascertain whether a diagnosis of CD can be reliably made in a proportion of patients without the need for small bowel biopsy and to re-evaluate the diagnostic guidelines used in our centre. Patients and methods A retrospective analysis was done in an unselected series of 270 adult patients who had small bowel biopsies and serum IgA-tissue transglutaminase antibody levels measured from 2009 to 2014. Results At an IgA-tissue transglutaminase antibody cut-off greater than 45 U/ml (>8×upper limit of normal+2SDs) the positive predictive value for CD in this cohort was 100%; 40% of cases were above this cut-off. Conclusion We have verified that a diagnosis of CD can be reliably made in a high proportion of adults based on serology alone using the IgA-tissue transglutaminase antibody method specified. These results add to the body of evidence that small bowel biopsy should no longer be considered mandatory for the diagnosis of CD. On the basis of these results the diagnostic guidelines in our centre have been modified.