Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of the Smart City Architecture, Speed and Traffic Density of Vehicles on the Performances of Vanets

Vehicular Ad-hoc Networks (VANET) is one of the emerging and actual research fields in automotive companies and Intelligent Transportation Systems (ITS) designers. In the Smart City the presence of such networks opens the way for a wide range of applications such as safety applications, mobility and connectivity for both driver and passengers to exploit the transport systems in a smoothly efficiently and safer way. The 802.11p is a draft amendment to the IEEE 802.11 standard for vehicular communications. VANET are characterized by a dynamic topology triggered by the vehiculars mobility. In the Smart City the main problems of inter-vehicle communication are the speed, density of vehicles and the size of the buildings. For this purpose, we first examine and then display the simulation findings of the impact of different radio propagation models on the performance of vehicular ad hoc networks in terms of the characteristics of the physical layer. In our study, we have compared the performances of two routing protocols (AODV and OLSR) for three propagation model (two-Ray ground, Rice and Nakagami). We study those protocols under varying metrics such as Traffic density, Smart City Architecture (size of the scenario areas) and the mobility of vehicle. Our objective is to provide a qualitative assessment of the protocols applicability in different vehicular scenarios. These two routing protocols are simulated and compared with Network Simulator-2 under Manhattan Grid Mobility Model. To conclude, the simulation findings are to be taken as a strong reference on the three routing protocols behaviour; however, it shouldn’t be considered as an exact representation of its behaviour and real environment because of several simulation constraints such as: the dimension of movement field of vehiculars, the traffic type and the simulation timing.
Context-Aware Symptom Checking for Disease Diagnosis Using Hierarchical Reinforcement Learning

Online symptom checkers have been deployed by sites such as WebMD and Mayo Clinic to identify possible causes and treatments for diseases based on a patient’s symptoms. Symptom checking first assesses a patient by asking a series of questions about their symptoms, then attempts to predict potential diseases. The two design goals of a symptom checker are to achieve high accuracy and intuitive interactions. In this paper we present our context-aware hierarchical reinforcement learning scheme, which significantly improves accuracy of symptom checking over traditional systems while also making a limited number of inquiries.
Genetic diversity in cytochrome c oxidase I gene of Anopheles mosquitoes

Abstract Genetic diversity in cytochrome c oxidase I (coxI) among 7 species of Anopheles mosquitoes from Pakistan, and 37 species from different geographical regions of the world, was recorded. Automatic Barcode Gap Discovery (ABGD) analysis revealed a clear gap between intraspecific and interspecific distances of 7 species from Pakistan. However, genetic distances of 37 Anopheles species failed to adequately differentiate species in a global context. Intraspecific and interspecific divergences for 7 Anopheles species of Pakistan varied from 0.0% to 2.5% (mean = 0.49%) and 8% to 22.3% (mean = 12.77%), respectively. Similarly, intraspecific distances for 37 species from different parts of world ranged from 0.0% to 11.2% (mean = 0.65%) while values of interspecific divergences ranged from 3.4% to 35% (mean = 11.75%). Although phylogenetic tree revealed separate clades for 7 Anopheles species of Pakistan, it failed to produce separate clades for 37 species of the world. It is concluded that although standard barcode region is helpful for identifying Anopheles mosquitoes, combination of multi-locus approaches and morphology may be required to accurately identify species in this genus.
Residual stress in thin films PECVD depositions: A review

The paper presents solutions for residual stress control in thin films deposition on plasma enhanced chemical vapor depositions (PECVD) reactors and some MEMS applications. The residual stress induced in the thin films is an important factor in the fabrication of thin and free standing MEMS structure such as membranes or cantilevers fabricated using surface or bulk micromachining. The main layers analyzed are: amorphous silicon, amorphous silicon carbide and amorphous silicon nitride. The main parameters analyzed are the temperature of the deposition process, pressure, gas composition, as well as the value of the power and the power mode (high frequency - 13.56 MHz or low frequency - 400 KHz. Due to annealing effect, the temperature can decrease the compressive value of the stress. The RF frequency mode presents a major influence of residual stress: in low frequency mode a relatively high compressive stress is achieved due to ion bombardment and, as a result, densification of the layer is achieved.
Experimental comparison of phase‐noise in cross‐coupled RC‐ and LC‐oscillators

Relaxation RC‐oscillators are notorious for their poor phase‐noise performance. However, there are reasons to expect a phase‐noise reduction in quadrature oscillators obtained by cross‐coupling two relaxation oscillators. We present measurements on 5 GHz oscillators, which show that in RC‐oscillators the coupling reduces both the phase‐noise and quadrature error, whereas in LC‐oscillators the coupling reduces the quadrature error, but increases the phase‐noise. A comparison using standard figures of merit indicates that quadrature RC‐oscillators may be a viable alternative to LC‐oscillators when area and cost are to be minimized. Copyright © 2009 John Wiley & Sons, Ltd.
SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked.
Relative influence of nitrogen and phosphorous availability on phytoplankton physiology and productivity in the oligotrophic sub‐tropical North Atlantic Ocean

Nutrient addition bioassay experiments were performed in the low‐nutrient, low‐chlorophyll oligotrophic subtropical North Atlantic Ocean to investigate the influence of nitrogen (N), phosphorus (P), and/or iron (Fe) on phytoplankton physiology and the limitation of primary productivity or picophytoplankton biomass. Additions of N alone resulted in 1.5‐2 fold increases in primary productivity and chlorophyll after 48 h, with larger (~threefold) increases observed for the addition of P in combination with N (NP). Measurements of cellular chlorophyll contents permitted evaluation of the physiological response of the photosynthetic apparatus to N and P additions in three picophytoplankton groups. In both Prochlorococcus and the picoeukaryotes, cellular chlorophyll increased by similar amounts in N and NP treatments relative to all other treatments, suggesting that pigment synthesis was N limited. In contrast, the increase of cellular chlorophyll was greater in NP than in N treatments in Synechococcus, suggestive of NP co‐limitation. Relative increases in cellular nucleic acid were also only observed in Synechococcus for NP treatments, indicating co‐limitation of net nucleic acid synthesis. A lack of response to relief of nutrient stress for the efficiency of photosystem II photochemistry, Fv :Fm, suggests that the low nutrient supply to this region resulted in a condition of balanced nutrient limited growth, rather than starvation. N thus appears to be the proximal (i.e. direct physiological) limiting nutrient in the oligotrophic sub‐tropical North Atlantic. In addition, some major picophytoplankton groups, as well as overall autotrophic community biomass, appears to be co‐limited by N and P.
Variation in Community Structure across Vertical Intertidal Stress Gradients: How Does It Compare with Horizontal Variation at Different Scales?

In rocky intertidal habitats, the pronounced increase in environmental stress from low to high elevations greatly affects community structure, that is, the combined measure of species identity and their relative abundance. Recent studies have shown that ecological variation also occurs along the coastline at a variety of spatial scales. Little is known, however, on how vertical variation compares with horizontal variation measured at increasing spatial scales (in terms of sampling interval). Because broad-scale processes can generate geographical patterns in community structure, we tested the hypothesis that vertical ecological variation is higher than fine-scale horizontal variation but lower than broad-scale horizontal variation. To test this prediction, we compared the variation in community structure across intertidal elevations on rocky shores of Helgoland Island with independent estimates of horizontal variation measured at the scale of patches (quadrats separated by 10s of cm), sites (quadrats separated by a few m), and shores (quadrats separated by 100s to 1000s of m). The multivariate analyses done on community structure supported our prediction. Specifically, vertical variation was significantly higher than patch- and site-scale horizontal variation but lower than shore-scale horizontal variation. Similar patterns were found for the variation in abundance of foundation taxa such as Fucus spp. and Mastocarpus stellatus, suggesting that the effects of these canopy-forming algae, known to function as ecosystem engineers, may explain part of the observed variability in community structure. Our findings suggest that broad-scale processes affecting species performance increase ecological variability relative to the pervasive fine-scale patchiness already described for marine coasts and the well known variation caused by vertical stress gradients. Our results also indicate that experimental research aiming to understand community structure on marine shores should benefit from applying a multi-scale approach.
Feeding behavior and activity budget of the southern yellow‐cheeked crested gibbons (Nomascus gabriellae) in a lowland tropical forest

The southern yellow‐cheeked crested gibbon (Nomascus gabriellae), an endangered species native to Vietnam and Cambodia, lives exclusively in undisturbed tropical forests and depends primarily on ripe fruit for food. Although this species is highly threatened, its ecology and conservation status remain relatively unknown. In order to understand how this heavily frugivorous primate adapts to the seasonal fluctuation of fruit resources in the forest, we collected feeding behavior and ranging activity data on one group of southern yellow‐cheeked crested gibbons in Cat Tien National Park, Vietnam, over 1‐year period. We compared these data to information on phenological patterns at the site gleaned during a prior study. We found that the gibbons gathered most of their food from 69 different plant species and also consumed insects and bird eggs. Fruits were the main dietary item (43.3%), followed by leaves (38.4%), flowers (11.6%), and other plant parts (6.0%). A significant seasonal shift in diet was observed; fruit generally dominated the diet in the rainy season and leaves in the dry season. The gibbons often started daily activities very early (05:10 am) in the morning and also ended quite early (16:45 pm) in the afternoon. Socializing was concentrated in the early morning, feeding had a bimodal pattern of high activity levels in mid‐morning and mid‐afternoon, and resting was most intense at the earliest and latest hours of the day and at midday, with proportionally less time used for traveling at these times. Averaged over the annual cycle, the gibbons spent 45% of their time feeding, 31.9% resting, 14.1% traveling, and 9.0% socializing. The percentage of time allocated to different activities varied significantly across months and between the dry and rainy seasons. Monthly variation in the activity budget was strongly related to changes in diet. In the rainy season, when the gibbons ate a higher percentage of fruit, they decreased their feeding time, while increasing traveling time in search of food; conversely, in the dry season, when they fed on a higher percentage of leaves, they decreased traveling time. Overall, our results show that the activity budget and diet of the southern yellow‐cheeked crested gibbon are associated with seasonal shifts in climate. This study provides information relevant to the conservation and management of this endangered species by identifying important habitat conditions for reintroducing captive animals into the wild and providing insight into dietary needs, which may be relevant to the maintenance of animals in rescue centers.
Structure of Apo- and Monometalated Forms of NDM-1—A Highly Potent Carbapenem-Hydrolyzing Metallo-β-Lactamase

The New Delhi Metallo-β-lactamase (NDM-1) gene makes multiple pathogenic microorganisms resistant to all known β-lactam antibiotics. The rapid emergence of NDM-1 has been linked to mobile plasmids that move between different strains resulting in world-wide dissemination. Biochemical studies revealed that NDM-1 is capable of efficiently hydrolyzing a wide range of β-lactams, including many carbapenems considered as “last resort” antibiotics. The crystal structures of metal-free apo- and monozinc forms of NDM-1 presented here revealed an enlarged and flexible active site of class B1 metallo-β-lactamase. This site is capable of accommodating many β-lactam substrates by having many of the catalytic residues on flexible loops, which explains the observed extended spectrum activity of this zinc dependent β-lactamase. Indeed, five loops contribute “keg” residues in the active site including side chains involved in metal binding. Loop 1 in particular, shows conformational flexibility, apparently related to the acceptance and positioning of substrates for cleavage by a zinc-activated water molecule.
Efficacy and Safety of Autologous Cell-based Therapy in Patients with No-option Critical Limb Ischaemia: A Meta-Analysis.

BACKGROUND Revascularisation therapy is the current gold standard of care for critical limb ischemia (CLI), although a significant proportion of patients with CLI either are not fit for or do not respond well to this procedure. Recently, novel angiogenic therapies such as the use of autologous cellbased therapy (CBT) have been examined, but the results of individual trials were inconsistent. OBJECTIVE To pool all published studies that compared the safety and efficacy of autologous CBT derived from different sources and phenotypes with non cell-based therapy (NCT) in CLI patients. METHODS We searched Medline, Embase, Cochrane Library and ClinicalTrials.gov from 1974-2017. Sixteen randomised clinical trials (RCTs) involving 775 patients receiving the following interventions: mobilised peripheral blood stem cells(m-PBSC), bone marrow mononuclear cells(BM-MNC), bone marrow mesenchymal stem cells(BM-MSC), cultured BM-MNC(Ixmyelocel-T), cultured PB cells(VesCell) and CD34+ cells were included in the meta-analysis. RESULTS High-quality evidence (QoE) showed similar all-cause mortality rates between CBT and NCT. AR reduction by approximately 60% were observed in patients receiving CBT compared to NCT (moderate QoE). CBT patients experienced improvement in ulcer healing, ABI, TcO2, pain free walking capacity and collateral vessel formation (moderate QoE). Low-to-moderate QoE showed that compared to NCT, intramuscular BM-MNC and m-PBSC may reduce amputation rate, rest pain, and improve ulcer healing and ankle-brachial pressure index, while intramuscular BM-MSC appeared to improve rest pain, ulcer healing and pain-free walking distance but not AR. Efficacy of other types of CBT could not be confirmed due to limited data. Cell harvesting and implantation appeared safe and well-tolerated with similar rates of adverse-events between groups. CONCLUSION Implantation of autologous CBT may be an effective therapeutic strategy for no-option CLI patients. BM-MNC and m-PSBC appear more effective than NCT in improving AR and other limb perfusion parameters. BM-MSC may be beneficial in improving perfusion parameters but not AR, however, this observation needs to be confirmed in a larger population of patients. Generally, treatment using various sources and phenotypes of cell products appeared safe and well tolerated. Large-size RCTs with long follow-up are warranted to determine the superiority and durability of angiogenic potential of a particular CBT and the optimal treatment regimen for CLI.
Effects of Light, Food Availability and Temperature Stress on the Function of Photosystem II and Photosystem I of Coral Symbionts

Background Reef corals are heterotrophic coelenterates that achieve high productivity through their photosynthetic dinoflagellate symbionts. Excessive seawater temperature destabilises this symbiosis and causes corals to “bleach,” lowering their photosynthetic capacity. Bleaching poses a serious threat to the persistence of coral reefs on a global scale. Despite expanding research on the causes of bleaching, the mechanisms remain a subject of debate. Methodology/Principal Findings This study determined how light and food availability modulate the effects of temperature stress on photosynthesis in two reef coral species. We quantified the activities of Photosystem II, Photosystem I and whole chain electron transport under combinations of normal and stressful growth temperatures, moderate and high light levels and the presence or absence of feeding of the coral hosts. Our results show that PS1 function is comparatively robust against temperature stress in both species, whereas PS2 and whole chain electron transport are susceptible to temperature stress. In the symbiotic dinoflagellates of Stylophora pistillata the contents of chlorophyll and major photosynthetic complexes were primarily affected by food availability. In Turbinaria reniformis growth temperature was the dominant influence on the contents of the photosynthetic complexes. In both species feeding the host significantly protected photosynthetic function from high temperature stress. Conclusions/Significance Our findings support the photoinhibition model of coral bleaching and demonstrate that PS1 is not a major site for thermal damage during bleaching events. Feeding mitigates bleaching in two scleractinian corals, so that reef responses to temperature stresses will likely be influenced by the coinciding availabilities of prey for the host.
Natural Polyphenol Chlorogenic Acid Protects Against Acetaminophen-Induced Hepatotoxicity by Activating ERK/Nrf2 Antioxidative Pathway

Hepatotoxicity due to acetaminophen (APAP) overdose is a leading cause of drug-induced acute liver failure in clinic. Chlorogenic acid (CGA), a dietary polyphenol, was reported to prevent APAP-induced liver injury in our previous studies. This study aims to investigate the protection provided by CGA against APAP-induced hepatotoxicity via focusing on nuclear factor erythroid 2-related factor 2 (Nrf2) and extracellular regulated protein kinases (ERK)1/2. CGA prevented APAP-induced oxidative liver injury and enhanced Nrf2 activation in mice and in hepatocytes in vitro. CGA-provided the protection against APAP-induced hepatotoxicity was diminished after the application of Nrf2 siRNA in vitro and Nrf2 knockout mice in vivo. CGA enhanced the expression of heme oxygenase-1 (HO-1) and NAD(P)H: quinone oxidoreductase-1 (NQO1), and their inhibitors reduced the protection provided by CGA against APAP-induced cytotoxicity in hepatocytes. Molecular docking results indicated the potential interaction of CGA with Nrf2 binding site in Kelch-like ECH-associating protein-1 (Keap1). CGA decreased the expression of protein phosphatases including PP2A subunit A (PP2A-A) and PP5, and induced the sustained ERK1/2 phosphorylation. Moreover, ERK1/2 inhibitors (U0126 and PD98059) and ERK2 siRNA abrogated CGA-induced Nrf2 phosphorylation and its subsequent transcriptional activation, and also reduced the protection provided by CGA against APAP-induced cytotoxicity in hepatocytes. These results suggest that CGA protects against APAP-induced hepatotoxicity by activating Nrf2 antioxidative signaling pathway via blocking the binding of Nrf2 to its inhibitor protein Keap1, and ERK1/2 plays a critical role in regulating CGA-induced Nrf2 transcriptional activation. CGA is a promising therapeutic agent for the detoxification of APAP-induced hepatotoxicity.
The CreC Regulator of Escherichia coli, a New Target for Metabolic Manipulations

ABSTRACT The CreBC (carbon source-responsive) two-component regulation system of Escherichia coli affects a number of functions, including intermediary carbon catabolism. The impacts of different creC mutations (a ΔcreC mutant and a mutant carrying the constitutive creC510 allele) on bacterial physiology were analyzed in glucose cultures under three oxygen availability conditions. Differences in the amounts of extracellular metabolites produced were observed in the null mutant compared to the wild-type strain and the mutant carrying creC510 and shown to be affected by oxygen availability. The ΔcreC strain secreted more formate, succinate, and acetate but less lactate under low aeration. These metabolic changes were associated with differences in AckA and LdhA activities, both of which were affected by CreC. Measurement of the NAD(P)H/NAD(P)+ ratios showed that the creC510 strain had a more reduced intracellular redox state, while the opposite was observed for the ΔcreC mutant, particularly under intermediate oxygen availability conditions, indicating that CreC affects redox balance. The null mutant formed more succinate than the wild-type strain under both low aeration and no aeration. Overexpression of the genes encoding phosphoenolpyruvate carboxylase from E. coli and a NADH-forming formate dehydrogenase from Candida boidinii in the ΔcreC mutant further increased the yield of succinate on glucose. Interestingly, the elimination of ackA and adhE did not significantly improve the production of succinate. The diverse metabolic effects of this regulator on the central biochemical network of E. coli make it a good candidate for metabolic-engineering manipulations to enhance the formation of bioproducts, such as succinate.