Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Phylogenetic and Occurrence Information for Risk Assessment of Pest and Pathogen Interactions with Host Plants

Phytosanitary agencies conduct plant biosecurity activities, including early detection of potential introduction pathways, to improve control and eradication of pest and pathogen incursions. For such actions, analytical tools based on solid scientific knowledge regarding plant-pest or pathogen relationships for pest risk assessment are needed. Recent evidence indicating that closely related species share a higher chance of becoming infected or attacked by pests has allowed the identification of taxa with different degrees of vulnerability. Here, we use information readily available online about pest-host interactions and their geographic distributions, in combination with host phylogenetic reconstructions, to estimate a pest-host interaction (in some cases infection) index in geographic space as a more comprehensive, spatially explicit tool for risk assessment. We demonstrate this protocol using phylogenetic relationships for 20 beetle species and 235 host plant genera: first, we estimate the probability of a host sharing pests, and second, we project the index in geographic space. Overall, the predictions allow identification of the pest-host interaction type (e.g., generalist or specialist), which is largely determined by both host range and phylogenetic constraints. Furthermore, the results can be valuable in terms of identifying hotspots where pests and vulnerable hosts interact. This knowledge is useful for anticipating biological invasions or spreading of disease. We suggest that our understanding of biotic interactions will improve after combining information from multiple dimensions of biodiversity at multiple scales (e.g., phylogenetic signal and host-vector-pathogen geographic distribution).
Have Recent Investigations into Remission from Childhood Asthma Helped in Understanding the Pathogenesis of this Disease?

Studies show that a significant proportion of young people suffering from childhood onset asthma later recovered, usually in adolescence. In this article we argue that an understanding of the differences between children who recover from asthma and those who do not would contribute to increased understanding of the pathogenic mechanisms of the disease and could provide new clues about prevention and treatment. We note that some researchers have recently published results from these kinds of investigations. This paper reports results regarding genetic determinants, distorted mechanisms of inflammation, and mind/body relationships. We also try to integrate findings from these 3 areas to formulate general conclusions about the pathogenesis of asthma.
The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

Knowing mutation rates and the molecular spectrum of spontaneous mutations is important to understanding how the genetic composition of viral populations evolves. Previous studies have shown that the rate of spontaneous mutations for RNA viruses widely varies between 0.01 and 2 mutations per genome and generation, with plant RNA viruses always occupying the lower side of this range. However, this peculiarity of plant RNA viruses is based on a very limited number of studies. Here we analyze the spontaneous mutational spectrum and the mutation rate of Tobacco etch potyvirus, a model system of positive sense RNA viruses. Our experimental setup minimizes the action of purifying selection on the mutational spectrum, thus giving a picture of what types of mutations are produced by the viral replicase. As expected for a neutral target, we found that transitions and nonsynonymous (including a few stop codons and small deletions) mutations were the most abundant type. This spectrum was notably different from the one previously described for another plant virus. We have estimated that the spontaneous mutation rate for this virus was in the range 10−6−10−5 mutations per site and generation. Our estimates are in the same biological ballpark that previous values reported for plant RNA viruses. This finding gives further support to the idea that plant RNA viruses may have lower mutation rates than their animal counterparts.
RELIABILITY EVALUATION OF DISTRIBUTION NETWORKS AND PERFORMANCE COMPARISON USING REPRESENTATIVE NETWORKS

The regulation of distribution network monopolies has been shifting from asset-based to performance-based regulation and therefore is becoming more depending on the quality of customer service. Consequently, there has been increasing interest in developing analysis capability and tools that can support quantitative assessments of alternative Distribution Network Operator (DNO) investment plans in terms of costs and benefits involved. Furthermore, it is very important to appreciate the differences in performances across DNO networks and understand the impact that various historical design and operation practices, different topology and population characteristics may have on the network performance. It is also important to understand cost associated with setting individual performance targets to DNOs. Clearly, there is a need for a framework that enables network performances to be objectively compared, the differences to be understood and explained, and cost and benefits of alternative distribution network investment strategies to be evaluated.
Electromagnetic infrastructure monitoring: The exploitation of GPR data and neural networks for multi-layered geometries

In this paper, an inversion ANN-based algorithm for the estimation of geophysical properties (i.e. thickness and permittivity) of subsurface layers in stratified geometries is presented. The basic procedure for the analysis of GPR scans of single subsurface layers placed over a uniform background recently proposed by the authors has been here extended and inserted into a general framework where each stratum is recursively processed.
Searching for the optimal racing line using genetic algorithms

Finding the racing line to follow on the track is at the root of the development of any controller in racing games. In commercial games this issue is usually addressed by using human-designed racing lines provided by domain experts and represents a rather time consuming process. In this paper we introduce a novel approach to compute the racing line without any human intervention. In the proposed approach, the track is decomposed into several segments where a genetic algorithm is applied to search for the best trade-off between the minimization of two conflicting objectives: the length and the curvature of the racing line. The fitness of the candidate solutions is computed through a simulation performed with The Open Racing Car Simulator (TORCS), an open source simulator used as testbed in this work. Finally, to test our approach we carried out an experimental analysis that involved 11 tracks provided with the TORCS distribution. In addition, we compared the performance of our approach to the one achieved by a related approach, previously introduced in the literature, and to the performance of the fastest controller available for TORCS. Our results are very promising and show that the presented approach is able to reach the best performance in almost all the tracks considered.
Imaging patterns of gray and white matter abnormalities associated with PASAT and SDMT performance in relapsing-remitting multiple sclerosis

Objectives: To map the regional patterns of white matter (WM) microstructural abnormalities and gray matter (GM) atrophy exclusively associated with reduced performance in the Symbol Digit Modalities Test (SDMT) and Paced Auditory Serial Addition Test (PASAT) in relapsing-remitting (RR) multiple sclerosis (MS) patients. Methods: In all, 177 RRMS patients and 80 healthy controls (HC) were studied. WM microstructural abnormalities were investigated on diffusion tensor images using tract-based spatial statistics analysis, and regional GM atrophy was estimated on three-dimensional (3D) T1-weighted images using voxel-based morphometry. Results: Compared to HC, RRMS patients showed the expected pattern of cortical–subcortical GM atrophy and WM microstructural abnormalities. In patients, diffusivity abnormalities of supratentorial WM tracts correlated with both SDMT and PASAT scores. Lower SDMT performance was also associated with WM damage in several infratentorial WM tracts. Lower SDMT scores correlated with atrophy of the right anterior cingulate cortex, left postcentral gyrus, and right middle temporal gyrus, whereas lower PASAT scores correlated with atrophy of the deep GM nuclei, bilaterally, and several fronto-temporo-occipital regions. Conclusion: In RRMS patients, regional damage of different neural systems helps explaining reduced performance in SDMT and PASAT. WM microstructural damage typified reduced SDMT performance, whereas atrophy of several GM regions distinguished reduced PASAT performance.
Signal strength sensitivity and its effects on routing in maritime wireless networks

Unlike terrestrial networks, the received signal strength in maritime wireless networks are subjected to perturbations due to the sea movement. Surface motions at sea cause variations in antenna heights and orientations of the communicating node (e.g. ships and buoys), thus affecting the received signal strength. In order to minimize such undesirable effects, we carried out a detailed study of the relationship between sea waves and the received signal strength. The effect of antenna gain variations due to tilting of antenna masts were studied by modeling sea waves. The channel path-loss variations were studied using a two-ray path-loss model for the maritime environment. Our analysis showed that the sea wave movements affect both short and longer links. We proposed a simple scheme to avoid the use of unstable links and implemented it on the QualNet network simulator. We carried out IEEE 802.16-based mesh network simulations with sea terrain and path loss models. We observed performance improvements in packet delay and throughput when the stable link selection scheme was used.
Identification of MIMO systems by input-output TS fuzzy models

A number of techniques have been introduced to construct fuzzy models from measured data. Most attention has been focused on multiple-input, single-output (MISO) systems. This article concentrates on the identification of multiple-input multiple-output (MIMO) systems by means of product-space fuzzy clustering with adaptive distance measure (the Gustafson-Kessel algorithm). The MIMO model is represented as a set of coupled input-output MISO models of the Takagi-Sugeno type. Knowledge of the physical structure can easily be incorporated in the structure of the model. Software implementation in the form of a MATLAB toolbox is briefly described. A simulation example of four cascaded tanks is given.
Motivation for continuous haptic gas pedal feedback to support car following

The last years, increased effort has been dedicated to the design of systems that assist the driver in car following. The need for assistance systems arises from the fallibility of the visual feedback loop, for example due to inattention. Existing driver assistance systems either automate the car-following task or support drivers with binary warning systems to redirect their attention when necessary. The goal of this paper is to discuss the benefits and limitations of these systems, and to show the possibilities of an alternative design approach. To attain the goal, a theoretic analysis is presented, that views car following as a closed-loop control task that requires sufficient feedback about the separation (relative distance, relative velocity) to a lead vehicle. A task analysis helps to identify the areas where the current systems assist the driver well, and where they do not. The new design approach aims to keep the human in the loop, by supplementing the semi-continuous visual feedback loop with an additional continuous feedback loop, namely haptic feedback applied directly at the gas pedal. Expected benefits compared to existing systems include: better situation awareness (even during periods of visual inattention) and faster responses (the haptic feedback is available directly at the gas pedal, allowing the use of fast reflexes). Several design issues are presented, such as the prevention of nuisance and fatigue, deciding which separation states the feedback is based upon, and challenges in determining the correct characteristics of the haptic signals. The benefits of the approach are illustrated through several examples from literature that describe experimental humanin-the-loop studies with continuous haptic feedback. It is concluded that haptic feedback on the gas pedal is a promising way of supporting drivers.
Inferring page models for web application analysis

Web applications are difficult to analyze using code-based tools because data-flow and control-flow through the application occurs via both server-side code and client-side pages. Client-side pages are typically specified in a scripting language that is different from the main server-side language; moreover, the pages are generated dynamically from the scripts. To address these issues we propose a static-analysis approach that automatically constructs a "model" of each page in a given application. A page model is a code fragment in the same language as the server-side code, which faithfully over-approximates the possible elements of the page as well as the control-flows and data-flows due to these elements. The server-side code in conjunction with the page models then becomes a standard (non-web) program, thus amenable to analysis using standard code-based tools.
The association of TNF-308 (G/A) gene polymorphisms and hepatocellular carcinoma risk: a meta-analysis

Objective Many studies have examined the association between the TNF-308 G/A polymorphism gene polymorphisms and hepatocellular carcinoma risk in various populations, but their results have been inconsistent. To assess this relationship more precisely, a meta-analysis was performed. Methods The PubMed and CNKI (China National Knowledge Infrastructure) database was searched for case-control studies. Odds ratios (OR) with 95% CIs were used to determine the strength of association between the TNF-308 G/A polymorphisms and HCC risk. The pooled ORs for the risk associated with the TNF-308 G/A genotype, the A carriers (A/G + A/A) vs. the wild-type homozygotes (G/G), A/A vs. G/G were calculated, respectively. Subgroup analyses were done by ethnicity and smoking status. Heterogeneity assumptions were assessed by chi-square-based Q-test. Results Ultimately, 21 studies, comprising 2,923 hepatocellular carcinoma cases and 4,323 controls were included. Overall, the A carriers (G/A + A/A) vs. the wild-type homozygotes (G/G), the pooled OR was 1.05 (95% CI, 0.93-1.19; P=0.000 for heterogeneity), for A/A vs. G/G the pooled OR was 1.07 (95% CI, 0.95-1.21; P=0.007 for heterogeneity). In the stratified analysis by ethnicity, the significantly risks were found among non-Asians. However, for Asians, significantly risks were not found. Conclusions The TNF-308 G/A polymorphisms are not associated with hepatocellular carcinoma risk among Asians, but for non-Asians.
Pulmonary function and respiratory muscle strength in chronic renal failure patients on hemodialysis.

OBJECTIVE To evaluate pulmonary function and respiratory muscle strength in chronic renal failure patients, correlating these variables with hemodialysis-related weight fluctuation; to study the correlation between the duration hemodialysis and potential respiratory alterations. METHODS Seventeen patients (median age, 47 years; interquartile range, 41-52 years), submitted to three weekly hemodialysis sessions for a median of 27 months (interquartile range, 14-55) were evaluated. Twelve of the patients were male. The patients underwent spirometry. Maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP) were measured prior to and after the first hemodialysis session of the week. Body weight was quantified prior to and after each of the three weekly sessions. RESULTS Before the first hemodialysis session of the week, 8 patients presented mild restrictive defect, which normalized after the session in 2 of those patients. After dialysis, there was a significant increase in forced vital capacity (p = 0.02) and a significant decrease in body weight (p = 0.0001). Weight fluctuation over 3 days without hemodialysis tended to correlate with the variation in forced vital capacity in the first weekly session (r = 0.47; p = 0.055). Duration of hemodialysis correlated with predialysis MIP (r = -0.3; p = 0.03) and MEP (r = -0.63; p = 0.006). CONCLUSIONS More pronounced weight gain in the interdialytic period is associated with worsening of lung function, which is almost fully reversible by hemodialysis. In addition, longer duration of hemodialysis is associated with decreased respiratory muscle strength.
Combined Reactive Power Injection Modulation and Grid Current Distortion Improvement Approach for H6 Transformer-Less Photovoltaic Inverter

In this paper, a combined reactive power modulation and grid current distortion improvement approach is proposed for an H6 transformer-less full-bridge single-phase photovoltaic (PV) grid-connected inverter. H6 transformer-less inverters with traditional modulation and control strategies may not satisfy the requirement of reactive power compensation or may result in more severe zero-crossing current distortion. Therefore, contrary to the traditional modulation, a novel reactive power injection space vector pulse width modulation (SVPWM) is proposed, which consists of two operation stages—inverter modulation and reactive power modulation. The implementation of SVPWM for reactive power modulation using a digital signal processor is also investigated. Furthermore, to suppress the current zero-crossing distortion in the reactive power injection mode, a global sliding mode function based on the proportion-integration-resonance current controller is designed, and the control law of the global sliding mode is derived. Using the segment modulation and grid current distortion improvement approach, the function of reactive current injection is implemented in commercial PV inverters, and the total harmonic distortion of the grid current is decreased significantly by more than 5% in the low-power segment, under the operating conditions of a lagging or leading power factor of 0.95. The effectiveness and feasibility of the proposed approach are verified through simulation and experiment using a 5-kVA prototype.
Surgery confounds biology: The predictive value of stage‐, grade‐ and prostate‐specific antigen for recurrence after radical prostatectomy as a function of surgeon experience

Statistical models predicting cancer recurrence after surgery are based on biologic variables. We have shown previously that prostate cancer recurrence is related to both tumor biology and to surgical technique. Here, we evaluate the association between several biological predictors and biochemical recurrence across varying surgical experience. The study included two separate cohorts: 6,091 patients treated by open radical prostatectomy and an independent replication set of 2,298 patients treated laparoscopically. We calculated the odds ratios for biological predictors of biochemical recurrence—stage, Gleason grade and prostate‐specific antigen (PSA)—and also the predictive accuracy (area under the curve, AUC) of a multivariable model, for subgroups of patients defined by the experience of their surgeon. In the open cohort, the odds ratio for Gleason score 8+ and advanced pathologic stage, though not PSA or Gleason score 7, increased dramatically when patients treated by surgeons with lower levels of experience were excluded (Gleason 8+: odds ratios 5.6 overall vs. 13.0 for patients treated by surgeons with 1,000+ prior cases; locally advanced disease: odds ratios of 6.6 vs. 12.2, respectively). The AUC of the multivariable model was 0.750 for patients treated by surgeons with 50 or fewer cases compared to 0.849 for patients treated by surgeons with 500 or more. Although predictiveness was lower overall for the independent replication set cohort, the main findings were replicated. Surgery confounds biology. Although our findings have no direct clinical implications, studies investigating biological variables as predictors of outcome after curative resection of cancer should consider the impact of surgeon‐specific factors.
On stability of invariance controlled linear systems

Invariance control addresses the problem of control of nonlinear systems in the presence of state constraints. Admissibility with the constraints is guaranteed by keeping an admissible subset of state space positively invariant by switching of the control on the boundary of the set. This paper discusses application of invariance control on the special case of linear systems. For low order systems controlled by linear state feedback, it is shown that the resulting switching invariance control loop is asymptotically stable. The effectiveness of the approach is demonstrated by simulations of an example system.
Read-out of visual information from inferior temporal cortex for object recognition

We are studying the properties of local field potentials (LFPs) in inferior temporal (IT) cortex of the macaque monkey. LFPs are thought to constitute an average mostly of excitatory post-synaptic potentials over large numbers of neurons. Therefore we ask whether the LFPs showed selective responses and we compared the selectivity of LFPs to that of spiking neurons. We are also interested in the topography of visual selectivity in IT and we explored this by comparing the responses from nearby recording sites.
Aphasia in Multiple Sclerosis

Aphasia has rarely been reported in multiple sclerosis (MS). In this article a case with MS presenting as purely global aphasia during an exacerbation of MS is reported with clinical and MRI (magnetic resonance imaging) findings. MRI demonstrated giant plaques mimicking a cerebral tumour with surroundings characterised by oedematous transformations in the left frontal and parietal lobes.
Perceived and measurable performance of daily brushing and rinsing with an essential oil mouthrinse.

AIMS To determine whether the oral health benefits of recommending twice daily brushing and rinsing with an essential oil mouthrinse (EOM) are perceived and measurable by dentists and also perceived by their patients at a 3-month recall visit. METHODS This is a monadic, open label, uncontrolled study involving 766 generally healthy Italian subjects aged 19-66 years, with mild to moderate levels of gingivitis, no pockets of more than 4 mm, and at least 20 scorable teeth. Eight dentists scored subjects for plaque and gingivitis at baseline and at 90 days using simplified 4-point plaque and gingivitis indices. All subjects brushed twice daily, immediately followed by rinsing for 30 sec with 20 ml of an essential oil mouthrinse (Listerine(®)). RESULTS 735 subjects completed the study (95.9%). Average score reductions were 51.9% and 45.7% for plaque and gingivitis, respectively. About 62% and 70% were judged by the dentists as improved for plaque control and gingival health. 85% of subjects judged the EOM as efficacious. CONCLUSION The oral health benefits of brushing and rinsing twice daily with an essential oil mouthrinse are perceived by patients and professionals alike and measurable by dentists at a 3-month recall visit.
The complete mitochondrial genome of the hymenopteran hunting robber fly Dasypogon diadema

Abstract The complete mitochondrial genome of Dasypogon diadema (Insecta: Diptera) was sequenced using the Illumina MiSeq` platform. Its mt-genome spans over 16,947 bp with a GC content of 26.6% containing 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogenetic relationship of Dasypogon diadema and 11 other dipteran species was reconstructed and the phylogenetic position confirmed.