Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In many Gram- negative bacteria, including the phytopathogen Pseudomonas syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. To capture the dynamic nature of virulence gene repertoires across P. syringae, we screened 11 diverse strains for novel TTE families and coupled this nearly saturating screen with the sequencing and assembly of 14 phylogenetically diverse isolates from a broad collection of diseased host plants. TTE repertoires vary dramatically in size and content across all P. syringae clades; surprisingly few TTEs are conserved and present in all strains. Those that are likely provide basal requirements for pathogenicity. We demonstrate that functional divergence within one conserved locus, hopM1, leads to dramatic differences in pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be used to identify functionally critical residues of TTEs. The dynamism of the TTE repertoire is mirrored by diversity in pathways affecting the synthesis of secreted phytotoxins, highlighting the likely role of both types of virulence factors in determination of host range. We used these 14 draft genome sequences, plus five additional genome sequences previously reported, to identify the core genome for P. syringae and we compared this core to that of two closely related non-pathogenic pseudomonad species. These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species.
Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing an average of 39,300 bp in 78 gene fragments from 97 isolates. These isolates included 34 pairs of sequential samples, which were sampled at intervals of 0.25 to 10.2 years. They also included single isolates from 29 individuals (average age: 45 years) from 10 families. The accumulation of sequence diversity increased with time of separation in a clock-like manner in the sequential isolates. We used Approximate Bayesian Computation to estimate the rates of mutation, recombination, mean length of recombination tracts, and average diversity in those tracts. The estimates indicate that the short-term mutation rate is 1.4×10−6 (serial isolates) to 4.5×10−6 (family isolates) per nucleotide per year and that three times as many substitutions are introduced by recombination as by mutation. The long-term mutation rate over millennia is 5–17-fold lower, partly due to the removal of non-synonymous mutations due to purifying selection. Comparisons with the recent literature show that short-term mutation rates vary dramatically in different bacterial species and can span a range of several orders of magnitude.
Tag-based social interest discovery

The success and popularity of social network systems, such as del.icio. us, Facebook, MySpace, and YouTube, have generated many interesting and challenging problems to the research community. Among others, discovering social interests shared by groups of users is very important because it helps to connect people with common interests and encourages people to contribute and share more contents. The main challenge to solving this problem comes from the difficulty of detecting and representing the interest of the users. The existing approaches are all based on the online connections of users and so unable to identify the common interest of users who have no online connections. In this paper, we propose a novel social interest discovery approach based on user-generated tags. Our approach is motivated by the key observation that in a social network, human users tend to use descriptive tags to annotate the contents that they are interested in. Our analysis on a large amount of real-world traces reveals that in general, user-generated tags are consistent with the web content they are attached to, while more concise and closer to the understanding and judgments of human users about the content. Thus, patterns of frequent co-occurrences of user tags can be used to characterize and capture topics of user interests. We have developed an Internet Social Interest Discovery system, ISID, to discover the common user interests and cluster users and their saved URLs by different interest topics. Our evaluation shows that ISID can effectively cluster similar documents by interest topics and discover user communities with common interests no matter if they have any online connections.
Quasi-static Multilayer Electrical Modeling of Human Limb for IBC ∗

Home health care system and long term physiologic parameters monitoring system are important for elevating the living quality of chronic disease patients and elderly. Elaborating towards a sophisticated and comprehensive home health care system, Intra-Body Communication (IBC) is believed to have advantages in power consumption, electromagnetic radiation, interference from external electromagnetic noise, security, and restriction in spectrum resource. In this article, we start from quasi-static Maxwell’s Equation and propose a mathematical model, which includes electrical properties and proportion of human tissues, for IBC on a human limb. By solving the mathematical model analytically and conducting in vivo experiment, our model has shown adequate agreement with experiments.
VOLATILITY ANALYSIS OF CRUDE OIL PRICES IN NIGERIA

This study investigates the symmetric and asymmetric characteristics as well as the persistence of shocks in the Nigerian crude oil returns, utilizing monthly and daily crude oil prices spanning from January 2006 to September 2022 and November 3, 2009, to November 4, 2022, respectively. Descriptive statistics, normality measures, time plots, and the Dickey-Fuller Generalized Least Squares unit root test were employed to analyze the series properties. Symmetric ARMA (1,1)-GARCH (2,1) and asymmetric ARMA (1,1)-TARCH (2,1) models for monthly and daily returns, with varying innovation densities, were utilized, alongside symmetric GARCH (1,1) and asymmetric TARCH (1,1) models. Model selection criteria including AIC, SIC, HQC, and log likelihood guided the order and error distribution selection. Results revealed non-normal distributions for both monthly and daily prices and returns, non-stationarity in prices, and weak stationarity in log returns with ARCH effects detected in both returns. Symmetric models exhibited volatility clustering, high shocks persistence, mean-reverting behaviour, and predictability in both returns. Asymmetric models identified asymmetry with leverage effects in both returns, indicating that negative shocks induce greater volatility than positive shocks of the same magnitude. Mean reversion and volatility half-life findings suggested that crude oil prices tend to revert to their long-run averages. The study recommended promoting market information flow and aggressive trading to enhance market depth and mitigate the volatile nature of the Nigerian crude oil market.
Ketamine Anesthesia, Efficacy of Electroconvulsive Therapy, and Cognitive Functions in Treatment-Resistant Depression

Objectives Electroconvulsive therapy (ECT) is the most effective treatment for drug-resistant depression (DRD). Because a single infusion of ketamine may exert both a rapid antidepressant effect and a quick improvement of cognition, the aim of the present study was to assess whether ketamine, as an anesthetic drug for ECT, can augment the antidepressant activity of the procedure and/or exert a beneficial effect on cognition. Methods A total of 11 male and 34 female patients with DRD, aged 21 to 75 years, were included in the study. Fifteen patients (group 1) received only thiopental anesthesia, 15 patients (group 2) had their second and third ECT sessions with ketamine, and 15 patients (group 3) had ketamine for the second, fourth, sixth, eighth, and tenth sessions. Depression intensity was measured by the 17-item Hamilton Depression Rating Scale. Cognitive functions were measured before and after ECT, assessing visual-spatial abilities, verbal auditory memory, working memory, and executive functions. Results Before the ECT, the mean (SD) intensity of depression was 32 (6) points on the Hamilton Depression Rating Scale and the mean number of ECT sessions was 10.8 (1.5), with no difference between groups. After the last ECT session, the intensity of depression was significantly lower in group 3, compared with group 1. Cognitive assessments after ECT showed a more marked worsening in verbal memory in patients with added ketamine anesthesia. Conclusions The addition of ketamine may be connected with better antidepressant efficacy of ECT, compared with only thiopental anesthesia. However, patients with added ketamine had worse results on some of the indices measuring verbal memory.
Adherence to Mediterranean Diet, Dietary Salt Intake, and Susceptibility to Nephrolithiasis: A Case–Control Study

Unhealthy dietary habits play a key role in the pathogenesis of nephrolithiasis (NL). The aims of this case–control study were to evaluate (i) the adherence to the Mediterranean Diet (MD) and the dietary salt intake in stone-forming patients (SF), (ii) the relationship occurring between MD adherence, salt intake and NL-related metabolic risk factors in SF, and (iii) the impact of combined high MD adherence and low salt intake on NL susceptibility. From 1 January 2018 to 31 December 2019, we recruited all SF consecutively referred to the Extracorporeal Shock Wave Lithotripsy (ESWL) center of Federico II University, and at least two control subjects without a personal history of NL, age-, sex-, and body mass index-matched to SF (NSF). All study participants were interviewed using the validated MEDI-LITE and MINISAL questionnaires. In an SF subgroup, the NL-related metabolic risk factors were also evaluated. SF showed a lower MD adherence and a higher salt intake compared with NSF. The NL susceptibility decreased by 36% [OR: 0.64 (0.59–0.70); p < 0.01] for each point of increase in MEDI-LITE score, while it increased by 13% [OR: 1.13 (1.03–1.25); p = 0.01] for each point of increase in MINISAL score. The SF prevalence was higher among subjects showing combined low MD adherence and high salt intake. In SF, the MEDI-LITE score directly correlated with 24 h-citraturia, whereas the MINISAL score directly correlated with urinary sodium and uric acid excretion. In conclusion, high MD adherence and low salt intake are associated with a reduced NL susceptibility, both separately and in combination.
Analysis and performance evaluation of axial flux permanent magnet motors

A two-dimensional analytical method for the performance evaluation of axial flux permanent magnet (AFPM) machine has been presented in this paper. The method computes the electromagnetic torque, magnetic field distribution, cogging torque and back EMF of the machine using quasi-3D modeling. Fourier Transform is used for the solution of Maxwell's equations in different regions of the AFPM machine. A surface mounted AFPM motor is tested and the experimental results validate the proposed method.
Family history studies: V. The genetics of mania.

In this study of the families of 59 manic-depressive, manic type probands, the predominant affective illness among the family members was depression without mania, although mania was frequent. The findings suggest that genetic transmission occurred by a sex-linked single or double dominant gene. In two families affective disorder was linked to color blindness, implying that the X-linked gene for manic-depressive psychosis is on the short arm of the X chromosome.
Using non-convex approximations for efficient analysis of timed automata

The reachability problem for timed automata asks if there exists a path from an initial state to a target state. The standard solution to this problem involves computing the zone graph of the automaton, which in principle could be infinite. In order to make the graph finite, zones are approximated using an extrapolation operator. For reasons of efficiency in current algorithms extrapolation of a zone is always a zone; and in particular it is convex. In this paper, we propose to solve the reachability problem without such extrapolation operators. To ensure termination, we provide an efficient algorithm to check if a zone is included in the so called region closure of another. Although theoretically better, closure cannot be used in the standard algorithm since a closure of a zone may not be convex. An additional benefit of the proposed approach is that it permits to calculate approximating parameters on-the-fly during exploration of the zone graph, as opposed to the current methods which do it by a static analysis of the automaton prior to the exploration. This allows for further improvements in the algorithm. Promising experimental results are presented.
Market Minds: Understanding Behavioral Finance Concepts

The topic of behavioural finance is challenging the traditional notion of rational decision-making in the ever-changing financial markets. This paradigm shift examines the interaction between psychology, cognitive biases, and financial decisions, offering insights into market anomalies and behaviours that contradict conventional economic theory. Behavioural finance is an interdisciplinary field that combines psychology, cognitive science, economics, and finance. Its purpose is to connect economic theory with actual financial behaviours seen in the real world.
Functional Ingredients from Seafood Processing Wastes: Protein Hydrolysate and Biocalcium

The fish processing industry generally generates large amounts of byproducts, including skin, bone, scale, or meat residues, etc. These byproducts contain a wide range of nutritional components such as protein, lipid, mineral, etc. These leftovers can be converted to functional ingredients or nutraceuticals. To produce high value-added functional ingredients, the remaining proteins in fish processing leftovers are hydrolyzed, in which hydrolysate containing different peptides and amino acids can be generated. Frame or backbone as well as scale can be converted to fish biocalcium, which serves as a potential source of calcium and minerals. Nevertheless, potential processing or technology must be adopted to obtain desired products with target bioactivitities. This review covers production, characteristics, and bioavailability of fish protein hydrolysate (FPH) and fish biocalcium (BC). This review also focuses on the recent applications of the FPH and BC in drink and foods. Overall, the review points out the better exploitation of fish processing leftovers and simultaneously lower pollution caused by the improper discard or disposal of those wastes to environment. Also, consumers have more choices to consume functional ingredients or nutraceutical from marine resources.
A Holistic View of Water Management Impacts on Future Droughts: A Global Multimodel Analysis

This study investigates the impacts of climate change and water management including agricultural irrigation, water withdrawal, and reservoir regulation on future meteorological, agricultural, and hydrological droughts and their connections. The analysis is based on the simulations from four global hydrological models forced with the projections from five global climate models for historical period 1971–2000 and future period 2070–2099 with and without water management. Three unified drought indices, the standardized precipitation index, standardized soil moisture index, and standardized streamflow index, are adopted to represent the meteorological, agricultural, and hydrological droughts, respectively. The analysis suggests that the climate‐induced drought changes in all three types of droughts are enhanced but in different directions, while water‐management‐induced changes in agricultural and hydrological droughts are more consistent across space and simulations. Overall, water management activities reduce both the duration and intensity of agricultural droughts by roughly 1 order of magnitude, while increase those of hydrological droughts by up to 50%. Basin‐scale analysis reveals that the higher is the intensity of irrigation, the larger will be the water‐management‐induced drought changes. Due to water management activities at some regions, the return periods of extreme agricultural droughts (in terms of severity) can change from 100 to 300 years or even longer, while typical 100‐year hydrological droughts are likely to occur more often for the regions located in 25°N–40°N and 15°S–50°S. This study provides a global view on drought modification in the Anthropocene, which will help improve adaptation strategies for future droughts.
An Approach for Collaborative Decision in Distributed Intrusion Detection System

Computers have virtually changed every aspect of our life. The rapid growth in the development of computers was focused on making the computer easy to use for all. The rapid growth did not give as much importance on the security of the computer system thereby leaving system as vulnerable to attacks. As internet and its applications are increasing, complex and hybrid networks are being used for communication. So many loopholes are being explored to intrude into other systems. There are many tools and techniques available for securing networks like Firewalls, IDS etc. and until now they are used very frequently by nearly all the organizations to safeguard information and other critical data but these are not sufficient for implementing complete security because the intruders have become smarter. Higher security being the priority of many organizations has led to the importance and promoting active research on efficient Intrusion Detection Systems. To deal with various types of attacks we need to have information of attacks from other sources as well. This can be done by sharing intrusion information with all. As hackers are becoming more intelligent we need to
Relieving loading on tidal turbines operating in a turbulent environment: proposal for load alleviation device for a marine turbine

Tidal turbines operate in marine currents characterised by strong turbulence. This environment impacts on the life of the device, blades, transmission and running train ancillaries, bearings and seals, for example. The reduction of the transient load on the turbine blade can be achieved through a range of measures; in this investigation, modifications to the blade comprising blowing actuators will be modelled using the FLUENT CFD RANS solver with the k-ω SST turbulence model. Different locations on the suction side for the blowing are explored. Different angles and pressures of the blowing are explored for steady state cases. The final chosen location for the ejection was near the trailing edge (TE) for unsteady simulations with sinusoidal jet excitation and an oscillating-flow inlet boundary condition. The most obvious effectiveness is at low actuation frequency and mid-to-high jet-strength. This results in reduction of lift at the higher angles of attack, α , and reduction of ∆L ∆α . The action of the unsteady ejection re-shapes the hysteresis lift curve with little change in drag and reduces drag in some cases. A counter-rotating pair of vortices is formed due to the TE ejection, which altered the direction of flow leaving the TE due to a small region of induced recirculating flow behind the TE. One of the vortices takes the form of a curtailed TE vortex. It is thought that this could, under the right conditions, be caused to merge with the wake and shed to result in a more docile stall. The CFD validation study performed first of all, consisted of a comparison between the two relative types of motion a pitching aerofoil and static aerofoil subjected to flow oscillation. This study uncovered substantial differences in the dynamic stall mechanics between wind tunnel experiments on a pitching aerofoil and the kind experienced by a turbine blade due to oscillating loads in highly unsteady flow. Many wind turbine data currently depends on the relative motion between aerofoil and flow.
Meliponicultura no Rio Grande do Norte

ABSTRACT. Maia U.M. , Jaffe R. , Carvalho A.T. & Imperatriz-Fonseca V.L. [Meliponiculture in Rio Grande do Norte. ] Meliponicultura no Rio Grande do Norte. Revista Brasileira de Medicina Veterinaria, 37(4):327-333, 2015. Departamento de Biologia, Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Avenida Bandeirantes, 3900, Monte Alegre, Ribeirao Preto, SP 14040-901, Brasil. E-mail: ummaia@usp.br This study aimed to assess the current status of stingless bee beekeeping (meliponiculture) in the State of Rio Grande do Norte, Brazil, with the aid of structured questionnaires made during visits to beekeepers. The results were compared with a previous census made in the state and with a similar study from Australia. Meliponiculture in Rio Grande do Norte is still informal and little standardized. The activity has grown in recent years considering the mean number of nests per beekeeper. Most apiaries are formed of up to 50 colonies, usually distributed in the backyards of homes. Twelve species of stingless bees were reared in the state, and the most common was the “Jandaira” bee (Melipona subnitida), whose honey is considered medicinal. While many beekeepers already know the importance of bees as pollinators, stingless bees are still not used for crop pollination. Compared to a recent analysis of beekeeping in Australia, meliponiculture in Brazil is more traditional, honey is the main product and the number of colonies per beekeeper is much higher. Our results highlight the need to reinforce knowledge about bees and promote specific training aimed at improving and standardizing management practices.
p80cdc25 mitotic inducer is the tyrosine phosphatase that activates p34cdc2 kinase in fission yeast.

We have investigated the mechanism by which fission yeast p80cdc25 induces mitosis. The in vivo active domain was localized to the C‐terminal 23 kDa of p80cdc25. This domain produced as a bacterial fusion protein (GST‐cdc25) caused tyrosyl dephosphorylation and activation of immunoprecipitated p34cdc2. Furthermore, GST‐cdc25 dephosphorylated both para‐nitrophenyl‐phosphate (pNPP) and casein phosphorylated on serine in vitro. Reaction requirements and inhibitor sensitivities were the same as those of phosphotyrosine phosphatases (PTPases). Analysis of cdc25 C‐terminal domains from a variety of species revealed a conserved motif having critical residues present at the active site of PTPases. Mutation of the cdc25 Cys480 codon, corresponding to an essential cysteine in the active site of PTPases, abolished the phosphatase activity of GST‐cdc25. These data indicate that cdc25 proteins define a novel subclass of eukaryotic PTPases, and strongly argue that cdc25 proteins directly dephosphorylate and activate p34cdc2 kinase to induce M‐phase.
Novel Orthobunyavirus in Cattle, Europe, 2011

In 2011, an unidentified disease in cattle was reported in Germany and the Netherlands. Clinical signs included fever, decreased milk production, and diarrhea. Metagenomic analysis identified a novel orthobunyavirus, which subsequently was isolated from blood of affected animals. Surveillance was initiated to test malformed newborn animals in the affected region.