Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza

Evaluating the impact of different social networks on the spread of respiratory diseases has been limited by a lack of detailed data on transmission outside the household setting as well as appropriate statistical methods. Here, from data collected during a H1N1 pandemic (pdm) influenza outbreak that started in an elementary school and spread in a semirural community in Pennsylvania, we quantify how transmission of influenza is affected by social networks. We set up a transmission model for which parameters are estimated from the data via Markov chain Monte Carlo sampling. Sitting next to a case or being the playmate of a case did not significantly increase the risk of infection; but the structuring of the school into classes and grades strongly affected spread. There was evidence that boys were more likely to transmit influenza to other boys than to girls (and vice versa), which mimicked the observed assortative mixing among playmates. We also investigated the presence of abnormally high transmission occurring on specific days of the outbreak. Late closure of the school (i.e., when 27% of students already had symptoms) had no significant impact on spread. School-aged individuals (6–18 y) facilitated the introduction and spread of influenza in households, but only about one in five cases aged >18 y was infected by a school-aged household member. This analysis shows the extent to which clearly defined social networks affect influenza transmission, revealing strong between-place interactions with back-and-forth waves of transmission between the school, the community, and the household.
An Entropy-Based Multipath Routing Algorithm in Mobile Ad Hoc Networks

A mobile ad hoc network (MANET) consists of a set of mobile hosts that can communicate with each other without the assistance of base stations. The multipath routing in mobile ad hoc networks is difficult because the network topology may change constantly, and the available alternative path is inherently unreliable. Multi-path routing represents a promising routing method for wireless mobile ad hoc networks. Multi-path routing achieves load balancing and is more resilient to route failures. Design and analysis of routing protocols are the key issues for MANET. This paper proposes a novel Entropy-based Multipath Routing algorithm in MANET (EMR). It is typically proposed in order to increase the reliability of data transmission or to provide load balancing. The simulation results show that the proposed approach and parameters provide an accurate and efficient method of estimating and evaluating the route stability in dynamic MANETs.
High Cerebrospinal Fluid (CSF) Penetration and Potent Bactericidal Activity in CSF of NZ2114, a Novel Plectasin Variant, during Experimental Pneumococcal Meningitis

ABSTRACT Plectasin is the first defensin-type antimicrobial peptide isolated from a fungus and has potent activity against gram-positive bacteria. By using an experimental meningitis model, the penetration of plectasin into the cerebrospinal fluid (CSF) of infected and uninfected rabbits and the bactericidal activities in CSF of the plectasin variant NZ2114 and ceftriaxone against a penicillin-resistant Streptococcus pneumoniae strain (NZ2114 and ceftriaxone MICs, 0.25 and 0.5 μg/ml, respectively) were studied. Pharmacokinetic analysis showed that there was a significantly higher level of CSF penetration of NZ2114 through inflamed than through noninflamed meninges (area under the concentration-time curve for CSF/area under the concentration-time curve for serum, 33% and 1.1%, respectively; P = 0.03). The peak concentrations of NZ2114 in purulent CSF were observed ∼3 h after the infusion of an intravenous bolus of either 20 or 40 mg/kg of body weight and exceeded the MIC >10-fold for a 6-h study period. Treatment with NZ2114 (40 and 20 mg/kg at 0 and 5 h, respectively; n = 11) caused a significantly higher reduction in CSF bacterial concentrations than therapy with ceftriaxone (125 mg/kg at 0 h; n = 7) at 3 h (median changes, 3.7 log10 CFU/ml [interquartile range, 2.5 to 4.6 log10 CFU/ml] and 2.1 log10 CFU/ml [interquartile range, 1.7 to 2.6 log10 CFU/ml], respectively; P = 0.001), 5 h (median changes, 5.2 log10 CFU/ml [interquartile range, 3.6 to 6.1 log10 CFU/ml] and 3.1 log10 CFU/ml [interquartile range, 2.6 to 3.7 log10 CFU/ml], respectively; P = 0.01), and 10 h (median changes, 5.6 log10 CFU/ml [interquartile range, 5.2 to 5.9 log10 CFU/ml] and 4.2 log10 CFU/ml [interquartile range, 3.6 to 5.0 log10 CFU/ml], respectively; P = 0.03) after the start of therapy as well compared to the CSF bacterial concentrations in untreated rabbits with meningitis (n = 7, P < 0.05). Also, significantly more rabbits had sterile CSF at 5 and 10 h when they were treated with NZ2114 than when they were treated with ceftriaxone (67% [six of nine rabbits] and 0% [zero of seven rabbits], respectively, at 5 h and 75% [six of eight rabbits] and 14% [one of seven rabbits], respectively, at 10 h; P < 0.05). Due to its excellent CSF penetration and potent bactericidal activity in CSF, the plectasin variant NZ2114 could be a promising new option for the treatment of CNS infections caused by gram-positive bacteria, including penicillin-resistant pneumococcal meningitis.
The structure of inverses in schema mappings

A schema mapping is a specification that describes how data structured under one schema (the source schema) is to be transformed into data structured under a different schema (the target schema). The notion of an inverse of a schema mapping is subtle, because a schema mapping may associate many target instances with each source instance, and many source instances with each target instance. In PODS 2006, Fagin defined a notion of the inverse of a schema mapping. This notion is tailored to the types of schema mappings that commonly arise in practice (those specified by “source-to-target tuple-generating dependencies”, or s-t tgds). We resolve the key open problem of the complexity of deciding whether there is an inverse. We also explore a number of interesting questions, including: What is the structure of an inverse? When is the inverse unique? How many nonequivalent inverses can there be? When does an inverse have an inverse? How big must an inverse be? Surprisingly, these questions are all interrelated. We show that for schema mappings M specified by full s-t tgds (those with no existential quantifiers), if M has an inverse, then it has a polynomial-size inverse of a particularly nice form, and there is a polynomial-time algorithm for generating it. We introduce the notion of “essential conjunctions” (or “essential atoms” in the full case), and show that they play a crucial role in the study of inverses. We use them to give greatly simplified proofs of some known results about inverses. What emerges is a much deeper understanding about this fundamental and complex operator.
Nitrate reduction in streambed sediments: Effects of flow and biogeochemical kinetics

The effect of retention time on redox sequences along the hydrological flow path of groundwater discharging through low‐relief coastal stream sediments and the subsequent impact on the fate of NO3− carried in the groundwater was examined in two intact cores. Rates of denitrification were determined for the organic‐rich streambed sediments, and a macroscopic, multispecies, reactive transport model based on multiple Monod kinetics was developed to interpret and extend the experimental results. Regionalized sensitivity analysis and parameter estimation were used to determine a set of parameters that best describe the experimental data for one column. The calibrated model successfully replicated the spatial profiles of nitrate under both steady and transient conditions in the second column operated under different conditions. A dimensionless form of the model was used to examine how coupled biogeochemical reactions and hydrological transport processes operate within the stream sediments could be understood in terms of Peclet (ratio of advection to dispersion) and Damkohler numbers (the ratio of the characteristic time of transport to the characteristic time for reaction). At the study site, the Peclet number and the Damkohler numbers for both oxygen and nitrate are high (Pe = 25, DaN = 47.5, and DaO = 40). When Pe > 5, Damkohler numbers explain observed variations in nitrate removal rates; as the flow rate increases, the solute residence time in the reactive zone is shortened resulting in a lesser extent of reaction, such that more NO3− is delivered to the stream water.
Assessing effectiveness of home care for persons with AIDS: Analysis of methodological problems

The aim of this paper is to assess the methodological problems of an unsuccessful randomized controlled trial (RCT) conducted to evaluate the effectiveness, in terms of survival and quality of life, of the early offer of home care (HC) to persons with AIDS (PWA). The study carried out was an intention-to-treat RCT. Persons in the treatment group (TG) received the offer of HC at the moment of AIDS diagnosis; those in the control group (CG) received it six months from diagnosis. Many problems have hindered the progress of the study: particularly, the low compliance to the offer and the failure to enroll the required sample size have made the results unreliable. Analogous problems have been reported within other trials evaluating HC in different fields. The present study thoroughly evaluates the specific ethical and methodological problems encountered in designing and conducting a RCT on HC for PWA. We conclude that, before designing and conducting a RCT in this field, it is advisable to examine some main issues carefully, such as the acceptability of the offer of treatment, the expected compliance and the required size of the study population. If one or more of these elements prove to be problematic, the results of the trial risk being seriously compromised, and alternative approaches should be considered.
Circannual basis of geographically distinct bird schedules

SUMMARY To anticipate seasonal change, organisms schedule their annual activities by using calendrical cues like photoperiod. The use of cues must be fitted to local conditions because schedules differ between species and habitats. In complete absence of temporal information, many species show persistent circannual cycles that are synchronised, but not driven, by photoperiod. The contribution of circannual rhythms to timing under natural photoperiodic conditions is still unclear. In a suite of experiments, we examined timing in two closely related songbirds (Siberian and European stonechats) that inhabit similar latitudes but differ in seasonal behaviour. Under a more continental climate, Siberian stonechats breed later, moult faster and migrate further than European stonechats. We tested hypotheses for seasonal timing mechanisms by comparing the birds under constant and naturally changing daylengths. The taxa retained characteristic reproductive and moult schedules and hybrids behaved roughly intermediately. Based on their distinct circannual cycles, we expected European and Siberian stonechats to differ in photoperiodic responses at a given time of year. We found that the taxa responded, as predicted, in opposite ways to photoperiodic simulations as experienced on different migration routes. The findings indicate that circannual rhythms reflect geographically distinct periodic changes in seasonal disposition and cue-response mechanisms. Under natural daylengths, the phase relationship of the underlying circannual rhythm to the external year determines the action of photoperiod. Circannual rhythms are widespread among long-lived species. Accordingly, responses to environmental change, range expansion and novel migration patterns may depend on the particulars of a species' underlying circannual programming.
The effect of regularization in motion compensated PET image reconstruction: a realistic numerical 4D simulation study

Following continuous improvement in PET spatial resolution, respiratory motion correction has become an important task. Two of the most common approaches that utilize all detected PET events to motion-correct PET data are the reconstruct-transform-average method (RTA) and motion-compensated image reconstruction (MCIR). In RTA, separate images are reconstructed for each respiratory frame, subsequently transformed to one reference frame and finally averaged to produce a motion-corrected image. In MCIR, the projection data from all frames are reconstructed by including motion information in the system matrix so that a motion-corrected image is reconstructed directly. Previous theoretical analyses have explained why MCIR is expected to outperform RTA. It has been suggested that MCIR creates less noise than RTA because the images for each separate respiratory frame will be severely affected by noise. However, recent investigations have shown that in the unregularized case RTA images can have fewer noise artefacts, while MCIR images are more quantitatively accurate but have the common salt-and-pepper noise. In this paper, we perform a realistic numerical 4D simulation study to compare the advantages gained by including regularization within reconstruction for RTA and MCIR, in particular using the median-root-prior incorporated in the ordered subsets maximum a posteriori one-step-late algorithm. In this investigation we have demonstrated that MCIR with proper regularization parameters reconstructs lesions with less bias and root mean square error and similar CNR and standard deviation to regularized RTA. This finding is reproducible for a variety of noise levels (25, 50, 100 million counts), lesion sizes (8 mm, 14 mm diameter) and iterations. Nevertheless, regularized RTA can also be a practical solution for motion compensation as a proper level of regularization reduces both bias and mean square error.
A Quest for Initiating Cells of Head and Neck Cancer and Their Treatment

The biology of head and neck squamous cell carcinomas (HNSCC) and other cancers have been related to cancer stem-like cells (CSC). Specific markers, which vary considerably depending on tumor type or tissue of origin, characterize CSC. CSC are cancer initiating, sustaining and mostly quiescent. Compared to bulk tumors, CSC are less sensitive to chemo- and radiotherapy and may have low immunogenicity. Therapeutic targeting of CSC may improve clinical outcome. HNSCC has two main etiologies: human papillomavirus, a virus infecting epithelial stem cells, and tobacco and alcohol abuse. Here, current knowledge of HNSCC-CSC biology is reviewed and parallels to CSC of other origin are drawn where necessary for a comprehensive picture.
Why Do Some Civil Wars Last So Much Longer than Others?

Five factors are shown to be strongly related to civil war duration. Civil wars emerging from coups or revolutions tend to be short. Civil wars in Eastern Europe and the former Soviet Union have also tended to be relatively brief, as have anti-colonial wars. By contrast, ‘sons of the soil’ wars that typically involve land conflict between a peripheral ethnic minority and state-supported migrants of a dominant ethnic group are on average quite long-lived. So are conflicts in which a rebel group derives major funding from contraband such as opium, diamonds, or coca. The article seeks to explain these regularities, developing a game model focused on the puzzle of what prevents negotiated settlements to long-running, destructive civil wars for which conflicting military expectations are an implausible explanation. In the model, regional autonomy deals may be unreachable when fluctuations in state strength undermine the government’s ability to commit. The commitment problem binds harder when the center has an enduring political or economic interest in expansion into the periphery, as in ‘sons of the soil’ wars, and when either government or rebels are able to earn some income during a conflict despite the costs of fighting, as in the case of contraband funding.
Periodontal condition of patients with autoimmune diseases and the effect of anti-tumor necrosis factor-α therapy.

BACKGROUND The aim of this study is to evaluate the effect of autoimmune diseases (AIs), as well as anti-tumor necrosis factor-α (TNF-α) therapy on the clinical and immunologic parameters of the periodontium. METHODS Thirty-six AI patients (12 rheumatoid arthritis [RA], 12 psoriatic arthritis, and 12 systemic sclerosis) were recruited together with 12 healthy (H) and 10 RA patients receiving anti-TNF-α therapy (RA+). Periodontal indices including plaque index, gingival index (GI), probing depth (PD), and bleeding on probing (BOP) were measured, and gingival crevicular fluid (GCF) was collected from five deepest pockets using papers strips. The TNF-α level was analyzed using enzyme-linked immunosorbent assay. Analysis of variance test was used for statistical comparison between groups, whereas Pearson linear correlation coefficient test was used to examine the association between TNF-α and periodontal status indices. RESULTS The three AI subgroups were very similar in clinical and immunologic parameters. GI was greater in the AI patients compared to the H and RA+ groups (1.91 ± 0.54, 1.21 ± 0.67, and 1.45 ± 0.30, respectively, P = 0.0005). AI patients exhibited significantly more BOP than H and RA+ (46.45% ± 17.08%, 30.08% ± 16.86%, and 21.13% ± 9.51%, respectively, P = 0.0002). PD in H and RA+ groups were lower than in the AI (3.47 ± 0.33, 3.22 ± 0.41, and 3.91 ± 0.49 mm, P = 0.0001). Number of sites with PD >4 mm was higher in AI patients compared to H and RA+ (42.44 ± 17.5 versus 24.33 ± 15.62 versus 33.3 ± 6.6, P = 0.0002). GCF TNF-α was higher among the AI patients (1.67 ± 0.58 ng/site) compared to 1.07 ± 0.33 ng/site for the H group and 0.97 ± 0.52 ng/site for the RA+ group (P = 0.0002). A significant positive correlation was found between PD and TNF-α levels in the GCF (r = 0.4672, P = 0.0002), BOP (r = 0.7491, P = 0.0001), and GI (r = 0.5420, P = 0.0001). CONCLUSIONS Patients with AI diseases have higher periodontal indices and higher TNF-α levels in GCF than H controls. Anti-TNF-α treatment appears to reverse this phenomenon.
Developmental Trends in Voice Onset Time: Some Evidence for Sex Differences

Abstract This study reports on an investigation into the voice onset time (VOT) patterns of the plosives /p b t d/ in a group of 30 children aged 7 (n = 10), 9 (n = 10) and 11 (n = 10) years. Equal numbers of girls and boys participated in the study. Each child named a series of letter objects to elicit /p b t d/ in a syllable onset position with a fixed vowel context. VOT data were examined for age, sex and plosive differences with the following hypotheses: Firstly, that there would be sex differences in the VOT patterns of preadolescent children. Secondly, that the sex differences in VOT patterns would be linked to age and development, and that these would eventually become marked by the age of 11 years, by which time adult-like VOT values should have been achieved. Finally, that the extent of sex and age differences would be dependent upon the plosive being investigated. Results indicated patterns of decrease with age in the VOT values of /p b/ for the boys, with some evidence of increases in the VOT values of /t/ for the girls. In addition, ‘voiced’ and ‘voiceless’ cognates showed a more marked bimodal distribution in the girls‘ VOT patterns. This bimodal distribution was investigated by examining the degree of difference between the VOT values of voiced and voiceless cognate pairs /p b/ and /t d/, and examining the effects of age, sex and cognate pair. These results indicated that more marked sex differences in the ‘voiced’/‘voiceless’ contrast emerged between the data of the 9- and 11-year-olds, a pattern, which was more marked for the alveolar plosives. These preliminary results confirmed all three hypotheses. The findings are presented and discussed both within a developmental and sociophonetic framework.
Bounding Carry-in Interference to Improve Fixed-Priority Global Multiprocessor Scheduling Analysis

The analysis of global multiprocessor scheduling is more difficult than its uniprocessor counterpart. Due to the unknown critical instant, existing techniques use over-approximations of task interference for efficient yet pessimistic analysis. In this paper, we proposed a new technique to improve the precision of interference estimation. The key is to identify and resolve contradicting assumptions made in the analysis procedure. The resulting new analysis method improves the analysis precision at the price of a higher complexity. Then we introduce techniques to optimize the new method for better efficiency. Experiments with randomly generated task sets are conducted to evaluate both the precision and efficiency of the proposed new method.
Probabilistic search with agile UAVs

Through their ability to rapidly acquire aerial imagery, Unmanned Aerial Vehicles (UAVs) have the potential to aid target search tasks. Many of the core algorithms which are used to plan search tasks use occupancy grid-based representations and are often based on two main assumptions. Firstly, the altitude of the UAV is constant. Secondly, the onboard sensors can measure the entire state of an entire grid cell. Although these assumptions are sufficient for fixed-wing, high speed UAVs, we do not believe that they are appropriate for small, lightweight, low speed and agile UAVs such as quadrotors. These platforms have the ability to change altitude and their low speed means that multiple measurements may easily overlap multiple cells for substantial periods of time. In this paper we extend a framework for probabilistic search based on decision making to incorporate multiple observations of grid cells and changes in UAV altitude. We account for observation areas that completely and partially cover multiple grid cells. We show the resultant impact on a number of simulation examples.
The Significance and Insignificance of Carbon Nanotube-Induced Inflammation

In the present review article immune responses induced by carbon nanotubes (CNTs) are addressed. As inhalation is considered to be the primary entry route, and concern has been raised by similar high aspect ratio materials, the main focus lies on immune responses upon pulmonary exposure. Inflammation-related findings from both in vivo studies and in vitro models are reviewed, and the major responsible characteristics, which may drive CNT-induced inflammation in the lung, are discussed. In a second part, responses upon intentional administration of CNTs via subcutaneous and intravenous application are addressed, including their potential benefits and drawbacks for immunotherapy. Finally, the gastrointestinal tract as an alternative exposure route is briefly discussed. While there are many studies identifying numerous other factors involved in CNT-driven toxicity, e.g., cytotoxicity, oxidative stress, and genotoxicity, the focus of this review was kept solely on CNT-induced inflammation. Overall the literature has shown that CNTs are able to induce inflammation, which in some cases was a particularly robust response coinciding with the development of pro-fibrotic conditions. In the majority of cases the greatest inflammatory responses were associated with CNTs of considerable length and a high aspect ratio, accompanied by other factors like dispersion and sample purity.