Miracle-dz/UniFAR-FTUs huggingface dataset:
The Asian house shrew Suncus murinus as a reservoir and source of human outbreaks of plague in Madagascar

Identifying key reservoirs for zoonoses is crucial for understanding variation in incidence. Plague re-emerged in Mahajanga, Madagascar in the 1990s but there has been no confirmed case since 1999. Here we combine ecological and genetic data, from during and after the epidemics, with experimental infections to examine the role of the shrew Suncus murinus in the plague epidemiological cycle. The predominance of S. murinus captures during the epidemics, their carriage of the flea vector and their infection with Yersinia pestis suggest they played an important role in the maintenance and transmission of plague. S. murinus exhibit a high but variable resistance to experimental Y. pestis infections, providing evidence of its ability to act as a maintenance host. Genetic analyses of the strains isolated from various hosts were consistent with two partially-linked transmission cycles, with plague persisting within the S. murinus population, occasionally spilling over into the rat and human populations. The recent isolation from a rat in Mahajanga of a Y. pestis strain genetically close to shrew strains obtained during the epidemics reinforces this hypothesis and suggests circulation of plague continues. The observed decline in S. murinus and Xenopsylla cheopis since the epidemics appears to have decreased the frequency of spillover events to the more susceptible rats, which act as a source of infection for humans. Although this may explain the lack of confirmed human cases in recent years, the current circulation of plague within the city highlights the continuing health threat.
Effects of enactment by professional actors at encoding and retrieval

This experiment investigated memory benefits similar to those found with subject-performed tasks (SPTs) but under widely differing circumstances. Almost all SPT research has shown that as long as enactment takes place at encoding, mode of recall (enactment vs. verbal recall) is immaterial. Using professional actors, the experimenters had previously shown (Noice & Noice, 1999) that movement that was not semantically congruent with the accompanying material produced enhanced recall at retrieval compared to a non-moving condition, a result that did not appear to be due to the fact that retrieval conditions closely resembled encoding conditions. Experiment 1 of the present study replicated and extended this finding, demonstrating that the effect can be found after a delay of five months with actors of varying age and experience, and that the enhancement is not dependent on physical context. Experiment 2 demonstrated that, even with purely verbal retrieval of material that had been equated for memorability, dialogue originally performed when the participants had been engaged in movement from place to place was better recalled than dialogue originally performed when the participants had remained in one location. Taken together, these results indicate that movement at retrieval is not necessary for the nonliteral enactment effect to occur, but that such movement can aid recall compared to a purely verbal mode of report.
Productivity and population density estimates of the dengue vector mosquito Aedes aegypti (Stegomyia aegypti) in Australia

New mosquito control strategies centred on the modifying of populations require knowledge of existing population densities at release sites and an understanding of breeding site ecology. Using a quantitative pupal survey method, we investigated production of the dengue vector Aedes aegypti (L.) (Stegomyia aegypti) (Diptera: Culicidae) in Cairns, Queensland, Australia, and found that garden accoutrements represented the most common container type. Deliberately placed ‘sentinel’ containers were set at seven houses and sampled for pupae over 10 weeks during the wet season. Pupal production was approximately constant; tyres and buckets represented the most productive container types. Sentinel tyres produced the largest female mosquitoes, but were relatively rare in the field survey. We then used field‐collected data to make estimates of per premises population density using three different approaches. Estimates of female Ae. aegypti abundance per premises made using the container‐inhabiting mosquito simulation (CIMSiM) model [95% confidence interval (CI) 18.5–29.1 females] concorded reasonably well with estimates obtained using a standing crop calculation based on pupal collections (95% CI 8.8–22.5) and using BG‐Sentinel traps and a sampling rate correction factor (95% CI 6.2–35.2). By first describing local Ae. aegypti productivity, we were able to compare three separate population density estimates which provided similar results. We anticipate that this will provide researchers and health officials with several tools with which to make estimates of population densities.
‘Spreading depression of Leão’ and its emerging relevance to acute brain injury in humans

A new research field in translational neuroscience has opened as a result of the recognition since 2002 that “spreading depression of Leão” can be detected in many patients with acute brain injury, whether vascular and spontaneous, or traumatic in origin, as well as in those many individuals experiencing the visual (or sensorimotor) aura of migraine. In this review, we trace from their first description in rabbits through to their detection and study in migraine and the injured human brain, and from our personal perspectives, the evolution of understanding of the importance of spread of mass depolarisations in cerebral grey matter. Detection of spontaneous depolarisations occurring and spreading in the periphery or penumbra of experimental focal cortical ischemic lesions and of their adverse effects on the cerebral cortical microcirculation and on the tissue glucose and oxygen pools has led to clearer concepts of how ischaemic and traumatic lesions evolve in the injured human brain, and of how to seek to improve clinical management and outcome. Recognition of the likely fundamental significance of spreading depolarisations for this wide range of serious acute encephalopathies in humans provides a powerful case for a fresh examination of neuroprotection strategies.
Essays in estimating air transport demand processes and the formation of oligopolies

This dissertation studies three different topics in estimating air transport demand processes and the formation of oligopolies. Chapter 1 provides an overview of the thesis. Chapter 2 investigates the sensitivity of demand for air travel by singleton passengers, couples, and families. It examines how the demand for air travel by these groups is potentially different. In this study, a compound Poisson structure of the demand of different passenger groups is considered and aggregate demand observations and decompounding techniques are used to estimate demand sensitivity of each group of customers to price, time, season, and the economic cycle. The methodology is applied to Canadian market data and the results indicate there are significant differences among the different groups of customers. In Chapter 3 a new decompounding procedure based on rudimentary number theory is developed. The advantages and disadvantages of this new framework are discussed, and the efficiency of these methodologies for certain class of problems is demonstrated. The framework is capable of decompounding when group sizes are either pairwise co-prime or composed of two elements. Under some conditions, the methodologies are generalized to cases where data are recorded in non-equal intervals. It is also not dependent on a restrictive assumption of having some zero observations that exists in conventional decompounding algorithms such as the Panjer recursion algorithm. Chapter 4 shows how hierarchical decision making and franchising is used as a finetuned strategy for brands to both compete aggressively and softly. In a hierarchical decision making process, as a part of long-run plan, the head office of a brand first decides on how many franchises they will grant. At the second stage, the flagships or company owned divisions decide on their level of output and lastly franchises decide how much to produce. We show brands can use this strategy both as a commitment not to compete fiercely with
Predictors of perceived susceptibility of breast cancer and changes over time: a mixed modeling approach.

OBJECTIVE To examine predictors of perceived susceptibility to breast cancer and assess differences across three dependent measures. DESIGN Annual surveys were completed by US women veterans (N = 3,758) participating in a repeat mammography intervention trial. Multivariable non-linear mixed model analyses examined individual- and group-level changes in perceived susceptibility to breast cancer. DEPENDENT MEASURES Three single-item measures of perceived susceptibility to breast cancer (percent risk, ordinal risk, and comparative risk likelihood). Predictors included demographic, health status, health behavior, affect, knowledge, and subjective norm variables. RESULTS Breast symptoms and greater cancer worry increased perceived susceptibility for all three measures. Other predictors varied by dependent measure. Random change, indicating individual variability, was observed for percent risk only. CONCLUSION Despite small model effect sizes, breast symptoms and cancer worry were consistent predictors and may be good targets for messages designed to influence women's perceived susceptibility to breast cancer. Researchers may benefit from using measures of perceived susceptibility with larger response scales, but additional measurement research is needed. Combining indicators of perceived susceptibility may be undesirable when different predictors are associated with different measures.
Pricing Convertible Bond Based on the Jump-diffusion Process

In this paper,we adopt the jump-diffusion equation as the underlying stock equation.First we set a fluctuating interval of stock price where the jump take place,so we can find the jump point easily.After that,we classify the stock prices according to the jump point,and every class is seen as a sample from the population,then we can estimate all the parameters of the jump-diffusion equation. Because our underlying stock equation is a one that including jump,so we cannot find a self-financing strategy that is completely hedged,but we can compute the price of convertible bond according to risk minimum principle.At last,Monte Carlo simulation is used for calculating the time 0 price of Nanjing Shuiyun.
Parametric studies of ethanol production form xylose and other sugars by recombinant Escherichia coli

The conversion of xylose to ethanol by recombinant Escherichia coli has been investigated in pH‐controlled batch fermentations. Chemical and environmental parameters were varied to determine tolerance and to define optimal conditions. Relatively high concentrations of ethanol (56 g/L) were produced from xylose with excellent efficiencies. Volumetric productivities of up to 1.4 g ethanol/L h were obtained. Productivities, yields, and final ethanol concentrations achieved from xylose with recombinant E. coli exceeded the reported values with other organisms. In addition to xylose, all other sugar constituents of biomass (glucose, mannose, arabinose, and galactose) were efficiently converted to ethanol by recombinant E. coli. Unusually low inocula equivalent to 0.033 mg of dry cell weight/L were adequate for batch fermentations. The addition of small amounts of calcium, magnesium, and ferrous ions stimulated fermentation. The inhibitory effects of toxic compounds (salts, furfural, and acetate) which are present in hemicellulose hydrolysates were also examined.
Characterization of the translational defect to fiber synthesis in monkey cells abortively infected with human adenovirus: role of ancillary leaders

Synthesis of the fiber protein of human adenovirus serotype 2 (Ad2) is 100-fold lower in abortively infected monkey cells, compared with productive infections, despite only a 5- to 10-fold reduction in fiber mRNA levels. Previously Anderson and Klessig (Proc. Natl. Acad Sci. USA 81:4023-4027, 1984) demonstrated a direct correlation between the productive nature of the infection, efficient synthesis of the fiber protein in vivo, and the presence of the x or y ancillary leaders on 10 to 25% of fiber messages. To determine at what level in translation these leaders might be important, the relative rate of initiation and elongation of each class of fiber message was assessed. The presence of the y ancillary leader in productively infected cells increased the rate of initiation about twofold, although translational elongation was similar on all fiber messages. However, the rate of elongation of all fiber messages was threefold slower in abortively infected than in productively infected cells. This reduced elongation rate in abortive infections was specific for fiber. The similar distribution of fiber mRNAs on polysomes in both infections suggests that initiation must also be partially blocked in abortive infections. Since the majority of the fiber mRNA even in productive infections did not contain the ancillary leaders, the initiation and elongation defects in the abortive infection cannot be fully explained by the absence of these leaders. Therefore, other factors in the infected cell must be influencing the rate of translation.
Embodied Conversational Agents: A New Kind of Tool for Motor Rehabilitation?

Abstract In this paper, we follow a pluridisciplinary approach topropose a concept of emotional and social interfaces. Thisconcept has been developed in a social and emotionalbehavioral model for Embodied Conversational Agents (ECA)in the context of virtual therapy 1 . In our paradigm, a virtualtherapist interacts with a patient in order to guide andencourage him to fulfill their exercises. We are interested in theproduction of a sense of immersion in the patient by theexpression of a social as well as emotional presence in ECA.This In order to improve the patient / virtual therapistinteraction and thus to stimulate the participation of patientduring the rehabilitation therapy.Keywords--- Embodied Conversational Agents, SocialImmersion, Emotional and Social Interaction, VirtualTherapy, Motor Rehabilitation 1. Introduction Social interaction in virtual worlds opens new horizons inthe field of information technologies. Introducing virtualcharacters with some level of social interaction, allows thedevelopment of many professional applications, which couldnot have only been developed until now in the field of human-machine interaction.Concerning therapy applications, virtual reality and virtualworlds make possible the creation of an interactiveenvironment, where the exercises could be controlled,quantified and modulated, reinforcing the cognitive abilities ofthe patient and minimizing the cost of rehabilitation.In this paper we propose a concept of emotional and socialinterfaces through the use of Embodied Conversational Agents(ECA). We describe a social and emotional behavioral modelfor Embodied Conversational Agents in the context of a virtualtherapist for the rehabilitation of people with brain injuriescaused by cerebral vascular accidents (CVA).
Degradation of extracellular matrix by the trophoblastic cells of first‐trimester human placentas

First‐trimester human placental villi were cultured on 3H‐leucine‐labeled extracellular matrices isolated from the PF HR9 and PYS‐2 cell lines. Both cell lines produced an extracellular matrix that contained basement membrane‐specific macromolecules, including type IV collagen, laminin and proteoglycan. Both matrices promoted outgrowth of cells from the villi which, according to morphological criteria, were identified as cytotrophoblastic cells. As the cells migrated from the attachment site, they caused a marked focal dissolution of the matrix which was accompanied by a concomitant release of 3H‐labeled material into the media. Approximately half of this material chromatographed near the inclusion volume of Sephadex G‐50, indicating that the labeled matrix components had been degraded. This phenomenon was dependent on the age of the placenta. Second‐trimester placental villi also adhered to the matrix, but no areas of dissolution were formed and no significant amounts of radioactivity were released into the medium. These results suggest that culture of first‐trimester human placental villi on extracellular matrices may be useful for the study of some of the early embryonic events leading to human implantation, during which the trophoblastic cells erode the uterine epithelium.
CD8 T Cell-Mediated Killing of Cryptococcus neoformans Requires Granulysin and Is Dependent on CD4 T Cells and IL-151

Granulysin is located in the acidic granules of cytotoxic T cells. Although the purified protein has antimicrobial activity against a broad spectrum of microbial pathogens, direct evidence for granulysin-mediated cytotoxicity has heretofore been lacking. Studies were performed to examine the regulation and activity of granulysin expressed by CD8 T cells using Cryptococcus neoformans, which is one of the most common opportunistic pathogens of AIDS patients. IL-15-activated CD8 T cells acquired anticryptococcal activity, which correlated with the up-regulation of granulysin. When granules containing granulysin were depleted using SrCl2, or when the gene was silenced using 21-nt small interfering RNA duplexes, the antifungal effect of CD8 T cells was abrogated. Concanamycin A and EGTA did not affect the antifungal effect, suggesting that the activity of granulysin was perforin independent. Following stimulation by the C. neoformans mitogen, CD8 T cells expressed granulysin and acquired antifungal activity. This activity required CD4 T cells and was dependent upon accessory cells. Furthermore, IL-15 was both necessary and sufficient for granulysin up-regulation in CD8 T cells. These observations are most consistent with a mechanism whereby C. neoformans mitogen is presented to CD4 T cells, which in turn activate accessory cells. The resultant IL-15 activates CD8 T cells to express granulysin, which is responsible for antifungal activity.
Imbalance of Osteoclastogenesis‐Regulating Factors in Patients With Celiac Disease

Celiac disease is an autoimmune disorder characterized by atrophy of the intestine villi triggered by ingestion of gluten in genetically susceptible individuals. The association between celiac disease and low BMD has been recognized, but the mechanisms of disturbance are poorly understood. We show imbalance of cytokines relevant to bone metabolism in celiac patients' sera and the direct effect of these sera on in vitro bone cell activity.
Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism

ABSTRACT With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to simultaneously assess HIV-1 susceptibilities to all drugs targeting the three viral enzymes and to predict HIV-1 coreceptor tropism. Patient-derived gag-p2/NCp7/p1/p6/pol-PR/RT/IN- and env-C2V3 PCR products were sequenced using the Ion Torrent Personal Genome Machine. Reads spanning the 3′ end of the Gag, protease (PR), reverse transcriptase (RT), integrase (IN), and V3 regions were extracted, truncated, translated, and assembled for genotype and HIV-1 coreceptor tropism determination. DeepGen HIV consistently detected both minority drug-resistant viruses and non-R5 HIV-1 variants from clinical specimens with viral loads of ≥1,000 copies/ml and from B and non-B subtypes. Additional mutations associated with resistance to PR, RT, and IN inhibitors, previously undetected by standard (Sanger) population sequencing, were reliably identified at frequencies as low as 1%. DeepGen HIV results correlated with phenotypic (original Trofile, 92%; enhanced-sensitivity Trofile assay [ESTA], 80%; TROCAI, 81%; and VeriTrop, 80%) and genotypic (population sequencing/Geno2Pheno with a 10% false-positive rate [FPR], 84%) HIV-1 tropism test results. DeepGen HIV (83%) and Trofile (85%) showed similar concordances with the clinical response following an 8-day course of maraviroc monotherapy (MCT). In summary, this novel all-inclusive HIV-1 genotypic and coreceptor tropism assay, based on deep sequencing of the PR, RT, IN, and V3 regions, permits simultaneous multiplex detection of low-level drug-resistant and/or non-R5 viruses in up to 96 clinical samples. This comprehensive test, the first of its class, will be instrumental in the development of new antiretroviral drugs and, more importantly, will aid in the treatment and management of HIV-infected individuals.
Partitioning Road Network Streams Based on Runtime Correlation Discovery

Distributed data stream management systems (DDSMS) are often used to analyze and process road network data streams. DDSMS are composed of upper layer relational query systems (RQS) and lower layer stream processing systems (SPS). DDSMS usually need to meet multiple query requests. This often converts RQS submitted by users into different quest tasks on SPS, and executes query plans on different nodes in parallel by partitioning stream according to the values of specific attributes or partitioning keys. However, executing multiple query plans can cause redundant and repetitive partitioning. This article presents the framework of data stream partitioning based on runtime correlation discovery. It combines the runtime positive-correlation partitioning (RPC-partitioning) and the clustering partitioning (Clu-partitioning). In the process of RPC-partitioning, we first use batching schemes to reduce the number of output buffers and then partition data streams using the correlation between different partitioning keys. In the process of Clu-partitioning, we re-partition data streams by clustering for skewed data. Experiments show that our method can reduce the network communication cost from 16% to 20% with two workloads of road network data streams and improve the throughput in DDSMS. It proves the effectiveness of our method, especially on reducing the operational cost in the cloud environment.
Generation and Characterisation of a Pax8-CreERT2 Transgenic Line and a Slc22a6-CreERT2 Knock-In Line for Inducible and Specific Genetic Manipulation of Renal Tubular Epithelial Cells

Genetically relevant mouse models need to recapitulate the hallmarks of human disease by permitting spatiotemporal gene targeting. This is especially important for replicating the biology of complex diseases like cancer, where genetic events occur in a sporadic fashion within developed somatic tissues. Though a number of renal tubule targeting mouse lines have been developed their utility for the study of renal disease is limited by lack of inducibility and specificity. In this study we describe the generation and characterisation of two novel mouse lines directing CreERT2 expression to renal tubular epithelia. The Pax8-CreERT2 transgenic line uses the mouse Pax8 promoter to direct expression of CreERT2 to all renal tubular compartments (proximal and distal tubules as well as collecting ducts) whilst the Slc22a6-CreERT2 knock-in line utilises the endogenous mouse Slc22a6 locus to specifically target the epithelium of proximal renal tubules. Both lines show high organ and tissue specificity with no extrarenal activity detected. To establish the utility of these lines for the study of renal cancer biology, Pax8-CreERT2 and Slc22a6-CreERT2 mice were crossed to conditional Vhl knockout mice to induce long-term renal tubule specific Vhl deletion. These models exhibited renal specific activation of the hypoxia inducible factor pathway (a VHL target). Our results establish Pax8-CreERT2 and Slc22a6-CreERT2 mice as valuable tools for the investigation and modelling of complex renal biology and disease.