instruction:
In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
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Reproduction numbers, defined as averages of the number of people infected by a typical case, play a central role in tracking infectious disease outbreaks. The aim of this paper is to develop methods for estimating reproduction numbers which are simple enough that they could be applied with limited data or in real time during an outbreak. I present a new estimator for the individual reproduction number, which describes the state of the epidemic at a point in time rather than tracking individuals over time, and discuss some potential benefits. Then, to capture more of the detail that micro-simulations have shown is important in outbreak dynamics, I analyse a model of transmission within and between households, and develop a method to estimate the household reproduction number, defined as the number of households infected by each infected household. This method is validated by numerical simulations of the spread of influenza and measles using historical data, and estimates are obtained for would-be emerging epidemics of these viruses. I argue that the household reproduction number is useful in assessing the impact of measures that target the household for isolation, quarantine, vaccination or prophylactic treatment, and measures such as social distancing and school or workplace closures which limit between-household transmission, all of which play a key role in current thinking on future infectious disease mitigation.
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Estimating Individual and Household Reproduction Numbers in an Emerging Epidemic


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The immunostimulatory effects of oligodeoxyribonucleotides (ODN) containing unmethylated CpG dinucleotides (CpG-ODN) in certain base contexts have been extensively studied in man and mice. One major action is their ability to trigger production of massive amounts of interferon-a (IFN-a) by plasmacytoid dendritic cells (PDC), also referred to as natural IFN-a/b producing cells (NIPC). The present study using porcine PBMC activated by CpG-ODN or plasmid DNA revealed a considerable variation in the IFN-a production in response to various CpG-ODN constructs. Several phosphodiester ODNs, such as 5 0 TTTTCAATTCGAAGATGAAT 3 0 (ODN H), and the plasmid pcDNA3 all required pre-incubation with lipofectin in order to induce IFN-a. Intact unmethylated CpGs were also important, because methylation or substitution of the cytosines and CpG-inversion strongly reduced the IFN-a induction by single-or double-stranded forms of ODN H. Certain CpG-ODNs that contained flanking phosphorothioate or phosphodiester poly-G sequences were potent inducers of IFN-a without pre-incubation with lipofectin, for instance the ODN 2216 (5 0 GGGGGACGATCGTCGGGGGG 3 0 ). While poly-G sequences have been suggested to increase uptake of ODNs by cells, they did not obviate the need for lipofectin when added to the ODN H. However, they resulted in up to five-fold increases of the IFN-a levels caused by ODN H upon lipofection, indicating other enhancing effects of poly-G sequences on the induction of IFN-a. The identity of the IFN-a producing cells (IPC) stimulated by CpG-ODN or plasmid DNA was studied by means of flow cytometry using combined staining for intracellular IFN-a and surface markers. Approximately 1-3 IPC/10 3 PBMC were detected, compared to only 3 IPC/10 4 PBMC stimulated by Aujeszky's disease virus. The IPC frequencies were confirmed by detection of IFN-a mRNA positive cells by in situ hybridisation. The IPC induced by CpG-ODN or plasmid DNA had a similar phenotype, expressing CD2 and CD4 and intermediate levels of MHC class II and the myeloid marker SWC3, but not the markers of T and B cells or
answer:
Characteristics of oligodeoxyribonucleotides that induce interferon (IFN)-a in the pig and the phenotype of the IFN-a producing cells monocytes (CD3, CD21 and CD14)


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HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease 1 , and is related to the zoonotic SARS 2 and MERS 3 betacoronaviruses, which have high fatality rates and pandemic potential. Cell tropism and host range is determined in part by the coronavirus spike (S) protein 4 , which binds cellular receptors and mediates membrane fusion. As the largest known class I fusion protein, its size and extensive glycosylation have hindered structural studies of the full ectodomain, thus preventing a molecular understanding of its function and limiting development of effective interventions. Here we present the 4.0 Å resolution structure of the trimeric HKU1 S protein determined using singleparticle cryo-electron microscopy. In the pre-fusion conformation, the receptor-binding subunits, S1, rest above the fusion-mediating subunits, S2, preventing their conformational rearrangement. Surprisingly, the S1 C-terminal domains are interdigitated and form extensive quaternary interactions that occlude surfaces known in other coronaviruses to bind protein receptors. These features, along with the location of the two protease sites known to be important for coronavirus entry, provide a structural basis to support a model of membrane fusion mediated by progressive S protein destabilization through receptor binding and proteolytic cleavage. These studies should also serve as a foundation for the structure-based design of betacoronavirus vaccine immunogens. Betacoronavirus S proteins are processed into S1 and S2 subunits by host proteases 5 . Like other class I viral fusion proteins, the two subunits trimerize and fold into a metastable pre-fusion conformation. The S1 subunit is responsible for receptor binding, while the S2 subunit mediates membrane fusion. Coronaviruses typically possess two domains within S1 capable of binding to host receptors: an amino (N)-terminal domain (NTD) and a carboxy (C)-terminal domain (CTD), with the latter recognizing protein receptors for SARS-CoV and MERS-CoV 6,7 . Although these individual domains have been structurally characterized, the organization of the complete spike has not yet been determined, preventing a mechanistic understanding of S protein function. Here, we present the structure of the HKU1 S protein ectodomain determined using cryo-electron microscopy (cryo-EM) to 4.0 Å resolution ( Fig. 1a and Extended Data Figs 1 and 2 and Extended Data Table 1 ). The protein construct contains a C-terminal T4 fibritin trimerization motif and a mutated S1/S2 furin-cleavage site (Extended Data Fig. 3 ). The S1 subunit adopts an extended conformation with short linkers between domains and sub-domains (Fig. 1b) . The S1 NTD (amino acids 14-297) has strong structural and sequence homology to the bovine coronavirus (BCoV) S1 NTD (Extended Data Fig. 4) , which recognizes acetylated sialic acids on glycosylated cell-surface receptors 8 . The glycan-binding site in the BCoV S1 NTD is conserved in the HKU1 S1 NTD and is located at the apex of the trimer, oriented towards target cells. Indeed, HKU1 S1 was recently shown to bind O-acetylated sialic
answer:

Pre-fusion structure of a human coronavirus spike protein