TASK DEFINITION: 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.
PROBLEM: strains of infectious bronchitis virus (IBV) were isolated from the vaccinated chicken flocks in Sichuan province, China. The S1 genes of the isolates were amplified and sequenced. Phylogenetic analysis revealed that the 19 isolates and 37 reference IBV strains can be grouped into eight genotypes. Although IBVs of Taiwan-I type, massachusetts type, and proventriculitis type were isolated, but most isolates were LX4 genotype. Homology analysis of the sequences of S1 genes of the 19 isolates and 37 reference IBV strains revealed that the identity of the nucleotides and amino acid sequences of the S1 genes between the 15 LX4-type isolates and other IBV strains were 71.9-99.3% and 72.1-99.1%, respectively, while those of the analyzed IBV of LX4 type were 96.0-99.9% and 94.3-99.8%, respectively. The results from this study and other published results in the GenBank database showed that isolates circulating in Sichuan province in recent years were mainly LX4 genotype, which is the predominant genotype circulated in China in recent years.

SOLUTION: Genetic analysis revealed LX4 genotype strains of avian infectious bronchitis virus became predominant in recent years in Sichuan area, China

PROBLEM: The foreign insert intended to be displayed via recombinant phage proteins can have a negative effect on protein expression and phage assembly. A typical example is the case of display of peptides longer than 6 amino acid residues on the major coat protein, protein VIII of the filamentous bacteriophages M13 and fd. A solution to this problem has been the use of ''two-gene systems'' generating chimeric phages that concomitantly express wild-type protein VIII along with recombinant protein VIII. Although the two-gene systems are much more permissive in regard to insert length and composition, some cases can still adversely affect phage assembly. Although these phages genotypically contain the desired DNA of the insert, they appear to be phenotypically wild type. To avoid false-negative results when using chimeric phages in binding studies, it is necessary to confirm that the observed lack of phage recognition is not due to faulty assembly and display of the intended insert. Here we describe a strategy for generating antibodies that specifically recognize recombinant protein VIII regardless of the nature of its foreign insert. These antibodies can be used as a general monitor of the display of recombinant protein VIII into phage particles. Ó 2011 Elsevier Inc. All rights reserved. Filamentous bacteriophages have proven to be an extremely useful tool for the study of protein-protein interactions [1,2] and have had a profound impact on the analysis of antibody-peptide binding [3] [4] [5] . Of the five structural proteins that make up filamentous phages, proteins III and VIII are most often used as N-terminal fusion proteins, displaying their foreign inserts on the phage surface [6] . Protein III most easily displays inserts and can express proteins hundreds of amino acids in length without a negative impact on assembly or titer of phages. Thus, protein III is routinely used in antibody phage display where either Fab or single-chain antibodies are expressed [7, 8] . Although this system is quite efficient and widely used, the number of antibody or insert copies is limited to the five copies of protein III per phage. In situations where higher insert density is desirable, protein VIII should be considered. This is due to the fact that the filament structure is composed of some 2700 copies of protein VIII, a short 50-aminoacid protein that associates with the phage single-stranded DNA at its carboxy terminus and displays its free N terminus on the surface of the phage [6]. Peptide inserts can be introduced at the Nterminal aspect of protein VIII without disrupting the assembly so long as they are kept shorter than 6 to 8 residues [9,10]. Expression of longer peptides on all copies of protein VIII interferes with proper phage assembly. Thus, for instance, Cesareni and coworkers reported that only 20% of phage clones inserted with random octapeptides and 1% of clones inserted with random decapeptides pro-duce viable phage particles [9] . Longer inserts can be displayed employing a ''two-gene system'' where two versions of protein VIII are expressed in the infected bacterium, one corresponding to unaltered wild-type protein VIII and the other being a recombinant that can display peptides even longer than 100 amino acids in its N-terminal aspect [11] . In this situation, assembly of the phage generates chimeric phages containing mostly wild-type protein VIII studded here and there with recombinant versions displaying their peptide insert at the phage surface [12] . Moreover, such chimeric phages may contain recombinant protein VIII displaying large inserts at extremely low levels [11, 13] . To complicate matters, it has been shown that not only the length but also the sequence of the insert can affect incorporation levels into phage particles by affecting the critical steps of protein VIII membrane insertion and processing [13] . Although expression of peptides using this two-gene system is generally efficient and has only a marginal effect on the titer of chimeric phages, in some instances the particular nature of the peptide might be incompatible with functional phage assembly with two possible outcomes: (i) the recombinant protein VIII causes a block in assembly, leading to a dramatic drop in phage titer [9], or (ii) provided that a wild-type gene is expressed, the problematic recombinant protein VIII is simply not incorporated into the assembling phage, generating phages that phenotypically are uniformly wild type. Such phages are misleading in binding experiments because no binding is observed, not due to lack of peptide recognition but rather due to faulty display. To discriminate between these two options, it would be useful to have a specific 0003-2697/$ -see front matter Ó

SOLUTION: A general insert label for peptide display on chimeric filamentous bacteriophages

PROBLEM: Background: We undertook a 2X2 factorial, randomized controlled trial (RCT) to assess whether vitamin D 3 supplementation (10,000 international units per week) versus placebo and gargling versus no gargling could prevent viral, clinical upper respiratory tract infection (URTI) in university students. Methods: We randomized 600 students into 4 treatment arms: 1) vitamin D 3 and gargling, 2) placebo and gargling, 3) vitamin D 3 and no gargling, and 4) placebo and no gargling. Students completed weekly electronic surveys and submitted self-collected mid-turbinate nasal flocked swabs during September and October in 2010 or 2011. Symptomatic students also completed an electronic symptom diary. The primary and secondary outcomes were the occurrence of symptomatic clinical URTI and laboratory confirmed URTI respectively. Results: Of 600 participants, 471 (78.5%) completed all surveys while 43 (7.2%) completed none; 150 (25.0%) reported clinical URTI. Seventy participants (23.3%) randomized to vitamin D 3 reported clinical URTI compared to 80 (26.7%) randomized to placebo (RR:0.79, CI 95 :0.61-1.03, p = 0.09). Eighty-five participants (28.3%) randomized to gargling reported clinical URTI compared to 65 participants (21.7%) randomized to the no gargling arm (RR:1.3, CI 95 :0.92-1.57, p = 0.19). Laboratory testing identified 70 infections (46.7 per 100 URTIs). Vitamin D 3 treatment was associated with a significantly lower risk for laboratory confirmed URTI (RR: 0.54, CI 95 :0.34-0.84, p = 0.007) and with a significantly lower mean viral load measured as log 10 viral copies/mL (mean difference: −0.89, CI 95: -1.7, −0.06, p = 0.04). Fewer students assigned to gargling experienced laboratory confirmed URTI, however this was not statistically significant (RR:0.82, CI 95 :0.53-1.26, p = 0.36). Conclusions: These results suggest that vitamin D 3 is a promising intervention for the prevention of URTI. Vitamin D 3 significantly reduced the risk of laboratory confirmed URTI and may reduce the risk of clinical infections. Trial registration: Clinical Trials Registration: NCT01158560.

SOLUTION:
Vitamin D 3 and gargling for the prevention of upper respiratory tract infections: a randomized controlled trial