instruction:
In this task, you are given a paragraph (from a research paper) and your task is to classify each sentence of the paragraph (assume n sentence) into the following categories: Background, Purpose, Method, Finding/Contribution, or Other. Return the output in this format: 1 - category of sentence 1, 2 - category of sentence 2, ..., n - category of sentence n; where each number indicates the order of the sentence. The categories can be identified using the following questions: 
 Background: - Why is this problem important? - What relevant works have been done before? - What did the previous works miss? - What are the high-level research questions? - How might this help other researchers?
 Purpose: - What specific things do the researchers want to do? - What specific knowledge do the researchers want to know? - What specific hypothesis do the researchers want to test?
 Method: - How did the researchers do it or find it out? - What are the procedures and steps of this research?
 Finding/Contribution: - What did the researchers find out? Did the proposed methods work? - Did things behave as the researchers expected?
Other: put every text fragment that does not fit into any of the categories above here. Put a sentence here if its not in English, is not part of the article, contains numbers and dates, is a caption of a figure or a table, is a formatting error, or you are not sure about it.
question:
Background: Respiratory viral infections can cause significant morbidity and mortality in immunocompromised patients. Conventional tests routinely available at most institutions are limited by the number of detectable pathogens, by a poor sensitivity and/or a long turnaround time. Objectives: To compare the performance of routine conventional testing with direct fluorescent antibody assays and viral culture to a customized TaqMan® array card (TAC) real-time PCR method, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. Study design: We collected 143 respiratory samples from 120 symptomatic immunocompromised patients. Samples for which conventional and TAC results were discordant underwent further verification testing. Results: The TAC assay identified viral pathogens in more samples than did conventional testing (77/143 versus 27/143; McNemar P < 0.0001), even when TAC results for viruses that could not be detected by conventional testing were excluded from analysis (59/143 versus 26/143; P < 0.0001). In addition, the TAC assay identified 18 samples with non-viral pathogens. Verification testing confirmed positive TAC results for 50 out of 55 samples for which conventional testing was negative. Two out of three samples with a positive conventional test but negative TAC result were confirmed positive. A viral and a total pathogen co-infection rate of 5.6% and 11.8% were found, respectively. Conclusions: The customized TAC assay resulted in a significantly increased identification of respiratory viruses. This study provides a practical real-life assessment of the performance of the TAC assay in a population for whom rapid and accurate diagnosis of viral and atypical pathogens is crucial for appropriate clinical management.
answer:
1 - background, 2 - background, 3 - background, 4 - purpose, 5 - purpose, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding


question:
June 19, 2017) from four Manatee County sites (Fig. 1a) . To avoid cross contamination of 33 mosquito viromes, each year eggs from each site were hatched independently in distilled 34 water, reared to adulthood, speciated and then frozen. Female abdomens were pooled (N= 35 20/pool) separately for the four collection sites for a total of eight individual pools. Total RNA 36 was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), and rRNA depleted with the 37 NEBNext rRNA Depletion Kit (New England BioLabs). The NEBNext Ultra II Directional RNA 38 Library Prep Kit (New England BioLabs) was used to prepare shotgun metagenomics libraries. 39 Reverse-transcribed RNA libraries were sequenced using a HiSeq 3000 (Illumina) instrument 40 in 2x101 run mode. The data were deposited into the NCBI Sequence Read Archive and 41 Biosample archive under BioProject PRJNA547758. 42 43 Initial assembly and metavirome analysis 44 BBduk was used to trim adaptor 45 sequences and remove contaminants. Ae. aegypti sequences were removed using BBsplit 46 author/funder. All rights reserved. No reuse allowed without permission. : bioRxiv preprint 9 assembly with Spades in meta mode [8] and classification using Diamond [9] for a complete 71 DENV4 genome. Read-mapping with Bowtie [10] revealed incorrect bases near the 3' end, 72 which were manually corrected. The genome was annotated using the Genome Annotation 73 Transfer Utility [16] from the Virus Pathogen Database and Analysis Resource (ViPR) [17]. 74 75 Phylogenetic and Molecular Clock analyses 76 Two hundred thirty-four DENV4 genome sequences from GenBank (Table S1) were aligned 77 using MAFFT version 7.407 [18] with the L-INS-I method [19]. IQ-TREE software [20] was 78 used to evaluate phylogenetic signal in the genomes by likelihood mapping [21] and to infer 79 maximum likelihood (ML) phylogeny based on the best-fit model according to the Bayesian 80 Information Criterion (BIC) [20, 22]. Statistical robustness for internal branching order was 81 assessed by Ultrafast Bootstrap (BB) Approximation (2,000 replicates), and strong statistical 82 support was defined as BB>90% [23]. 83 84 To estimate when DENV4 entered Florida, we used 145 strains including all isolates from the 85 Americas, related Asian and African isolates, and randomly reduced oversampled Brazilian 86 isolates. The strains in this dataset were not recombinant, as assessed by scanning the 87 alignments for possible recombination points using the RDP, GENECONV, MaxChi, 88 CHIMAERA, and 3Seq algorithms implemented in the RDP4 software [24]. Correlation between root-to-tip genetic 90 divergence and date of sampling was conducted [25] to assess clock signal before Bayesian 91 phylodynamic analysis. Time-scaled trees were reconstructed using the Bayesian 92 phylodynamic inference framework in BEAST v.1.8.4 [26,27]. Markov Chain Monte Carlo 93 (MCMC) samplers were run until 200/250 million generations to ensure Markov chain mixing, 94 author/funder. All rights reserved. No reuse allowed without permission.
answer:
1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - other, 13 - method, 14 - other, 15 - other, 16 - method, 17 - finding, 18 - finding, 19 - method, 20 - method, 21 - method, 22 - method, 23 - finding, 24 - method, 25 - method, 26 - method, 27 - method, 28 - finding, 29 - finding, 30 - finding, 31 - finding, 32 - finding, 33 - finding, 34 - finding, 35 - other, 36 - other


question:
Attaching and effacing Escherichia coli are involved in diarrhea in 2 to 8-week old calves. The virulence factors of these bacteria include: (i) the secretion of proteins (i.e. EspB) involved in microvilli effacement, (ii) the production of the intimin, a 94 kDa outer membrane protein encoded by the eaeA gene and involved in the intimate attachment of bacteria to epithelial cell and (iii) the production of verotoxins: VT1 and/or VT2. We investigated the presence and the pathotype of these strains in several calf populations by colony hybridization or by genetic amplification. Using the colony hybridization method we showed first that only 5% of calves who died from diarrhea presented EaeA E. coli strains and secondly that 19% of healthy calves showed an asymptomatic carriage. However, using colony hybridization and genetic amplification, we identified EaeA strains in 91% of calves living in farms with recurrent diarrhea problems. In 66% of the calves, there was a correlation between the presence of AEEC and diarrhea. At the pathotype level, most of the EaeA isolates were negative for VT probes. In VT bacteria, the majority were VT1. The number of VT positive bacteria was significantly higher in calves who died from diarrhea than in healthy or sick calves. This underlined the aggravating role of verotoxins in the disease. Moreover, only 25% of the bovine AEEC were positive with the EaeB probe. Surprisingly, the proportion of EaeB strains was significantly higher in healthy calves than in other populations. # 1998 Elsevier Science B.V. All rights reserved.
answer:

1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding