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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.
Example Input: Conclusions and Clinical Importance: Results suggested that nasopharyngeal carriage of M. bovis was detrimental to health and growth of dairy calves in small herds with a high incidence of BRD.
Example Output: 1 - finding
Example Input: This paper assesses the impact of the September 11 terrorist attacks and its after-effects on U.S. airline demand. Using monthly time-series data from 1986 to 2003, we find that September 11 resulted in both a negative transitory shock of over 30% and an ongoing negative demand shock amounting to roughly 7.4% of pre-September 11 demand. This ongoing demand shock has yet to dissipate (as of November 2003) and cannot be explained by economic, seasonal, or other factors.
Example Output: 1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding
Example Input: The complexities of the dynamic processes and their control associated with biological and ecological systems offer many challenges for the control engineer. Over the past decades the application of dynamic modelling and control has aided understanding of their complexities. At the same time using such complex systems as test-beds for new control methods has highlighted their limitations (e.g. in relation to system identification) and has thus acted as a catalyst for methodological advance. This paper continues the theme of exploring opportunities and achievements in applying modelling and control in the bio-and ecological domains. #
Example Output: | 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - other
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
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:
Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 1212 |
answer:
1 - other
question:
We thank Héctor R. Morbidoni for critical reading of this manuscript and Paola Gallo for English revisions.
answer:
1 - background
question:
Results: Plasmids differed in core-expression capacity: mouse fibroblasts transfected with pCMVcore, pCMVcoreIRES and pCMVcoreKozak expressed 0.22 ± 0.18, 0.83 ± 0.5, and 13 ± 5 ng core per cell, respectively. Single immunization with highly expressing pCMVcoreKozak induced specific IFN- and IL-2, and weak antibody response. Single immunization with plasmids directing low levels of core expression induced similar levels of cytokines, strong T-cell proliferation
answer:
| 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding
| 9 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Q: Conclusions Infection immunity to a recent human H3N2 virus confers minimal cross-protection against a European swine H3N2 virus. We discuss our findings with regard to the recent zoonotic infections of humans in the United States with a swine-origin H3N2 variant virus. Please cite this paper as: Qiu et al. (2013) Prior infection of pigs with a recent human H3N2 influenza virus confers minimal cross-protection against a European swine H3N2 virus.
A: 1 - finding, 2 - finding, 3 - finding
****
Q: The method specifically detected S. pyogenes within 8 min from clinical specimens and can be potentially use within a point-of-care setting.
A: 1 - finding
****
Q: We evaluated if interventions aimed at air travellers can delay establishment of a SARS-CoV-2 outbreak in a previously unaffected country. Methods: For countries with no sustained SARS-CoV-2 transmission and with no shared border with affected regions we simulated arriving infected air travellers. We assessed the effectiveness of syndromic screening at departure and/or arrival & traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduce the average number of secondary cases. We report the minimal expected delay achievable in 50% (75% & 97.5%) of simulations. In the simulations we account for uncertainty in the number of secondary cases in the absence of air traveller targeted interventions and the arrival times of infected cases and also present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. Results: Under baseline assumptions exit and entry screening combined with traveller sensitisation can delay a local SARS-CoV-2 outbreak by at least 83 (75% of simulations: at least 36, 97.5% 8) days while there is no more than 1 infected traveller per week. The benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by at least 76 (75%: 33, 97.5%: 7) days. With increasing rates of infected travellers, less effective sensitisation or without screening these delays shrink rapidly to a week or less. Conclusion: Syndromic screening and traveller sensitisation in combination could delay outbreaks in yet unaffected countries and support local containment efforts, but only if infected traveller numbers are very low.
A: | 1 - background, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
****
| 4 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Input: Consider Input: Inhibition of extracellular matrix (ECM) degradation may represent a mechanism for cardiac protection against ischemia. Extracellular matrix metalloproteinase inducer (EMMPRIN) is highly expressed in response to acute myocardial infarction (AMI), and induces activation of several matrix metalloproteinases (MMPs), including gelatinases MMP-2 and MMP-9. We targeted EMMPRIN with paramagnetic/fluorescent micellar nanoparticles conjugated with the EMMPRIN binding peptide AP-9 (NAP9), or an AP-9 scrambled peptide as a negative control (NAPSC). We found that NAP9 binds to endogenous EMMPRIN in cultured HL1 myocytes and in mouse hearts subjected to ischemia/reperfusion (IR). Injection of NAP9 at the time of or one day after IR, was enough to reduce progression of myocardial cell death when compared to Control and NAPSC injected mice (infarct size in NAP9 injected mice: 32%±6.59 vs Control: 46%±9.04 or NAPSC injected mice: 48%±7.64). In the same way, cardiac parameters were recovered to almost healthy levels (LVEF NAP9 63% ± 7.24 vs Control 42% ± 4.74 or NAPSC 39% ± 6.44), whereas ECM degradation was also reduced as shown by inhibition of MMP-2 and MMP-9 activation. Cardiac magnetic resonance (CMR) scans have shown a signal enhancement in the left ventricle of NAP9 injected mice with respect to non-injected, and to mice injected with NAPSC. A positive correlation between CMR enhancement and Evans-Blue/TTC staining of infarct size was calculated (R:0.65). Taken together, these results point to EMMPRIN targeted nanoparticles as a new approach to the mitigation of ischemic/reperfusion injury.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding
Input: Consider Input: Coronavirus-like particles were identified by electronmicroscopy in the feces of homosexual men. The particles banded at a density of 1.21 g/ml after cesium chloride density gradient centrifugation. To determine whether the presence of this virus might be related to clinical symptoms, several patient groups were studied prospectively. In 8 of 16 (50%) homosexual males with acquired immunodeficiency syndrome (AIDS) or unexplained lymphadenopathy syndrome (LAS), coronavirus particles were found. In contrast, such particles were found in none of 18 heterosexual controls and in only 3 of 20 homosexual males without AIDS or LAS. Thus, coronavirus excretion correlated significantly (2c~<0.01) with the clinical diagnosis of AIDS or with syndromes belonging to the AIDS-related complex. In addition, such particles identified in the serum of one patient with LAS and diarrhea suggest invasion and systemic spread of the agent and underline that this virus behaves differently from" common cold" human coronaviruses.
Output: 1 - background, 2 - background, 3 - purpose, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding
Input: Consider Input: www.ajpmonline.org
| Output: 1 - other
| 2 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Ex Input:
An event-based model of superspreading A. James et al. 747
Ex Output:
1 - other
Ex Input:
Virus replicate inside prokaryotic and eukaryotic cells. Outside cells, they exist as independent particles (i.e. virions) generally composed of a protein shell (sometimes covered with a lipid bilayer) that contains their genetic material made of RNA or DNA. Virus genome replication and transcription are catalyzed by virally encoded polymerases. Although all these enzymes show some homology and share structural features and their catalytic mechanism, they also have important differences that reflect diverse virus replication strategies.
Ex Output:
1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding
Ex Input:
Objectives: Many patients with influenza have more than one viral agent with co-infection frequencies reported as high as 20%. The impact of respiratory virus copathogens on influenza disease is unclear. We sought to determine if respiratory virus co-infection with pandemic H1N1 altered clinical disease. Methods: Respiratory samples from 229 and 267 patients identified with and without H1N1 influenza respectively were screened for the presence of 13 seasonal respiratory viruses by multiplex RT-PCR. Disease severity between coinfected and monoinfected H1N1 patients were quantified using a standardized clinical severity scale. Influenza viral load was calculated by quantitative RT-PCR. Results: Thirty (13.1%) influenza samples screened positive for the presence of 31 viral copathogens. The most prominent copathogens included rhinovirus (61.3%), and coronaviruses (16.1%). Median clinical severity of both monoinfected and coinfected groups were 1. Patients coinfected with rhinovirus tended to have lower clinical severity (median 0), whereas non-rhinovirus co-infections had substantially higher clinical severity (median 2). No difference in H1N1 viral load was observed between coinfected and monoinfected groups. Conclusions: Respiratory viruses co-infect patients with influenza disease. Patients coinfected with rhinovirus had less severe disease while non-rhinovirus co-infections were associated with substantially higher severity without changes in influenza viral titer.
Ex Output:
| 1 - purpose, 2 - purpose, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding
| 1 | NIv2 | task352_coda-19_classification | fs_opt |
Teacher: 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.
Teacher: Now, understand the problem? If you are still confused, see the following example:
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Reason: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Now, solve this instance: Geo-social interaction patterns Geo-social scale Location-based social network Agent-based epidemic models Social network analysis Infectious disease transmission and control High performance computing A B S T R A C T Cities play an important role in fostering and amplifying the transmission of airborne diseases (e.g., influenza) because of dense human contacts. Before an outbreak of airborne diseases within a city, how to determine an appropriate containment area for effective vaccination strategies is unknown. This research treats airborne disease spreads as geo-social interaction patterns, because viruses transmit among different groups of people over geographical locations through human interactions and population movement. Previous research argued that an appropriate scale identified through human geo-social interaction patterns can provide great potential for effective vaccination. However, little work has been done to examine the effectiveness of such vaccination at large scales (e.g., city) that are characterized by spatially heterogeneous population distribution and movement. This article therefore aims to understand the impact of geo-social interaction patterns on effective vaccination in the urbanized area of Portland, Oregon. To achieve this goal, we simulate influenza transmission on a large-scale location-based social network to 1) identify human geo-social interaction patterns for designing effective vaccination strategies, and 2) and evaluate the efficacy of different vaccination strategies according to the identified geo-social patterns. The simulation results illustrate the effectiveness of vaccination strategies based on geosocial interaction patterns in containing the epidemic outbreak at the source. This research can provide evidence to inform public health approaches to determine effective scales in the design of disease control strategies.
Student: | 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - finding, 12 - finding | 2 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: www.nature.com/reviews/molcellbio
Example Output: 1 - other
Example Input: Abbreviations: B16M -B16 melanoma; ELISA -enzyme-linked immunosorbent assay; IL-18 -interleukin-18; i.p.intraperitoneal; LPS -lipopolysaccharide; MHV -Mouse Hepatitis Virus; TNF-a -tumor necrosis factor a
Example Output: 1 - finding
Example Input: The hydroalcoholic extract of Punica granatum (pomegranate) leaves was previously demonstrated to be anti-inflammatory in a rat model of lipopolysaccharide-(LPS-) induced acute peritonitis. Here, we investigated the anti-inflammatory effects of the ethyl acetate fraction obtained from the pomegranate leaf hydroalcoholic extract (EAFPg) on the LPS-induced acute lung injury (ALI) mouse model. Male Swiss mice received either EAFPg at different doses or dexamethasone (per os) prior to LPS intranasal instillation. Vehicle-treated mice were used as controls. Animals were culled at 4 h after LPS challenge, and the bronchoalveolar lavage fluid (BALF) and lung samples were collected for analysis. EAFPg and kaempferol effects on NO and cytokine production by LPS-stimulated RAW 264.7 macrophages were also investigated. Pretreatment with EAFPg (100-300 mg/kg) markedly reduced cell accumulation (specially neutrophils) and collagen deposition in the lungs of ALI mice. The same animals presented with reduced lung and BALF TNF-α and IL-1β expression in comparison with vehicle controls (p < 0 05). Additionally, incubation with either EAFPg or kaempferol (100 μg/ml) reduced NO production and cytokine gene expression in cultured LPS-treated RAW 264.7 macrophages. Overall, these results demonstrate that the prophylactic treatment with EAFPg attenuates acute lung inflammation. We suggest this fraction may be useful in treating ALI.
Example Output: | 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: Conclusions: Preliminary results show that there is significant air motion associated with a cough (on the order of 0.5 m/s) as far away as 1 m from the mouth of the healthy person who coughs. The results from this pilot study provide the framework for a more extensive participant recruitment campaign that will encompass a statisticallysignificant cohort.
Example Output: 1 - finding, 2 - finding
Example Input: The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals.
Example Output: 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Example Input: Saudi communities still lack awareness of available protective measures to prevent the transmission of the virus. It is necessary to explore the current information-seeking strategies and preferences for communication tools among the Saudi population to promote dissemination of accurate information. Guided by McGuire's Input-Output Persuasion Model and focusing on input variables (receiver characteristics, sources, message, channel and destination), we explored the current information-seeking strategies and preferences for different communication tools among residents of Riyadh (n ¼ 658). Preferred and sought-after information sources on MERS. Most participants in the sample were female (61.7%), and the majority (98.2%) had internet access at home. The internet was the most commonly used source of information (39.5%) and the most endorsed channel for a MERS awareness campaign. Physicians were the preferred source of information (45.6%), followed by other health care providers (31.3%). In univariate multinomial logistic regression models, males and individuals aged 27 years were more likely to seek information from the internet than from physicians. Residents of southern and western Riyadh preferred physicians as a credible source of information over the Ministry of Health. The results of this survey provide valuable information on how to reach this population and for understanding how to launch an effective MERS risk communication campaign in a Saudi population.
Example Output: | 1 - background, 2 - background, 3 - background, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
You will be given a definition of a task first, then an example. Follow the example to solve a new instance of the task.
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.
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Why? The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
New input: Published: xx xx xxxx opeN www.nature.com/scientificreports/
Solution: | 1 - other | 0 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Q: The hydroalcoholic extract of Punica granatum (pomegranate) leaves was previously demonstrated to be anti-inflammatory in a rat model of lipopolysaccharide-(LPS-) induced acute peritonitis. Here, we investigated the anti-inflammatory effects of the ethyl acetate fraction obtained from the pomegranate leaf hydroalcoholic extract (EAFPg) on the LPS-induced acute lung injury (ALI) mouse model. Male Swiss mice received either EAFPg at different doses or dexamethasone (per os) prior to LPS intranasal instillation. Vehicle-treated mice were used as controls. Animals were culled at 4 h after LPS challenge, and the bronchoalveolar lavage fluid (BALF) and lung samples were collected for analysis. EAFPg and kaempferol effects on NO and cytokine production by LPS-stimulated RAW 264.7 macrophages were also investigated. Pretreatment with EAFPg (100-300 mg/kg) markedly reduced cell accumulation (specially neutrophils) and collagen deposition in the lungs of ALI mice. The same animals presented with reduced lung and BALF TNF-α and IL-1β expression in comparison with vehicle controls (p < 0 05). Additionally, incubation with either EAFPg or kaempferol (100 μg/ml) reduced NO production and cytokine gene expression in cultured LPS-treated RAW 264.7 macrophages. Overall, these results demonstrate that the prophylactic treatment with EAFPg attenuates acute lung inflammation. We suggest this fraction may be useful in treating ALI.
A: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
****
Q: Quantification of physiologic defensin concentrations in vivo is complex, as defensins are present at high local concentrations within specific cell types or upon release from cells into confined anatomical niches (e.g., crypts of the small intestine) but can become diluted in extracellular fluids. For the myeloid -defensins, Daher et al. estimated ~3 mM (10 mg/ml) HNPs in neutrophils, with even higher local concentrations in the azurophilic granules in which they are stored 1 . For the enteric -defensins, Ayabe et al. estimated concentrations of ≥3.5 mM (15-100 mg/ml) in the crypt lumen, the site of Paneth cell degranulation 31 . These concentrations are likely similar in the human small intestine, where HD5 expression exceeds that of HD6 by 6-fold 32 . In healthy patients, epithelial lining fluid of the lung contains 31-79 nM HNP1-3, nasal fluid contains ~2.7 M HNP1-3, saliva contains 0.3-3 M HNP1-3, and vaginal secretions contain ~1.5 M HNPs and 0.3-14 M HD5 23; 33; 34; 35; 36; 37; 38 . For the -defensins, 5-10 nM HBD2 has been measured in nasal fluid 37; 39 . However, in certain disease states defensin levels can be highly elevated. For example, 57 M to 2.4 mM concentrations of HNP1 have been found in epithelial lining fluid of cystic fibrosis patients 36 . Overall, the concentrations of defensins present in vivo are generally within the range that is needed for direct antiviral activity by -defensins and generally below the concentrations required for direct antiviral activity by -defensins. Wilson et al.
A: 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - other
****
Q: within the receptor binding domain (RBD) of the MERS-CoV S protein. We used a complex consisting of the epitope peptide of the MERS-CoV S protein and CpG-DNA encapsulated in liposome complex to immunize mice, and produced the monoclonal antibodies 506-2G10G5 and 492-1G10E4E2. The western blotting data showed that both monoclonal antibodies detected the S protein and immunoprecipitated the native form of the S protein. Indirect immunofluorescence and confocal analysis suggested strong reactivity of the antibodies towards the S protein of MERS-CoV virus infected Vero cells. Furthermore, the 506-2G10G5 monoclonal antibody significantly reduced plaque formation in MERS-CoV infected Vero cells compared to normal mouse IgG and 492-1G10E4E2. Thus, we successfully produced a monoclonal antibody directed against the RBD domain of the S protein which could be used in the development of diagnostics and therapeutic applications in the future. [BMB Reports 2019; 52(6): 397-402] BMB Rep. 2019; 52(6): 397-402 www.bmbreports.org
A: | 1 - background, 2 - method, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - other
****
| 4 | NIv2 | task352_coda-19_classification | fs_opt |
You will be given a definition of a task first, then an example. Follow the example to solve a new instance of the task.
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.
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Why? The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
New input: This study aimed to determine the aetiology of community-acquired pneumonia (CAP) by adding polymerase chain reaction (PCR) to conventional methods and to describe the clinical and laboratory features between patients with bacterial pneumonia (BP) and viral pneumonia (VP). Adults with CAP admitted from November 2009 to October 2010 were included. Demographics, comorbidities, severity and clinical features were recorded. Conventional microbiological methods included blood and sputum cultures, acute and convalescent serologic samples, and antigen urinary detection. New methods included multiplex PCR for Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae, Bordetella pertussis and 15 respiratory viruses. A total of 169 patients were included. Using conventional methods, we identified a pathogen in 51 % of cases. With PCR, up to 70 % of cases had an aetiological diagnosis. Fortyfive patients had BP (34 %), 22 had VP (17 %) and 25 (19 %) had co-infection (BP and VP). Pneumococci and respiratory syncytial virus (RSV) were the most frequently identified pathogens. Procalcitonin (PCT) and C-reactive protein (CRP) median values were significantly higher in BP than in VP patients. Shaking chills, higher CURB score and shock were significantly more frequent in BP. A viral infection was identified in more than one-third of patients with CAP. Clinical and laboratory features could help to differentiate between VP and BP and to guide empirical therapy. A. Sangil : E. Calbo : S. Benet : M. E. Viladot : V. Pascual :
Solution: | 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding | 0 | NIv2 | task352_coda-19_classification | fs_opt |
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: European populations of free-living wildcats have been shown to be exposed to cat viruses. Luxembourg has a high degree of habitat fragmentation, and hybridisation rates between domestic cats and wildcats are high. We therefore assessed the seroprevalence of six viruses in 34 serum samples collected between 2001 and 2016 from wildcats in Luxembourg. The values for feline leukemia virus (FeLV; 52.9%) and feline coronavirus (FCoV; 47.1%) were amongst the highest reported for wildcats. We found evidence for the cumulative likelihood of exposure to FCoV affecting its seroprevalence. Routine monitoring of viral agents in this strictly protected species should be considered.
Answer: 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - finding, 6 - finding, 7 - finding
Question: M. Heiliö • M. Jabłońska-Sabuka ( )
Answer: 1 - other
Question: This study aimed to determine the aetiology of community-acquired pneumonia (CAP) by adding polymerase chain reaction (PCR) to conventional methods and to describe the clinical and laboratory features between patients with bacterial pneumonia (BP) and viral pneumonia (VP). Adults with CAP admitted from November 2009 to October 2010 were included. Demographics, comorbidities, severity and clinical features were recorded. Conventional microbiological methods included blood and sputum cultures, acute and convalescent serologic samples, and antigen urinary detection. New methods included multiplex PCR for Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae, Bordetella pertussis and 15 respiratory viruses. A total of 169 patients were included. Using conventional methods, we identified a pathogen in 51 % of cases. With PCR, up to 70 % of cases had an aetiological diagnosis. Fortyfive patients had BP (34 %), 22 had VP (17 %) and 25 (19 %) had co-infection (BP and VP). Pneumococci and respiratory syncytial virus (RSV) were the most frequently identified pathogens. Procalcitonin (PCT) and C-reactive protein (CRP) median values were significantly higher in BP than in VP patients. Shaking chills, higher CURB score and shock were significantly more frequent in BP. A viral infection was identified in more than one-third of patients with CAP. Clinical and laboratory features could help to differentiate between VP and BP and to guide empirical therapy. A. Sangil : E. Calbo : S. Benet : M. E. Viladot : V. Pascual :
Answer: | 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding
| 7 | NIv2 | task352_coda-19_classification | fs_opt |
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.
[Q]: 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.
[A]: 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
[Q]: : Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of general population from emerging and reemerging viral diseases reinforcing the arsenal of available antiviral options. Here, we reviewed discovery and development of BSAAs and summarized the information on 119 safe-in-man agents in freely accessible database. Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections.
[A]: 1 - background, 2 - background, 3 - background, 4 - method, 5 - finding, 6 - finding, 7 - finding
[Q]: A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.
[A]: | 1 - method, 2 - method, 3 - finding, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding
| 5 | NIv2 | task352_coda-19_classification | fs_opt |
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.
One example is below.
Q: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
A: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Rationale: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Q: Prism 7 software is used for statistical analysis. Student's t test was performed for twogroup analysis. Pearson's correlation coefficients were calculated. P values less than 0.05 were considered to be statistically significant.
A: | 1 - method, 2 - method, 3 - method, 4 - method | 9 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Example solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Example explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Problem: A series of etacrynic acid derivatives was synthesized and screened for their in vitro activity against Plasmodium falciparum, as well as their activity against recombinantly expressed falcipain-2 and -3. The two most active compounds of the series displayed IC 50 values of 9.0 and 18.8 μM against Plasmodia.
| Solution: 1 - method, 2 - method, 3 - finding | 5 | NIv2 | task352_coda-19_classification | fs_opt |
TASK DEFINITION: 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.
PROBLEM: The results of this study showed that simultaneous colonization of the intestinal mucosa by adherent non-ETEC E. coli and Enterococcus spp. can be involved in the pathogenesis of neonatal porcine diarrhea. These bacteria should be considered in diagnosis of diarrhea in piglets, when detection of common, well-known enteric agents is unsuccessful.
SOLUTION: 1 - finding, 2 - finding, 3 - finding
PROBLEM: Background: Respiratory protection effi ciency of facemasks is critically important in the battle against communicable respiratory infections such as infl uenza and severe acute respiratory syndrome (SARS). We studied the spatial distributions of simulated virus-laden respiratory droplets when human subjects wore facemasks and were exposed to regulatory viral droplets by conducting in vivo experiments in facemask use. Methods: Transmission pathway of aerosols of Fluorescein-KCl solution through facemasks and protective effi ciency of facemasks were examined by using normal surgical facemasks and two facemasks with exhaust valves (Facemask A) and exhaust holes (Facemask B) covered with the same surgical fi lters situated at the back of the facemasks. Fluorescein-KCl solution was sprayed onto the faces of participants wearing the facemasks and performing intermittent exercises on a treadmill in a climatic chamber. Results: Experimental results showed that when droplets spread onto a person face-to-face over short distances, 92.3% to 99.5% of droplets were blocked by the front surface of the facemask, whereas only 0.5% to 7.7% of droplets reached the back of the facemask. Both facemasks A and B had near or over 99% protection effi ciency, compared with that of 95.5% to 97% of surgical facemasks. Using the same fi lters as normal surgical masks, facemasks A and B provided more effective respiratory protection against communicable respiratory infections such as infl uenza and SARS by the location of the breathing pathway to the back of the facemasks. Conclusions: Separating the breathing pathway from the virus-contaminated area in facemasks can provide more effective protection against communicable respiratory infections such as infl uenza and SARS.
SOLUTION: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
PROBLEM: An antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) method was developed for the efficient detection of the UL24 antigen of the duck enteritis virus (DEV) using polyclonal antibodies. Ducks and rabbits were immunized, respectively, with expressed UL24 recombinant protein. The IgG antibodies against UL24 from ducks and rabbits were purified and used as the capture antibodies. The specificity of the optimized AC-ELISA was evaluated by use of DEV, duck hepatitis virus (DHV), duck hepatitis B virus (DHBV), gosling plague virus (GPV), Riemerella anatipestifer (R.A.), Escherichia coli (E. coli), Pasteurella multocida (P.M.) and Salmonella Enteritidis (S.E.). Only DEV specimens yielded a specific and strong signal. The limit of the sensitivity of this method for the detection of DEV was 46 ng/100 l. Compared with PCR and virus isolation, the rate of agreement for the detection of experimentally infected sera was 100%. A comparative test used on clinical specimens between the neutralization test and the AC-ELISA showed that the proportions of true positives and true negatives by the AC-ELISA were 0.90 and 0.67 respectively. These results indicated that the AC-ELISA approach is rapid, sensitive, and reliable for specific detection of DEV antigen.
SOLUTION: | 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding
| 8 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Example solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Example explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Problem: Genetically encoded fluorescent proteins are extensively utilized for labeling and imaging proteins, organelles, cell tissues, and whole organisms. In this study, we explored the feasibility of mRFP1 and its variants for measuring intracellular temperature. A linear relationship was observed between the temperature and fluorescence intensity of mRFP1 and its variants. Temperature sensitivities of E. coli expressing mRFP1, mRFP-P63A and mRFP-P63A[(4R)-FP] were -1.27%, -1.26% and -0.77%/°C, respectively. Finally, we demonstrated the potentiality of mRFP1 and its variants as an in vivo temperature sensor.
| Solution: 1 - background, 2 - background, 3 - purpose, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding | 5 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: Bovine respiratory disease (BRD) often occurs when active respiratory virus infections (BHV-1, etc.) impair resistance to Mannheimia haemolytica infection in the lower respiratory tract. The interactions that occur when the respiratory epithelium encounters these viral and bacterial pathogens are poorly understood. We used Agilent bovine gene microarray chips containing 44,000 transcripts to elucidate bovine bronchial epithelial cell (BBEC) responses following in vitro exposure to BHV-1 alone, M. haemolytica alone, or both BHV-1 and M. haemolytica. Microarray analysis revealed differential regulation (>2-fold) of 978 transcripts by BHV-1 alone, 2040 transcripts by M. haemolytica alone, and 2189 genes by BHV-1 and M. haemolytica in combination. M. haemolytica treatment produced significantly greater inductions (>10-fold) of several inflammation associated genes, such as CXCL2, IL-6, IL-1␣, e-selectin, and IL-8, than to BHV-1 alone. Functional analysis of the microarray data revealed a significant upregulation of genes involved in important biological processes such as inflammation (TNF-␣, IL-8, Tlr-2, IL-1, CXCL2, CSF2), vascular functions (VEGF, EDN2) and leukocyte migration (ICAM1, IL-16) during a co-infection with BHV-1 and M. haemolytica compared to either pathogen alone. This study provides evidence to support that lung epithelial cells are a source of mediators that may promote inflammatory changes observed during bovine respiratory disease.
Example Output: 1 - background, 2 - background, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding
Example Input: The role of respiratory viruses in the pathogenesis of Kawasaki disease (KD) remains controversial. In this study we showed that 8.8 % of KD patients had documented respiratory viral infections. Patients with concomitant viral infections had a higher frequency of coronary artery dilatations and were significantly more often diagnosed with incomplete KD. The presence of a concomitant viral infection should not exclude the diagnosis of KD.
Example Output: 1 - background, 2 - finding, 3 - finding, 4 - finding
Example Input: Conclusions and Clinical Importance: Results suggested that nasopharyngeal carriage of M. bovis was detrimental to health and growth of dairy calves in small herds with a high incidence of BRD.
Example Output: | 1 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example input: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Example output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Example explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Q: In the present work, a single-step purification of recombinant nucleocapsid protein (NP) of the Newcastle disease virus (NDV) directly from unclarified feedstock using an expanded bed adsorption chromatography (EBAC) was developed. Streamline 25 column (ID = 25 mm) was used as a contactor and Streamline chelating adsorbent immobilized with Ni 2+ ion was used as affinity adsorbent. The dynamic binding capacity of Ni 2+ -loaded Streamline chelating adsorbent for the NP protein in unclarified feedstock was found to be 2.94 mg ml À1 adsorbent at a superficial velocity of 200 cm h À1 . The direct purification of NP protein from unclarified feedstock using expanded bed adsorption has resulted in a 31% adsorption and 9.6% recovery of NP protein. The purity of the NP protein recovered was about 70% and the volume of processing fluid was reduced by a factor of 10. The results of the present study show that the IMA-EBAC developed could be used to combine the clarification, concentration and initial purification steps into a single-step operation.
A: | 1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding | 3 | NIv2 | task352_coda-19_classification | fs_opt |
You will be given a definition of a task first, then an example. Follow the example to solve a new instance of the task.
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.
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Why? The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
New input: 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.
Solution: | 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 | 0 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.
Example Output: 1 - background, 2 - background, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Example Input: C. Xu et al.
Example Output: 1 - other
Example Input: The limit of blanks (LoBs) of the RT-dPCR assays were ~1.6, ~1.6 and ~0.8 copies/reaction for ORF 1ab, N and E genes, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients.
Example Output: | 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Example solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Example explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Problem: Conclusions: Normal cough produced a turbulent jet about 0.7 m towards the end of the bed from the recumbent subject. N95 mask was more effective than surgical mask in preventing expelled air leakage during coughing but there was still significant sideway leakage.
| Solution: 1 - finding, 2 - finding | 5 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Q: The hydroalcoholic extract of Punica granatum (pomegranate) leaves was previously demonstrated to be anti-inflammatory in a rat model of lipopolysaccharide-(LPS-) induced acute peritonitis. Here, we investigated the anti-inflammatory effects of the ethyl acetate fraction obtained from the pomegranate leaf hydroalcoholic extract (EAFPg) on the LPS-induced acute lung injury (ALI) mouse model. Male Swiss mice received either EAFPg at different doses or dexamethasone (per os) prior to LPS intranasal instillation. Vehicle-treated mice were used as controls. Animals were culled at 4 h after LPS challenge, and the bronchoalveolar lavage fluid (BALF) and lung samples were collected for analysis. EAFPg and kaempferol effects on NO and cytokine production by LPS-stimulated RAW 264.7 macrophages were also investigated. Pretreatment with EAFPg (100-300 mg/kg) markedly reduced cell accumulation (specially neutrophils) and collagen deposition in the lungs of ALI mice. The same animals presented with reduced lung and BALF TNF-α and IL-1β expression in comparison with vehicle controls (p < 0 05). Additionally, incubation with either EAFPg or kaempferol (100 μg/ml) reduced NO production and cytokine gene expression in cultured LPS-treated RAW 264.7 macrophages. Overall, these results demonstrate that the prophylactic treatment with EAFPg attenuates acute lung inflammation. We suggest this fraction may be useful in treating ALI.
A: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
****
Q: From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/ 4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.
A: 1 - background, 2 - purpose, 3 - background, 4 - background, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding
****
Q: To optimize the preparation process of chitosan microspheres and study its loading capacity, chitosan microsphere was prepared by crosslinking with glutaraldehyde, and bovine serum albumin (BSA) was absorbed onto chitosan microsphere. Scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FITR), TA instruments and zeta potentiometer analyzer were used to characterize the parameters with respect to size, thermal characters, morphology, and zeta potential of the microspheres. The loading capability and in vitro release tests were carried out. The results showed that chitosan microsphere with particle size less than 10 μm and positively charged (+25.97±0.56 mV) can be obtained under the aldehyde group to amino group ratio at 1:1. A loading capacity of BSA at 28.63±0.15 g/100 g with corresponding loading effi ciency at 72.01±1.44% was obtained for chitosan microsphere. In vitro test revealed a burst release followed by sustained-release profi le.
A: | 1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding
****
| 4 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example input: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Example output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Example explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Q: Conclusion-ABS complicates 8% of URI in young children. Girls have more frequent ABS episodes than boys. Presence of rhinovirus and M. catarrhalis during URI are positively correlated with the risk for ABS complication.
A: | 1 - finding, 2 - finding, 3 - finding | 3 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: Glycyrrhiza glabra L. has become an endangered medicinal plant due to the unabated extraction of glycyrrhizin. Glycyrrhizin is a triterpenoid saponin that is a root centric secondary metabolite having numerous pharmacological properties, such as anti-inflammatory, immunomodulatory, antiallergic, antiulcer, and is found to be effective even against HIV. Harvesting of the roots for high value glycyrrhizin destroys the whole plant causing existential threat to the plant itself and consequent damage to biodiversity. The present study establishes that hairy root cultures of G. glabra, using an optimized elicitor, can dramatically enhance focused production of glycyrrhizin at a much faster pace year-round without causing destruction of the plant. Hairy root cultures of G. glabra were developed using the Agrobacterium rhizogenes A4 strain. The glycyrrhizin content was enhanced using different biotic and abiotic elicitors, for example, PEG (polyethylene glycol), CdCl 2 , cellulase, and mannan at different concentrations and durations. PEG at 1% concentration enhanced the yield of glycyrrhizin up to 5.4fold after 24 h of exposure, whereas 200 µg mL −1 cellulase enhanced glycyrrhizin yield to 8.6-fold after 7 days of treatment. Mannan at 10 mg L −1 concentration enhanced the production of glycyrrhizin up to 7.8-fold after 10 days of stress. Among different antioxidant enzymes, SOD activity was significantly enhanced under drought, cellulase and mannan stress. This identification of elicitors can result in abundant supply of valuable glycyrrhizin to meet broad spectrum demand through commercial production without endangering G. glabra L.
Example Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - purpose, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding
Example Input: Fig. 6. Input mzML/mzXML les were processed with OpenMS 34 and low-quality MS/MS spectra .
Example Output: 1 - method, 2 - other
Example Input: Conclusion-ABS complicates 8% of URI in young children. Girls have more frequent ABS episodes than boys. Presence of rhinovirus and M. catarrhalis during URI are positively correlated with the risk for ABS complication.
Example Output: | 1 - finding, 2 - finding, 3 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
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.
One example is below.
Q: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
A: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Rationale: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Q: FilmArray Respiratory Panel (RP) (Idaho Technology, Inc., Salt Lake City, UT, USA) performance was retrospectively evaluated in respiratory samples collected from neonates in 2 reference neonatology units. Using the FilmArray RP assay, 121/152 (79.6%) samples were positive for at least 1 respiratory virus, while 31/ 152 (20.4%) were negative. FilmArray RP results were concordant in 68/72 (94.4%) respiratory samples tested with laboratory-developed real-time PCR assays, while in 4/72 (5.6%) samples, the FilmArray RP assay detected an additional virus (2 human rhinovirus/enterovirus and 2 bocavirus). In addition, FilmArray RP results for 70 of 80 (87.5%) respiratory samples tested were concordant with the Seegene Seeplex RV15® detection assay (Seegene, Inc., Seoul, South Korea), while 10/80 (12.5%) were discordant. The advantages of the FilmArray RP are the rapid detection of respiratory viruses (1 hour), the wide number of pathogens detectable in a single assay, and the reduced hands-on time.
A: | 1 - method, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding | 9 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Q: Mycoplasma haemofelis" and "Candidatus Mycoplasma turicensis" are feline hemoplasmas that induce hemolytic anemia. Protection from homologous re-challenge was recently demonstrated in cats recovered from primary infection. Here, we determined if cats recovered from "Cand. M. turicensis" infection were protected against infections with the more pathogenic M. haemofelis. Ten specified pathogen-free cats were exposed to M. haemofelis. Five of the ten cats had recovered from "Cand. M. turicensis" bacteremia (group A), and five cats were naïve controls (group B). No cross-protection was observed. By contrast, the "Cand. M. turicensis"-recovered cats displayed faster M. haemofelis infection onset (earlier PCR-positive and anemic) than the controls. No "Cand. M. turicensis" was detected in any cat. M. haemofelis shedding was observed in saliva, feces and urine. In both groups, evidence of a Th1 response was observed (high IFN-γ, low IL-4), but IL-10 levels were also high. In group A, total, CD4+ and CD8+ T cells increased within days after M. haemofelis exposure. At times of maximal bacteremia, macrocytic hypochromic anemia, neutropenia, monocytosis and a decrease in leukocyte, eosinophil, and lymphocyte counts and subsets thereof (B-and T-cells, CD4+, CD8+ and CD4+CD25+ cells) were particularly significant in group A. Moreover, an increase in protein concentrations, hypoalbuminemia and a polyclonal hypergammaglobulinemia were observed. Five of ten M. haemofelis-infected cats subsequently cleared bacteremia without antibiotic treatment. In conclusion, the study suggests that a previous hemoplasma infection, even when the cat has ostensibly recovered, may influence subsequent infections, lead to an enhancement phenomenon and other differences in infection kinetics.
A: 1 - background, 2 - background, 3 - purpose, 4 - background, 5 - method, 6 - method, 7 - method, 8 - method, 9 - background, 10 - finding, 11 - finding, 12 - background, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding, 27 - finding, 28 - finding
****
Q: Hepatocytes are key effector cells in anti-Coxsackievirus immunity PLOS Pathogens.
A: 1 - other
****
Q: This study investigates and compares the virucidal performances of photocatalytic (PC) and photoelectrocatalytic (PEC) treatments in the presence and absence of halides, such as Br À and Cl À , under comparable experimental conditions. The results confirm that the PC virucidal efficiency can be enhanced in the presence of low halide concentrations (e.g., X = Br À or Cl À ) and further enhanced by applying potential bias onto the photoanode in a PEC system. The PEC treatment in the presence of 1.0 mM Br (PEC-Br) shows the highest virucidal efficiency, enabling complete inactivation of a $1000 TCID50 replication-deficient recombinant adenovirus (RDRADS) population within 31.7 s. The superior virucidal performances of PEC-X treatments can be attributed to the increased production of active oxygen species and additional viricides resulting from the PEC halide oxidation, as well as prolonged lifetime of photoholes (h + ) for direct inactivation. The findings of this work confirm that new forms of active species generated in situ via a PC or PEC process are effective for viruses.
A: | 1 - purpose, 2 - purpose, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding
****
| 4 | NIv2 | task352_coda-19_classification | fs_opt |
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.
One example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution is here: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Now, solve this: The estimated costs and TAT were 8.2€ and 2 h for DFA, 31.8€ and 1.5 h for Simplexa™ and 55€ and 3 h for TAC testing. Conclusions: Performing the Simplexa™ test 24 h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly.
Solution: | 1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding | 6 | NIv2 | task352_coda-19_classification | fs_opt |
Teacher: 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.
Teacher: Now, understand the problem? If you are still confused, see the following example:
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Reason: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Now, solve this instance: She was treated successfully with a corticosteroid and anti-mycobacterial therapy. Our observations suggest that pulmonary M. abscessus infection should be added to the list of infectious conditions associated with OP.
Student: | 1 - finding, 2 - finding | 2 | NIv2 | task352_coda-19_classification | fs_opt |
Given the task definition, example input & output, solve the new input case.
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.
Example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
New input case for you: Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. Based on that and using an in silico approach, we evaluated SARS-CoV-2 main protease as a target for HIV-1 protease inhibitors to reveal the structural features related to their antiviral effect. Our results showed that several HIV inhibitors such as lopinavir, ritonavir, and saquinavir produce strong interaction with the active site of SARS-CoV-2 main protease. Furthermore, broad library protease inhibitors obtained from PubChem and ZINC (www.zinc.docking.org) were evaluated. Our analysis revealed 20 compounds that could be clustered into three groups based on their chemical features. Then, these structures could serve as leading compounds to develop a series of derivatives optimizing their activity against SARS-CoV-2 and other coronaviruses. Altogether, the results presented in this work contribute to gain a deep understanding of the molecular pharmacology of SARS-CoV-2 treatment and validate the use of protease inhibitors against SARS-CoV-2.
Output: | 1 - background, 2 - background, 3 - background, 4 - background, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding | 1 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Let me give you an example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
The answer to this example can be: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Here is why: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
OK. solve this:
After 3-day acclimation, pigs in the challenged group were inoculated with a prototype US PEDV isolate US/Iowa/18984/ 2013 (GenBank accession #KF804028) (Hoang et al., 2013), 10 3 plaque-forming units/pig, via oro-gastric gavage as previously described (Madson et al., 2014). Pigs in the control group received virus-free cell culture media. Some of these pigs were inoculated again with the same strain in the identical manner at day 56 post-inoculation (PI).
Answer: | 1 - finding, 2 - finding, 3 - finding, 4 - finding | 8 | NIv2 | task352_coda-19_classification | fs_opt |
Detailed Instructions: 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.
See one example below:
Problem: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Problem: Journal of Infection (2012) 64, 96e103 sampled elderly (>65 years, 3.2%) than in middle aged adults (25e65 years; 2.0%) and teenagers (14e25 years; 0.9%). During the study period, hMPV infections showed a biennial rhythm of seasonality, peaking from
Solution: | 1 - background, 2 - background, 3 - finding | 4 | NIv2 | task352_coda-19_classification | fs_opt |
Part 1. Definition
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.
Part 2. Example
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Answer: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Part 3. Exercise
An event-based model of superspreading A. James et al. 747
Answer: | 1 - other | 7 | NIv2 | task352_coda-19_classification | fs_opt |
TASK DEFINITION: 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.
PROBLEM: A 1520 bp region of Cochlosoma anatis mtDNA 16S gene was subjected to DNA sequencing and a 466 bp portion was compared with other protozoan 16S sequences to develop PCR primers specific for C. anatis. This PCR diagnostic method allowed identification of C. anatis from house flies, Musca domestica L., turkey gut, and fecal samples within 6 h after fieldcollected samples reached the laboratory. House flies detected carrying C. anatis using the diagnostic 374 bp amplicons represented the first record of this protozoan in house flies. #
SOLUTION: 1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - other
PROBLEM: The method specifically detected S. pyogenes within 8 min from clinical specimens and can be potentially use within a point-of-care setting.
SOLUTION: 1 - finding
PROBLEM: Journal of Infection (2012) 64, 96e103 sampled elderly (>65 years, 3.2%) than in middle aged adults (25e65 years; 2.0%) and teenagers (14e25 years; 0.9%). During the study period, hMPV infections showed a biennial rhythm of seasonality, peaking from
SOLUTION: | 1 - background, 2 - background, 3 - finding
| 8 | NIv2 | task352_coda-19_classification | fs_opt |
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.
[EX Q]: Immunization with different EV types allowed to produce a variety of monoclonal antibodies (MAbs) that are either type-specific (i.e., responsible of virus neutralization) or directed to conserved regions of capsid proteins 15-18 . Reactivity of the latter antibodies may be limited to sets of different EV types or may be directed to a wider range of EV types. Though molecular methods are held to be more informative than classical serologic methods for virus identification 19 , "pan-EV antibodies" capable of reacting with all or with the majority of EV types remain desirable reagents for detecting these agents both in the diagnosis of infectious diseases 20-23 and in immunohistochemistry 24 .
[EX A]: 1 - finding, 2 - finding, 3 - finding, 4 - finding
[EX Q]: Acute respiratory distress syndrome (28.36%), acute cardiac injury (7.89%) and acute kidney 35 injury (7.60%) were the most common complications recorded. 36 37 Conclusions: Clinical and epidemiological characteristics of COVID-19 patients were mostly 38 heterogeneous and non-specific. This is the most comprehensive report of the characteristics of 39
[EX A]: 1 - finding, 2 - finding, 3 - finding, 4 - finding
[EX Q]: Abbreviations: B16M -B16 melanoma; ELISA -enzyme-linked immunosorbent assay; IL-18 -interleukin-18; i.p.intraperitoneal; LPS -lipopolysaccharide; MHV -Mouse Hepatitis Virus; TNF-a -tumor necrosis factor a
[EX A]: | 1 - finding
| 6 | NIv2 | task352_coda-19_classification | fs_opt |
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.
[EX Q]: Purpose Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. Methodology Published sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between coinfection and disease outcome was assessed using logistic regression. Results The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients
[EX A]: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding
[EX Q]: This study investigates and compares the virucidal performances of photocatalytic (PC) and photoelectrocatalytic (PEC) treatments in the presence and absence of halides, such as Br À and Cl À , under comparable experimental conditions. The results confirm that the PC virucidal efficiency can be enhanced in the presence of low halide concentrations (e.g., X = Br À or Cl À ) and further enhanced by applying potential bias onto the photoanode in a PEC system. The PEC treatment in the presence of 1.0 mM Br (PEC-Br) shows the highest virucidal efficiency, enabling complete inactivation of a $1000 TCID50 replication-deficient recombinant adenovirus (RDRADS) population within 31.7 s. The superior virucidal performances of PEC-X treatments can be attributed to the increased production of active oxygen species and additional viricides resulting from the PEC halide oxidation, as well as prolonged lifetime of photoholes (h + ) for direct inactivation. The findings of this work confirm that new forms of active species generated in situ via a PC or PEC process are effective for viruses.
[EX A]: 1 - purpose, 2 - purpose, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding
[EX Q]: The aim in this study was to assess the effectiveness of a quaternary ammonium chloride (QAC) surfactant in reducing surface staphylococcal contamination in a routinely operating medical ward occupied by patients who had tested positive for methicillin-resistant Staphylococcus aureus (MRSA). The QAC being tested is an antibacterial film that is sprayed onto a surface and can remain active for up to 8 h. A field experimental study was designed with the QAC plus daily hypochlorite cleaning as the experimental group and hypochlorite cleaning alone as the control group. The method of swabbing on moistened surfaces was used for sampling. It was found that 83% and 77% of the bedside surfaces of MRSA-positive and MRSA-negative patients respectively were contaminated with staphylococci at 08:00 hours, and that the staphylococcal concentrations increased by 80% at 1200 h over a 4-hour period with routine ward and clinical activities. Irrespective of the MRSA status of the patients, high-touch surfaces around the bed-units within the studied medical ward were heavily contaminated (ranged 1 to 276 cfu/cm 2 amongst the sites with OPEN ACCESS Int. J. Environ. Res. Public Health 2015, 12 3027 positive culture) with staphylococcal bacteria including MRSA, despite the implementation of daily hypochlorite wiping. However, the contamination rate dropped significantly from 78% to 11% after the application of the QAC polymer. In the experimental group, the mean staphylococcal concentration of bedside surfaces was significantly (p < 0.0001) reduced from 4.4 ± 8.7 cfu/cm 2 at 08:00 hours to 0.07 ± 0.26 cfu/cm 2 at 12:00 hours by the QAC polymer. The results of this study support the view that, in addition to hypochlorite wiping, the tested QAC surfactant is a potential environmental decontamination strategy for preventing the transmission of clinically important pathogens in medical wards.
[EX A]: | 1 - purpose, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - other, 10 - other, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding
| 6 | NIv2 | task352_coda-19_classification | fs_opt |
Given the task definition, example input & output, solve the new input case.
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.
Example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
New input case for you: Background: Hand hygiene is crucial for safe healthcare. Although the use of alcohol hand rubs is encouraged in clinics, there are few studies that focus on the proper use of alcohol hand rubs among nursing students. Objectives: The aim of this study is to evaluate the effectiveness of alcohol-based hand rub application and proper hand washing techniques which influence nursing students' hand hygiene compliance to make recommendations for future practice of hand hygiene training. Design: This cross-sectional study was carried out from May 3/June 3 2016 with the participation of 257 nursing students. Their hand hygiene techniques were analyzed using a UV lamp and an alcohol-based mix marked with fluorescence. Results: Of the participants, 77.0% were first-year students and 55.3% were males. The percentage of skin surface covered by alcohol-based hand rub was 82.0% on both hands. The lowest percentages of skin area covered by fluorescent-labelled hand rub were identified in the metacarpal area near the wrist and thumbs. While there was a difference between points for using proper hand-rub technique on the dorsal and palmar surfaces of the hands (p < 0.01), no difference was determined between the right and left hands (p > 0.05). It was found that the largest fluorescent remains were on fingers after hand-washing, and there was a difference in terms of hand-washing points between right-left hands and dorsal-palmar surfaces (p < 0.01). Conclusions: There is a need to improve nursing students' compliance with hand hygiene. It is suggested that the use of hand-rub among students should be popularized, and new techniques that prevent the frequently omitted areas of the hands should be integrated into the curriculum.
Output: | 1 - background, 2 - background, 3 - background, 4 - purpose, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding | 1 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Input: Consider Input: Background: Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat. Next generation sequencing (NGS) helps us to identify viruses without the design of a specific PCR primer. The major task in NGS data analysis is taxonomic identification for vast numbers of sequences. However, taxonomic identification via a BLAST search against all the known sequences is a computational bottleneck. Description: Here we propose an enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data. To reduce the computational cost, ELM uses a customized database composed only of viral sequences for the BLAST search. At the same time, ELM adopts a novel criterion to suppress the rise in false positive assignments caused by the small database. As a result, identification by ELM is more than 1,000 times faster than the conventional methods without loss of accuracy. Conclusions: We anticipate that ELM will contribute to direct diagnosis of viral infections. The web server and the customized viral database are freely available.
Output: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding
Input: Consider Input: Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.
Output: 1 - background, 2 - background, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Input: Consider Input: Homogenates obtained by a Dounce homogeniser of oligodendrocyte and whole brain from 2-day-old rats were suspended in Published by Elsevier Science Publishers B. V.
| Output: 1 - method
| 2 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: 0 1992 Academic PVE.S. Inc.
Example Output: 1 - other, 2 - other
Example Input: The copyright holder for this preprint (which was not peer-reviewed) is . 1101 updating the predictions with the use of fresh data and using more complicated mathematical models.
Example Output: 1 - other, 2 - other, 3 - other
Example Input: Design, synthesis and biological evaluation of a series of 5-chloropyridine ester-derived severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors is described. Position of the carboxylate functionality is critical to potency. Inhibitor 10 with a 5-chloropyridinyl ester at position 4 of the indole ring is the most potent inhibitor with a SARS 3Clpro IC 50 value of 30 nM and antiviral EC 50 value of 6.9 μM. Molecular Docking studies have provided possible binding modes of these inhibitors.
Example Output: | 1 - background, 2 - background, 3 - background, 4 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
Teacher: 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.
Teacher: Now, understand the problem? If you are still confused, see the following example:
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Reason: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Now, solve this instance: In particular, 63% (12 of 19) of fecal samples from Miniopterus pusillus were positive for the virus. These findings suggest that this virus might be commonly circulating in M. pusillus in Hong Kong.
Student: | 1 - finding, 2 - finding | 2 | NIv2 | task352_coda-19_classification | fs_opt |
You will be given a definition of a task first, then an example. Follow the example to solve a new instance of the task.
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.
In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Why? The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
New input: Wedzicha JA: Respiratory syncytial virus, airway inflammation, and FEV1 decline in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2006, 173:871-876. This paper demonstrated that persistent respiratory syncytial virus infection could contribute to the progression of COPD severity. Models of infection and exacerbations in COPD Papi et al. 263 www.sciencedirect.com
Solution: | 1 - background, 2 - background, 3 - other, 4 - finding, 5 - other | 0 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Conclusion-ABS complicates 8% of URI in young children. Girls have more frequent ABS episodes than boys. Presence of rhinovirus and M. catarrhalis during URI are positively correlated with the risk for ABS complication.
1 - finding, 2 - finding, 3 - finding
Acute otitis media (AOM) is an inflammatory response to microbes in the middle ear, sometimes associated with rupture of the tympanic membrane. Human leukocytes produce different patterns of inflammatory mediators in vitro when stimulated with Gram-positive and Gram-negative bacteria, respectively. Here, we investigated the cytokine and prostaglandin E 2 (PGE 2 ) responses in middle ear fluids (MEFs) from children with spontaneously perforated AOM, and related the mediator levels to the presence of pathogens detected by culture (live) or PCR (live or dead). Furthermore, the in vivo cytokine pattern was compared with that induced in leukocytes stimulated by dead bacteria in vitro. MEFs with culturable pathogenic bacteria contained more interleukin (IL)-1b (median: 110 lg/L vs. <7.5 lg/L), tumour necrosis factor (TNF) (6.3 lg/L vs. <2.5 lg/L), IL-8 (410 lg/L vs. 38 lg/L) and IL-10 (0.48 lg/L vs. <0.30 lg/L) than culture-negative fluids, irrespective of PCR findings. IL-6 and PGE 2 were equally abundant (69-110 lg/L) in effusions with live, dead or undetectable bacteria. Cytokine levels were unrelated to bacterial species and to the presence or absence of virus. Similar levels of TNF and IL-6 as found in the MEFs were obtained by in vitro stimulation of leukocytes, whereas 11 times more IL-1b and 3.5 times more IL-8 were produced in vivo, and 22 times more IL-10 was produced in vitro. Vigorous production of proinflammatory cytokines accompanies AOM with membrane rupture, regardless of the causative agent, but the production seems to cease rapidly once the bacteria are killed and fragmented. IL-6 and PGE 2 , however, remain after bacterial disintegration, and may play a role in the resolution phase.
1 - background, 2 - background, 3 - background, 4 - purpose, 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, 18 - finding, 19 - finding
A total of 123 community paediatricians and 23 microbiology laboratories studied the clinical and bacteriological efficacy of treatment of group A streptococcal pharyngitis in Italy. Of 1065 patients, from whom Streptococcus pyogenes was isolated, 723 returned to follow up and of these 138 (19%) still had a positive throat culture. The erythromycin resistance (ER) rate was 23.7% with resistance phenotype distribution of: 31.7% constitutive (CR), 26.6% inducible (IR) and 41.7% efflux pump (M) resistance phenotype. All strains were susceptible to the b-lactam agents tested. CR strains were highly resistant to all 14, 15 and 16 membered macrolides with the exception of rokitamycin which showed activity against 37.8% of isolates. All phenotype M and some IR isolates were susceptible to clindamycin, rokitamycin, josamycin and spiramycin; clarithromycin was active against a small percentage of strains belonging to the IR and M phenotype. Bacterial eradication was found in 85.5, 78.7 and 75.8% of the penicillin, macrolide and cephalosporin treated groups. Genotyping of strains showed that 8.7% of the 19% of cases classified as 'failed bacterial eradication' were due to recolonization with a different isolate, observed exclusively among b-lactams treated patients. Clinical cure was achieved in a high percentage of cases, irrespective of the antibiotic prescribed, with the best clinical efficacy being found following therapy with amoxycillin and clarithromycin (90.9%).
| 1 - method, 2 - method, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding
| 0 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Input: Consider Input: Objectives: Many patients with influenza have more than one viral agent with co-infection frequencies reported as high as 20%. The impact of respiratory virus copathogens on influenza disease is unclear. We sought to determine if respiratory virus co-infection with pandemic H1N1 altered clinical disease. Methods: Respiratory samples from 229 and 267 patients identified with and without H1N1 influenza respectively were screened for the presence of 13 seasonal respiratory viruses by multiplex RT-PCR. Disease severity between coinfected and monoinfected H1N1 patients were quantified using a standardized clinical severity scale. Influenza viral load was calculated by quantitative RT-PCR. Results: Thirty (13.1%) influenza samples screened positive for the presence of 31 viral copathogens. The most prominent copathogens included rhinovirus (61.3%), and coronaviruses (16.1%). Median clinical severity of both monoinfected and coinfected groups were 1. Patients coinfected with rhinovirus tended to have lower clinical severity (median 0), whereas non-rhinovirus co-infections had substantially higher clinical severity (median 2). No difference in H1N1 viral load was observed between coinfected and monoinfected groups. Conclusions: Respiratory viruses co-infect patients with influenza disease. Patients coinfected with rhinovirus had less severe disease while non-rhinovirus co-infections were associated with substantially higher severity without changes in influenza viral titer.
Output: 1 - purpose, 2 - purpose, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding
Input: Consider Input: A capsid protein of porcine circovirus 2 (PCV 2) serves as a diagnostic antigen for the detection of PCV 2-associated disease known as a postweaning multisystemic wasting syndrome (PMWS). In this report, a bacterial expression system was developed for the expression and purification of the full-length PCV 2 capsid (Cap) protein from a codon-optimized cap gene. Replacement of rare arginine codons located at the 5 end of the cap reading frame with codons optimal for E. coli was found to overcome the poor expression of the viral protein in the prokaryotic system. The Cap protein was purified to greater than 95% homogeneity by using a single cation-exchange chromatography at a yield of 10 mg per litre of bacterial culture. Despite the failure of the E. coli-expressed Cap protein to self-assemble into virus-like particles (VLPs), the immunization of mice with recombinant Cap yielded antibodies with the same specificity as those raised against native PCV 2 virions. In addition, the antigenic properties of the purified Cap protein were employed in a subunit-based indirect ELISA to monitor the levels of PCV 2 specific antibodies in piglets originating from a herd which was experiencing PCV 2 infection. These results pave the way for a straightforward large-scale production of the recombinant PCV 2 capsid protein and its use as a diagnostic antigen or a PCV 2 subunit vaccine.
Output: 1 - background, 2 - method, 3 - finding, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding
Input: Consider Input: Cooperative interactions play a central role in the regulation of protein functions. Here we show that in multi-site systems like ion channels the application of the Hill formalism could require a combination of different experiments, even involving site-directed mutagenesis, to identify the different sources of cooperativity and to discriminate between genuine and apparent cooperativity. We discuss the implications for the channel function in the bacterial porins PorA (N. meningitidis) and OmpF (E. coli ) and the viroporin SARS-CoV E.
| Output: 1 - background, 2 - finding, 3 - finding, 4 - finding
| 2 | NIv2 | task352_coda-19_classification | fs_opt |
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.
One example: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
Solution is here: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Explanation: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Now, solve this: Bordetella bronchiseptica isolate KM22 has been used in experimental infections of swine as a model of clinical B. bronchiseptica infection and to study host-to-host transmission. The draft genome sequence of KM22 was reported in 2014. Here, we report the complete genome sequence of KM22.
Solution: | 1 - background, 2 - background, 3 - purpose | 6 | NIv2 | task352_coda-19_classification | fs_opt |
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: Public Health jo urnal homepage: www .e lse vi er.co m/ pu he p u b l i c h e a l t h 1 5 0 ( 2 0 1 7 ) 1 4 9 e1 5 1.
Answer: 1 - other, 2 - other
Question: A multiplex quantitative real-time polymerase chain reaction (mqPCR) assay was developed and validated for the detection and differentiation of porcine circovirus type 3 (PCV3) and type 2 (PCV2) strains. The assay coverage was 97.9% (184/188) for PCV3 and 99.1% (1889/1907) for PCV2 sequences that were available from the current GenBank database. The PCR amplification efficiencies were 98-99% for plasmids, and 92-96% for diagnostic samples, with correlation coefficients all greater than 0.99. The limit of detection (LOD) determined as plasmid copies per reaction was 17 for PCV3 and 14 for PCV2. The assay specifically detected the targeted viruses without cross reacting to each other or to other common porcine viruses. Among 336 swine clinical samples collected in 2018, 101 (30.1%) were PCV3 positive, 56 (16.7%) were PCV2 positive and 18 (5.4%) were co-positives. Sixty selected PCV3 positives were confirmed by Sanger sequencing, and 53 of the 56 PCV2 positive samples were tested positive by another validated PCR assay.
Answer: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding
Question: Statistics. Statistical analyses were conducted using SPSS software (version 20 SPSS, Inc., Chicago, IL). For normally distributed variables, Student's t-test and one-way ANOVA were used for comparisons, and the data are presented as the mean ± SE. The Mann-Whitney U and Kruskal-Wallis tests were used for comparisons of variables that were not normally distributed. Correlations were assessed with Pearson's correlation coefficient for parametric distributions. Statistical significance was set at P < 0.05.
Answer: | 1 - method, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding
| 7 | NIv2 | task352_coda-19_classification | fs_opt |
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.
One example is below.
Q: In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.
A: 1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose
Rationale: The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study.
Q: The spike protein of Porcine epidemic diarrhea virus is the main surface glycoprotein involved in virus attachment and entry and therefore is the target of neutralizing antibodies. Here, the immunogenicity of a novel antigenic domain found on the carboxy-terminal of the spike protein characterized by the peptide motif GPRLQPY, was evaluated. A synthetic peptide whose linear sequence is identical to the 24 a.a. carboxy-terminal portion of the spike protein (S-CT24) elicited a strong antibody response in BALB/c mice that had specific reactivity against the S-CT24 and PEDV. These antibodies were shown to have a specific affinity to the GPRLQPY motif, as demonstrated by non-reactivity with a peptide that lacks this motif. In addition, antiS-CT24 antibodies exhibited neutralizing activities against KPEDV-9 in focus reduction neutralization tests suggesting that the GPRLQPY motif induces neutralizing antibodies against PEDV.
A: | 1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding | 9 | NIv2 | task352_coda-19_classification | fs_opt |
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.
Example Input: Purpose Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. Methodology Published sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between coinfection and disease outcome was assessed using logistic regression. Results The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients
Example Output: 1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding
Example Input: Prism 7 software is used for statistical analysis. Student's t test was performed for twogroup analysis. Pearson's correlation coefficients were calculated. P values less than 0.05 were considered to be statistically significant.
Example Output: 1 - method, 2 - method, 3 - method, 4 - method
Example Input: The spike protein of Porcine epidemic diarrhea virus is the main surface glycoprotein involved in virus attachment and entry and therefore is the target of neutralizing antibodies. Here, the immunogenicity of a novel antigenic domain found on the carboxy-terminal of the spike protein characterized by the peptide motif GPRLQPY, was evaluated. A synthetic peptide whose linear sequence is identical to the 24 a.a. carboxy-terminal portion of the spike protein (S-CT24) elicited a strong antibody response in BALB/c mice that had specific reactivity against the S-CT24 and PEDV. These antibodies were shown to have a specific affinity to the GPRLQPY motif, as demonstrated by non-reactivity with a peptide that lacks this motif. In addition, antiS-CT24 antibodies exhibited neutralizing activities against KPEDV-9 in focus reduction neutralization tests suggesting that the GPRLQPY motif induces neutralizing antibodies against PEDV.
Example Output: | 1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding
| 3 | NIv2 | task352_coda-19_classification | fs_opt |
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