xingqiang/medical-entity-qa-data · Datasets at Hugging Face

instruction stringclasses 27 values	input stringclasses 694 values	output stringlengths 27 1.26k	system stringclasses 1 value	qa_type stringclasses 8 values
What diseases are mentioned in the text?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: Lyme arthritis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What pathological states are described?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: Lyme disease, erythema migrans, arthritis, neuroborreliosis, and carditis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the viruses referenced in this text.	Please analyze the following medical literature and extract entities and relationships:	The virus mentioned is: Rabies virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
Identify the bacterial organisms referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacteria mentioned is: Clostridium tetani	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
List all medical conditions discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: rabies, hydrophobia, and viral encephalitis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What pathogens (viruses, bacteria, fungi, parasites) are mentioned?	Please analyze the following medical literature and extract entities and relationships:	The pathogens mentioned are: Parasite: Taenia solium	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
How are the entities in this text related?	Please analyze the following medical literature and extract entities and relationships:	The relationships are: - Human T-lymphotropic virus has relationship adult T-cell leukemia	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
Identify the parasites referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The parasite mentioned is: Trichinella spiralis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
What diseases are mentioned in the text?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: bubonic plague	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
How many distinct pathogens are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	There are 8 virus(es) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
What is the relationship between the pathogens and diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - EV71 causes hand foot and mouth disease - EV71 causes aseptic meningitis - EV71 is a Enterovirus 71	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What bacteria are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacterias mentioned are: Escherichia coli O157:H7, enterohemorrhagic E. coli, and EHEC	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
Identify the parasites referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The parasites mentioned are: Trypanosoma cruzi, triatomine bugs, and T. cruzi	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
What is the relationship between the pathogens and diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - Trypanosoma cruzi causes Chagas disease - Chagas disease is a American trypanosomiasis - Trypanosoma cruzi causes acute infection - acute infection causes mild symptoms - acute infection causes fever - acute infection causes chronic cardiomyopathy - chronic cardiomyopathy causes heart failure - chronic cardiomyopathy causes arrhythmias - chronic cardiomyopathy causes sudden cardiac death - T. cruzi is a Trypanosoma cruzi - TcII associated with severe chronic cardiac manifestations - TcVI associated with severe chronic cardiac manifestations	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What pathological states are described?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: cryoglobulinemia	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the viruses referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The virus mentioned is: Marburg virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What parasites are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The parasites mentioned are: Toxoplasma gondii, and T. gondii	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
List all medical conditions discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: tuberculosis, TB, pulmonary tuberculosis, granulomatous inflammation, caseous necrosis, and human tuberculosis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What pathological states are described?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: hydatid disease	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
How many diseases are referenced in this passage?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	There are 5 disease(s) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The disease mentioned is: meningoencephalitis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
List all medical conditions discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: meningoencephalitis, and HIV/AIDS	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the diseases and conditions referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The disease mentioned is: bronchitis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What viruses are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The virus mentioned is: Influenza A virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What pathogens (viruses, bacteria, fungi, parasites) are mentioned?	Please analyze the following medical literature and extract entities and relationships:	The pathogens mentioned are: Fungus: Aspergillus fumigatus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
Which viruses are associated with the diseases mentioned?	Please analyze the following medical literature and extract entities and relationships:	The virus mentioned is: Human T-lymphotropic virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What pathogens (viruses, bacteria, fungi, parasites) are mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The pathogens mentioned are: Parasite: Trypanosoma cruzi, triatomine bugs, reduviid bugs, T. cruzi, TcII, TcVI	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
What pathological states are described?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: diphtheria	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the parasites referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The parasite mentioned is: Trypanosoma cruzi	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
Identify the diseases and conditions referenced in this text.	Spontaneous inflammatory bowel disease in multiple mutant mouse lines: association with colonization by Helicobacter hepaticus. BACKGROUND: Both genetic and microbial factors are thought to play a role in the development of inflammatory bowel disease (IBD): however, no causative microbial agent has been clearly defined for humans or animals. Normal flora or previously unrecognized intestinal pathogens may contribute to the development of disease in susceptible hosts. A newly recognized murine Helicobacter, H. hepaticus, causes hepatitis in mice and in one strain of mice is linked to liver cancer. This study investigates the association between colonization of the lower intestinal tract of multiple genetically altered lines of mice with H. hepaticus, and the occurrence of IBD.MATERIALS AND METHODS: Rectal prolapse noted clinically in multiple genetically altered mouse lines was evaluated for the presence of H. hepaticus and histologic evidence of IBD. Fifty-five mice representing 11 different genetic alterations were evaluated.RESULTS: H. hepaticus was detected in 85% of mutant mice with rectal prolapse. Histologic evidence of proliferative typhlitis, colitis or proctitis was present in 65% of the animals examined, 89% of which were positive for H. hepaticus as detected by species specific PCR.CONCLUSION: The presence of H. hepaticus in association with IBD in multiple lines of genetically altered mice suggests further studies are needed to test experimentally the role H. hepaticus plays in the development of IBD in susceptible mice. Additionally, specific mutant mouse lines infected with H. hepaticus in this study may provide additional models for elucidation of microbial and genetic factors in the pathogenesis of IBD.	The disease mentioned is: inflammatory bowel disease	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
List all parasitic organisms discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The parasites mentioned are: Schistosoma mansoni, freshwater snails, Biomphalaria, humans, and cercariae	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
Count the number of viruses mentioned.	Please analyze the following medical literature and extract entities and relationships:	There are 1 virus(es) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
List all viral pathogens discussed in this passage.	Please analyze the following medical literature and extract entities and relationships:	The virus mentioned is: Hepatitis C virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What pathological states are described?	The Global Epidemiology of Scleritis: A Systematic Review and Meta-analysis. Purpose: Scleritis, a severe inflammatory condition of the sclera, causes significant ocular pain and potential tissue damage. Often linked with systemic diseases, scleritis can be either infectious or noninfectious. Despite its clinical importance, the global incidence and detailed epidemiology of scleritis are poorly understood due to its heterogeneity and rarity. This systematic review and meta-analysis aim to elucidate the worldwide incidence and epidemiological trends of scleritis, examining variations across geographic regions, etiologies, and time periods. Design: Systematic Review and Meta-analysis. Clinical relevance: Understanding scleritis epidemiology is crucial for enhancing diagnostic accuracy and treatment, especially concerning systemic illnesses commonly associated with this condition. Identifying epidemiological trends can inform healthcare policies and resource allocation, improving patient outcomes. Methods: We systematically reviewed literature across databases, including Embase, PubMed, Virtual Health Library, The Cochrane Library, and medRxiv. Population-based, cohort, case-control, cross-sectional, and claims database studies reporting the frequency, prevalence, or incidence of scleritis diagnosed through clinical or imaging techniques, were included. The screening was based on titles and abstracts, followed by a full-text review. We assessed the risk of bias using standardized tools and systematically extracted data for qualitative and quantitative synthesis. This review is registered with PROSPERO (CRD42022330948). Results: This review included 74 studies with 169,871 scleritis patients. The incidence was 2.67 per 100,000 in ophthalmological centers and 1.38 per 100,000 in broader population-based studies, both showing a decreasing trend over time. The patient population was predominantly female (67.24%), with an average age of 48.3 years. Epidemiological patterns were significantly influenced by etiology, geographic region, and publication period, with idiopathic cases being the most common. Scleritis was notably associated with systemic diseases such as rheumatoid arthritis, granulomatosis with polyangiitis, Sjögren's syndrome, sarcoidosis, and infectious agents like Mycobacterium tuberculosis and herpes virus. Conclusion: This is the most extensive study on scleritis to date, providing comparative insights across geographic regions, age groups, and genders. Our meta-analysis highlights significant regional differences in scleritis incidence, reflecting variations in medical practice, access to care, and potential genetic and environmental factors. These findings underscore the need for further research to explore these patterns and their global health implications.	The disease mentioned is: Scleritis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the parasites referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The parasites mentioned are: Plasmodium falciparum, and Anopheles mosquito	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
Describe the associations between pathogens and conditions.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - Treponema pallidum subsp. pallidum causes syphilis - Treponema pallidum subsp. pallidum causes chronic sexually transmitted infection - syphilis associated with painless chancres - syphilis associated with secondary syphilis - syphilis associated with tertiary complications - syphilis associated with cardiovascular - syphilis associated with neurosyphilis - T. pallidum is a Treponema pallidum subsp. pallidum	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
List all viral pathogens discussed in this passage.	Please analyze the following medical literature and extract entities and relationships:	The virus mentioned is: Epstein-Barr virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What is the relationship between the pathogens and diseases mentioned?	Please analyze the following medical literature and extract entities and relationships:	The relationships are: - Bartonella henselae has relationship cat scratch disease	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
How are the entities in this text related?	Please analyze the following medical literature and extract entities and relationships:	The relationships are: - Streptococcus pyogenes has relationship acute glomerulonephritis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What is the relationship between the pathogens and diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - Borrelia burgdorferi causes erythema migrans - Borrelia burgdorferi causes Lyme disease - Borrelia burgdorferi causes Lyme arthritis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
Identify the diseases and conditions referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The disease mentioned is: trachoma	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What is the relationship between the pathogens and diseases mentioned?	The pathogenesis of viral-induced diabetes. Serologic case-control studies have suggested an association between coxsasckie group B viruses and insulin-dependent diabetes mellitus (IDDM). New investigations have identified enteroviral nucleic acid in the peripheral blood mononuclear cells of newly-diagnosed patients with IDDM. The disease pathogenesis is dependent on several factors. including the genetics of the host, strain of virus, activation status of autoreactive T-cells, upregulation of pancreatic MHC-1 antigens, molecular mimicry between viral and beta cell epitopes and direct islet cell destruction by viral cytolysis. Epitopes (IDDM-E1 and E2) on glutamate decarboxylase 65 (GAD65) are the most common targets for antibody and cellular-mediated autoimmune beta cell destruction.	The relationships are: - coxsasckie group B viruses has relationship insulin-dependent diabetes mellitus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
List all infectious agents discussed in this text.	Please analyze the following medical literature and extract entities and relationships:	The pathogens mentioned are: Bacteria: Vibrio cholerae	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
How many diseases are referenced in this passage?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	There are 2 disease(s) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
Identify the viruses referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The viruss mentioned are: Hepatitis B virus, and HBV	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
List all medical conditions discussed in this passage.	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: thrombocytopenia	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
List all infectious agents discussed in this text.	Exploring Treatments for a Rare Guillain-Barré Variant: A Case Report of Miller-Fisher Syndrome. The symptoms of Miller-Fisher syndrome (MFS) are a triad of areflexia, ataxia, and ophthalmoplegia. The condition is a rare variant of Guillain-Barré syndrome (GBS), an acute immune-mediated nerve disorder. Both conditions involve abnormal autoimmune responses that may often be triggered by infections such as Campylobacter jejuni, human immunodeficiency virus, Epstein-Barr virus, and Zika virus, among others. As a result, the immune system mistakenly attacks the body's own nerve tissues. MFS is characterised by ophthalmoparesis, which can progress to complete external ophthalmoplegia and may include ptosis, facial nerve paralysis, sensory impairments, and muscle weakness. Diagnosis is supported by lumbar puncture, revealing albumin-cytologic dissociation, although initial tests may not always be indicative. A diagnostic marker for MFS is the presence of anti-GQ1b antibodies, which target the GQ1b ganglioside in nerves and affect oculomotor function in particular. Electrodiagnostic studies often show absent or reduced sensory responses without reduced conduction velocity. Treatment options include intravenous immunoglobulin therapy and plasmapheresis, which are both equally effective. This case study demonstrated significant clinical improvement in a patient undergoing plasmapheresis due to financial constraints, highlighting the efficacy of this treatment approach. A 50-year-old female presented with limb paraesthesia, progressive ptosis, imbalance, and transient diplopia following a recent fever. Examination revealed stable vitals, decreased deep tendon reflexes, reduced vibratory sensation, cerebellar ataxia, and cranial nerve abnormalities. Cerebrospinal fluid analysis showed elevated protein, suggesting MFS. Normal magnetic resonance imaging and nerve conduction studies indicated GBS, with positive anti-GQ1b antibodies. After five plasma exchange cycles, the patient improved substantially and was discharged with no residual symptoms after one month.	The pathogens mentioned are: Virus: 1. human immunodeficiency virus 2. Campylobacter jejuni 3. Epstein-Barr virus 4. Zika virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
Which viruses are associated with the diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The virus mentioned is: SARS-CoV	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
List all bacterial pathogens discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacterias mentioned are: Chlamydophila pneumoniae, and C. pneumoniae	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
Identify the bacterial organisms referenced in this text.	Please analyze the following medical literature and extract entities and relationships:	The bacteria mentioned is: Klebsiella pneumoniae	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
Identify the diseases and conditions referenced in this text.	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: antibiotic-associated diarrhea	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the viruses referenced in this text.	Please analyze the following medical literature and extract entities and relationships:	The virus mentioned is: Epstein-Barr virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
List all parasitic organisms discussed in this passage.	Please analyze the following medical literature and extract entities and relationships:	The parasite mentioned is: Paragonimus westermani	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
How are the entities in this text related?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - HIV-1 is a Human immunodeficiency virus type 1 - Human immunodeficiency virus type 1 causes HIV-positive - Mycobacterium tuberculosis causes tuberculosis - HIV-1 associated with Mycobacterium tuberculosis - HIV-1 causes active tuberculosis - M. tuberculosis causes tuberculosis - IRIS is a immune reconstitution inflammatory syndrome	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: pseudomembranous colitis, and C. difficile infection	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Count the number of viruses mentioned.	Please analyze the following medical literature and extract entities and relationships:	There are 0 virus(es) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: bacterial meningitis, invasive disease, acute purulent meningitis, fever, headache, neck stiffness, altered mental status, and invasive meningococcal disease	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Describe the associations between pathogens and conditions.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - Influenza B virus causes pneumonia - Influenza B virus causes bronchitis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The disease mentioned is: pericarditis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
How are the entities in this text related?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - M. tuberculosis causes pulmonary tuberculosis - M. tuberculosis causes miliary tuberculosis - M. tuberculosis is a Mycobacterium tuberculosis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What bacteria are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacterias mentioned are: Neisseria meningitidis, and N. meningitidis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
What bacteria are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacteria mentioned is: Campylobacter jejuni	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
Identify the diseases and conditions referenced in this text.	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: talaromycosis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
How are the entities in this text related?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - MDR-TB is a Multidrug-resistant tuberculosis - Mycobacterium tuberculosis complex causes Multidrug-resistant tuberculosis - XDR-TB is a extensively drug-resistant tuberculosis - Multidrug-resistant tuberculosis associated with mortality rates exceeding 50%	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
Identify the diseases and conditions referenced in this text.	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: tinea pedis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: dengue fever, severe dengue, dengue hemorrhagic fever, DHF, dengue shock syndrome, and DSS	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What parasites are mentioned in the text?	Please analyze the following medical literature and extract entities and relationships:	The parasite mentioned is: Wuchereria bancrofti	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
What fungi are mentioned in the text?	Please analyze the following medical literature and extract entities and relationships:	The fungus mentioned is: Malassezia furfur	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_fungus
List all viral pathogens discussed in this passage.	Identification of antiviral RNAi regulators, ILF3/DHX9, recruit at ZIKV stem loop B to protect against ZIKV induced microcephaly. Zika virus (ZIKV) is a member of the Flaviviridae family and causes congenital microcephaly and Guillain-Barré syndrome. Currently, there is a lack of approved vaccines or therapies against ZIKV infection. In this study, we profile vRNA‒host protein interactomes at ZIKV stem‒loop B (SLB) and reveal that interleukin enhancer binding factor 3 (ILF3) and DEAH-box helicase 9 (DHX9) form positive regulators of antiviral RNA inference in undifferentiated human neuroblastoma cells and induced pluripotent stem cell-derived human neural stem cells (iPSC-NSCs). Functionally, ablation of ILF3 in brain organoids and Nestin-Cre ILF3 cKO foetal mice significantly enhance ZIKV replication and aggravated ZIKV-induced microcephalic phenotypes. Mechanistically, ILF3/DHX9 enhance DICER processing of ZIKV vRNA-derived siRNAs (vsiR-1 and vsiR-2) to exert anti-flavivirus activity. VsiR-1 strongly inhibits ZIKV NS5 polymerase activity and RNA translation. Treatment with the vsiR-1 mimic inhibits ZIKV replication in vitro and in vivo and protected mice from ZIKV-induced microcephaly. Overall, we propose a novel therapeutic strategy to combat flavivirus infection.	The viruss mentioned are: Zika virus, and ZIKV	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What bacteria are mentioned in the text?	Please analyze the following medical literature and extract entities and relationships:	The bacteria mentioned is: Cryptosporidium	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
How many distinct pathogens are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	There are 2 distinct pathogen(s) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
Describe the associations between pathogens and conditions.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - Schistosoma mansoni causes intestinal schistosomiasis - S. mansoni is a Schistosoma mansoni - Schistosoma mansoni causes hepatosplenomegaly - Schistosoma mansoni causes portal hypertension - Schistosoma mansoni associated with bladder cancer - S. mansoni causes immune modulation - S. mansoni associated with parasitic infections	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
What pathological states are described?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: Ebola virus disease, EVD, hemorrhagic fever, fever, fatigue, muscle pain, headache, sore throat, vomiting, diarrhea, rash, internal and external bleeding, disseminated intravascular coagulation, multi-organ failure, arthritis, uveitis, and neurological symptoms	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Identify the viruses referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The viruss mentioned are: Herpes simplex virus type 1, HSV-1, and HSV-2	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
List all bacterial pathogens discussed in this passage.	Please analyze the following medical literature and extract entities and relationships:	The bacteria mentioned is: Clostridium tetani	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
List all medical conditions discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: tuberculosis, HIV-positive, disease progression, immunosuppression, mycobacterial replication, HIV viral load, CD4+ T cell depletion, diagnostic challenges, atypical radiographic presentations, tuberculin skin test sensitivity, drug interactions, antiretroviral therapy, anti-tuberculosis medications, and rifampicin's effect on cytochrome P450 metabolism	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Which viruses are associated with the diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The viruss mentioned are: West Nile virus, and WNV	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
How are the entities in this text related?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - Salmonella enterica causes gastroenteritis - Salmonella enterica causes bacteremia - Salmonella enterica causes salmonellosis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
List all medical conditions discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: gastroenteritis, Guillain-Barré syndrome, and campylobacteriosis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What pathogens (viruses, bacteria, fungi, parasites) are mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The pathogens mentioned are: Bacteria: Treponema pallidum subsp. pallidum, T. pallidum	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
Which bacteria are associated with the conditions mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacteria mentioned is: Mycobacterium tuberculosis complex	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
Identify the viruses referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The virus mentioned is: Rabies virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
List all bacterial pathogens discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacteria mentioned is: Clostridium perfringens	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
What pathological states are described?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The disease mentioned is: aseptic meningitis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What pathological states are described?	Relationship between rheumatoid arthritis and Mycoplasma pneumoniae: a case-control study. OBJECTIVE: Rheumatoid arthritis (RA) has a complex and multifactorial aetiology. Infectious agents could start this disease. The majority of the characteristics of this infirmity can be observed in chronic arthritis produced by mycoplasmas in animals. In this study the association between Mycoplasma pneumoniae and RA has been evaluated.METHODS: A case-control study was performed. Sera taken from 78 RA patients and from 156 controls were analysed to ascertain the levels of immunoglobulin G (IgG) against M. pneumoniae. Other variables, like age, gender, work status, history of pneumonia, etc., were recorded in a questionnaire.RESULTS: The presence of antibodies against M. pneumoniae was associated with RA (odds ratio=2.34, P<0.001).CONCLUSIONS: The results suggest that M. pneumoniae could be a cofactor in the pathogenesis of RA; however, more studies need to be done.	The disease mentioned is: Rheumatoid arthritis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
How many distinct pathogens are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	There are 0 virus(es) mentioned in the text.	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_count
Identify the fungal organisms referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The fungus mentioned is: Mucor	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_fungus
What is the relationship between the pathogens and diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The relationships are: - NiV causes Nipah virus infection - NiV is a Nipah virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_relationship
List all infectious agents discussed in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The pathogens mentioned are: Virus: Rabies virus, Rabies lyssavirus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_all_pathogens
Identify the viruses referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The virus mentioned is: Measles virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The disease mentioned is: giardiasis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
List all fungal pathogens discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The fungus mentioned is: Mucor	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_fungus
Identify the bacterial organisms referenced in this text.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacteria mentioned is: Rickettsia rickettsii	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria
What diseases are mentioned in the text?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: Burkitt lymphoma	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
Which viruses are associated with the diseases mentioned?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The virus mentioned is: Variola virus	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_virus
List all parasitic organisms discussed in this passage.	Please analyze the following medical literature and extract entities and relationships:	The parasite mentioned is: Strongyloides stercoralis	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_parasite
What diseases are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: pneumonia, and liver abscess	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
List all medical conditions discussed in this passage.	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The diseases mentioned are: Multidrug-resistant tuberculosis, MDR-TB, extensively drug-resistant tuberculosis, XDR-TB, drug-resistant TB, persistent cough, fever, night sweats, and weight loss	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What pathological states are described?	Please analyze the following medical literature and extract entities and relationships:	The disease mentioned is: common cold	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_disease
What bacteria are mentioned in the text?	Extract all medical entities (pathogens, diseases, evidence) and their relationships from the following text. Output as JSON.	The bacterias mentioned are: Escherichia coli O157:H7, Shiga toxin-producing E. coli, STEC, and E. coli O157:H7	You are a medical entity recognition expert. Answer questions about entities in the provided medical text accurately and concisely.	entity_bacteria

What diseases are mentioned in the text?

Please analyze the following medical literature and extract entities and relationships:

The disease mentioned is: Lyme arthritis