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prion_0000 | AIMS: Creutzfeldt-Jakob disease (CJD) is a rare, progressive, fatal neurodegenerative disorder caused by an abnormal glycoprotein known as the prion protein.
The core features include progressive cognitive decline, cerebellar dysfunction, personality changes, and visual disturbances.
Although psychiatric symptoms are r... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 6,
"end": 31,
"text": "Creutzfeldt-Jakob disease",
"spans": [
{
"start": 6,
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"is_discontinuous": null
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{
"id": "T1",
"label": "Generic_Prion",
"start": 33,
"end": 36,
... |
prion_0001 | Aims: Creutzfeldt–Jakob Disease (CJD) is a rare, fatal neurodegenerative disorder caused by prion proteins, leading to progressive brain damage.
CJD has sporadic, variant, genetic, and iatrogenic forms, with sporadic being the most common, affecting 1–2 people per million annually.
It typically presents with rapid cogn... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 6,
"end": 31,
"text": "Creutzfeldt–Jakob Disease",
"spans": [
{
"start": 6,
"end": 31
}
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"is_discontinuous": null
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{
"id": "T3",
"label": "Generic_Prion",
"start": 33,
"end": 36,
... |
prion_0004 | BACKGROUND: TSEs present diagnostic and infection control (IC) challenges.
Creutzfeldt-Jakob Disease (CJD) is the most common human TSE, occurring in 1–2/million/year in the United States, but other zoonotic factors or transmissions remain incompletely understood.
Prompted by the occurrence of four suspected cases from... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 12,
"end": 16,
"text": "TSEs",
"spans": [
{
"start": 12,
"end": 16
}
],
"is_discontinuous": null
},
{
"id": "T3",
"label": "Generic_Prion",
"start": 75,
"end": 100,
"text": "Creutzfel... |
prion_0006 | BACKGROUND: Creutzfeldt‐Jakob disease (CJD) is a progressive, irreversible, and fatal disease associated with the misfolding of a protein in the central nervous system.
Several surveillance programs emerged worldwide after the epidemic of the early 2000s.
In Mexico, information about its epidemiology is scarce.
A case ... | [
{
"id": "T21",
"label": "Generic_Prion",
"start": 12,
"end": 37,
"text": "Creutzfeldt‐Jakob disease",
"spans": [
{
"start": 12,
"end": 37
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{
"id": "T2",
"label": "Generic_Prion",
"start": 39,
"end": 42,
... |
prion_0007 | INTRODUCTION: Creutzfeldt‐Jakob disease (CJD) is a rare, fatal neurodegenerative disorder caused by misfolded prion proteins that accumulate in the brain, leading to spongiform encephalopathy.
It is characterized by rapidly progressive mental decline and other neurological symptoms, typically resulting in death within ... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 14,
"end": 39,
"text": "Creutzfeldt‐Jakob disease",
"spans": [
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"start": 14,
"end": 39
}
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{
"id": "T3",
"label": "Generic_Prion",
"start": 41,
"end": 44,
... |
prion_0008 | BACKGROUND: The unfavorable prognosis of prion diseases highlights the need for a robust diagnostic approach system to accurately distinguish them from other etiologies of dementia.
Correlating biomarkers is crucial for advancing therapies and optimizing patient selection in clinical trials.
METHOD: We prospectively en... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 41,
"end": 55,
"text": "prion diseases",
"spans": [
{
"start": 41,
"end": 55
}
],
"is_discontinuous": null
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{
"id": "T27",
"label": "Differential_Diagnosis",
"start": 152,
"end": 180,
... |
prion_0011 | PURPOSE: To report on quantitative electroencephalograph (EEG) activity during polysomnography (PSG) in a rare case of confirmed Fatal Familial Insomnia (FFI).
METHODS: Sleep/wake characteristics of a 32-year-old male patient were quantitatively analysed using central EEG recordings during two PSGs (FFI-1 and FFI-2) fi... | [
{
"id": "T32",
"label": "Electrophysio_test",
"start": 35,
"end": 56,
"text": "electroencephalograph",
"spans": [
{
"start": 35,
"end": 56
}
],
"is_discontinuous": null
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{
"id": "T33",
"label": "Electrophysio_test",
"start": 58,
"end"... |
prion_0013 | BACKGROUND: Fatal Familial Insomnia (FFI) is a rare autosomal dominant prion disease.
Herein, we present a case of a patient who was diagnosed with FFI, with symptoms initially resembling dementia with Lewy bodies (DLB).
METHOD: A 48‐year‐old Brazilian male with a six‐year history of insomnia presented with rapidly pro... | [
{
"id": "T2",
"label": "FFI",
"start": 12,
"end": 35,
"text": "Fatal Familial Insomnia",
"spans": [
{
"start": 12,
"end": 35
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],
"is_discontinuous": null
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{
"id": "T3",
"label": "FFI",
"start": 37,
"end": 40,
"text": "FFI",
"... |
prion_0015 | BACKGROUND: Creutzfeld‐Jakob disease (CJD) is an extremely rare neurodegenerative disorder, caused by the deposition of pathogenic protein components, known as prions, in the central nervous system.
It may present a variable combination of symptoms that include rapidly progressive dementia, ataxia, extrapyramidal sympt... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 12,
"end": 36,
"text": "Creutzfeld‐Jakob disease",
"spans": [
{
"start": 12,
"end": 36
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"is_discontinuous": null
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{
"id": "T3",
"label": "Generic_Prion",
"start": 38,
"end": 41,
... |
prion_0077 | BACKGROUND: Prion diseases are a group of neurodegenerative diseases associated with prion protein.
The disease can be caused by mutations in the PRNP gene, the gene that encodes prion protein.
An octapeptide repeat on the N‐terminus of prion protein plays an important role in normal intercellular function of prion pro... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 12,
"end": 26,
"text": "Prion diseases",
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"start": 12,
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{
"id": "T14",
"label": "Differential_Diagnosis",
"start": 42,
"end": 68,
... |
prion_0081 | Creutzfeldt-Jakob disease (CJD) belongs to a group of prion diseases that may be infectious, sporadic, or hereditary.
The 200K point mutation in the PRNP gene is the most frequent cause of hereditary CJD, accounting for >70% of families with CJD worldwide.
Prevalence of the 200K variant of familial CJD is especially hi... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 0,
"end": 25,
"text": "Creutzfeldt-Jakob disease",
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"start": 0,
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"id": "T3",
"label": "Generic_Prion",
"start": 27,
"end": 30,
... |
prion_0109 | Clinical differential diagnosis of early-onset dementia (EOD) includes familial Alzheimer disease (FAD) and hereditary prion disease.
In both disease entities, postmortem brain histopathological examination is essential for unambiguous diagnosis.
Mutations in the genes encoding the presenilins (PS1 and PS2) and amyloid... | [
{
"id": "T2",
"label": "Symptom",
"start": 35,
"end": 55,
"text": "early-onset dementia",
"spans": [
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"start": 35,
"end": 55
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{
"id": "T42",
"label": "Symptom",
"start": 57,
"end": 60,
"text": "EOD",... |
prion_0111 | Since a report in 1996 of 10 cases of Creutzfeldt-Jakob disease (CJD) with onset in a younger than usual age, a pattern of the disease has emerged.
This includes early neuropsychiatric features and sensory symptoms and neurological signs such as ataxia and involuntary movements later in the course of the disease.
Three... | [
{
"id": "T2",
"label": "Time_point",
"start": 18,
"end": 22,
"text": "1996",
"spans": [
{
"start": 18,
"end": 22
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{
"id": "T3",
"label": "Generic_Prion",
"start": 38,
"end": 63,
"text": "Creutzfeldt-J... |
prion_0121 | The clinical presentation and evolution, neuropathological findings, and genotyping of three members of a Spanish family affected with fatal familial insomnia are reported.
The mother and two of her offspring developed a rapidly evolving disease with insomnia and behavioural disorders as the initial symptoms and died b... | [
{
"id": "T17",
"label": "Autopsy",
"start": 41,
"end": 58,
"text": "neuropathological",
"spans": [
{
"start": 41,
"end": 58
}
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"is_discontinuous": null
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{
"id": "T18",
"label": "Genetic_test",
"start": 73,
"end": 83,
"text": "ge... |
prion_0122 | This study examined trends in mortality from sporadic Creutzfeldt-Jakob disease in France for 1992-7 by age, genotype at the codon 129 of the prion protein gene, and geographical area.
Case ascertainment was based on notifications by neurologists, neuropathologists, and laboratories; 324 deaths from definite or probabl... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 54,
"end": 79,
"text": "Creutzfeldt-Jakob disease",
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"id": "T3",
"label": "Duration",
"start": 94,
"end": 100,
"t... |
prion_0141 | A total of 65 cases of Creutzfeldt-Jakob disease with a history of cadaveric dura transplantation in Japan were analysed to clarify the epidemiologic features of such patients and to explore whether other such patients will appear in the future.
The age at transplantation averaged 44.4 years with a standard deviation o... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 23,
"end": 48,
"text": "Creutzfeldt-Jakob disease",
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{
"id": "T18",
"label": "Treatment",
"start": 67,
"end": 97,
"... |
prion_0159 | A postmortem case of an atypical form of dural graft associated Creutzfeldt-Jakob disease (CJD) is described.
A 42 year old man developed progressive spastic paresis 163 months after a cadaveric dura mater graft.
He presented with no myoclonus and very late occurrence of periodic synchronous discharges on EEG.
The prio... | [
{
"id": "T2",
"label": "iCJD",
"start": 41,
"end": 89,
"text": "dural graft associated Creutzfeldt-Jakob disease",
"spans": [
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"start": 41,
"end": 89
}
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"is_discontinuous": null
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{
"id": "T3",
"label": "Generic_Prion",
"start": 91,
... |
prion_0164 | OBJECTIVES: The detection of the protein 14-3-3 in the CSF has been shown to be a reliable and sensitive marker for sporadic Creutzfeldt-Jakob disease (CJD).
Other brain-specific proteins such as neuron specific enolase (NSE), S-100b, and tau protein have also been reported to be increased in the CSF of patients with s... | [
{
"id": "T44",
"label": "Blood_biomarker_test",
"start": 55,
"end": 58,
"text": "CSF",
"spans": [
{
"start": 55,
"end": 58
}
],
"is_discontinuous": null
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{
"id": "T2",
"label": "Generic_Prion",
"start": 125,
"end": 150,
"text": "C... |
prion_0165 | Three members of a family with inherited prion disease are reported.
One additional family member had a progressive neurological disease without details.
Two developed symptoms of ataxia, dementia, myoclonus, rigidity, and hemiparesis, and one had a different phenotype with the combination of lower motor neuron deficit... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 31,
"end": 54,
"text": "inherited prion disease",
"spans": [
{
"start": 31,
"end": 54
}
],
"is_discontinuous": null
},
{
"id": "T20",
"label": "Symptom",
"start": 104,
"end": 136,
"te... |
prion_0170 | OBJECTIVES: To describe the clinical presentation of patients with Alzheimer's disease (AD) or dementia with Lewy bodies (DLB) who were suspected of having Creutzfeldt-Jakob disease (CJD) and to investigate whether current clinical diagnostic criteria cover these atypical forms of AD and DLB.
METHODS: Brains from necro... | [
{
"id": "T2",
"label": "Differential_Diagnosis",
"start": 67,
"end": 86,
"text": "Alzheimer's disease",
"spans": [
{
"start": 67,
"end": 86
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"is_discontinuous": null
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{
"id": "T3",
"label": "Differential_Diagnosis",
"start": 95,
"... |
prion_0200 | OBJECTIVE: To compare conventional and diffusion-weighted MR imaging in terms of their depiction of the abnormalities occurring in Creutzfeldt-Jakob disease.
MATERIALS AND METHODS: We retrospectively analyzed the findings of conventional (T2-weighted and fluid-attenuated inversion recovery) and diffusion-weighted MR im... | [
{
"id": "T23",
"label": "Imaging_sequence",
"start": 22,
"end": 68,
"text": "conventional MR imaging",
"spans": [
{
"start": 22,
"end": 34
},
{
"start": 58,
"end": 68
}
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"is_discontinuous": true
},
{
"id": "T2",
"l... |
prion_0214 | We report the use of diffusion-weighted MR imaging in the early diagnosis and monitoring of the progression of a histopathologically proved case of sporadic Creutzfeldt-Jakob disease.
Ribbon-like areas of hyperintensity in the cerebral cortex on diffusion-weighted images corresponded to the localization of periodic sha... | [
{
"id": "T2",
"label": "Imaging_sequence",
"start": 21,
"end": 39,
"text": "diffusion-weighted",
"spans": [
{
"start": 21,
"end": 39
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],
"is_discontinuous": null
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{
"id": "T8",
"label": "Imaging_test",
"start": 40,
"end": 50,
"te... |
prion_0217 | Prions have emerged in the past 5 years as serious transmissible infective agents.
Ocular tissue transplantation has come under scrutiny after potential infected tissue was transplanted into healthy patients.
In this review we examine the evidence for the risk of transmission of prions after scleral transplantation and... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 0,
"end": 6,
"text": "Prions",
"spans": [
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"start": 0,
"end": 6
}
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"is_discontinuous": null
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{
"id": "T3",
"label": "Treatment",
"start": 83,
"end": 112,
"text": "Ocular tissue t... |
prion_0223 | OBJECTIVE: To gain a better understanding of how mutations of the prion protein (PrP) gene are responsible for progressive dementia syndrome and to clarify the correlation between genotype and phenotype, which should help to explain how the prion promotes neurological symptoms. BACKGROUND: Genetic prion diseases are as... | [
{
"id": "T3",
"label": "Differential_Diagnosis",
"start": 111,
"end": 140,
"text": "progressive dementia syndrome",
"spans": [
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"start": 111,
"end": 140
}
],
"is_discontinuous": null
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{
"id": "T5",
"label": "Symptom",
"start": 256,
"... |
prion_0224 | A 47 year old man is described who developed pathology proven Creutzfeldt-Jakob disease (CJD) 38 years after receiving a low dose of human derived growth hormone (hGH) as part of a diagnostic procedure.
The patient presented with a cerebellar syndrome, which is compatible with iatrogenic CJD.
This is the longest incuba... | [
{
"id": "T2",
"label": "Age",
"start": 2,
"end": 13,
"text": "47 year old",
"spans": [
{
"start": 2,
"end": 13
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"is_discontinuous": null
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{
"id": "T11",
"label": "Autopsy",
"start": 45,
"end": 54,
"text": "pathology",
"spa... |
prion_0228 | A quantitative assessment of eye movements and a detailed neuropsychological profile were conducted at predementia stage in a patient who later had histological confirmation of sporadic Creutzfeldt-Jakob disease (CJD).
The patient was a middle aged man who presented with abnormal eye movements and poor balance.
Neurops... | [
{
"id": "T11",
"label": "Symptom",
"start": 29,
"end": 42,
"text": "eye movements",
"spans": [
{
"start": 29,
"end": 42
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],
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{
"id": "T2",
"label": "sCJD",
"start": 177,
"end": 211,
"text": "sporadic Creu... |
prion_0233 | BACKGROUND AND PURPOSE: Diffusion-weighted imaging can disclose distinct hyperintense lesions in Creutzfeldt-Jakob disease (CJD).
However, these findings and chronologic changes of CJD at diffusion-weighted imaging have not been fully investigated.
Our purpose was to assess the diagnostic value of diffusion-weighted im... | [
{
"id": "T2",
"label": "Imaging_sequence",
"start": 24,
"end": 50,
"text": "Diffusion-weighted imaging",
"spans": [
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"end": 50
}
],
"is_discontinuous": null
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{
"id": "T4",
"label": "Imaging_finding",
"start": 73,
"end": ... |
prion_0242 | OBJECTIVES: To characterise the nature of cognitive change in Creutzfeldt-Jakob disease (CJD).
METHODS: Case histories are reported of four patients with sporadic (sCJD) and two with familial CJD (fCJD), with postmortem pathological findings in four cases.
The data derived from cognitive examination are examined with r... | [
{
"id": "T22",
"label": "Symptom",
"start": 42,
"end": 58,
"text": "cognitive change",
"spans": [
{
"start": 42,
"end": 58
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{
"id": "T2",
"label": "Generic_Prion",
"start": 62,
"end": 87,
"text": "Cre... |
prion_0281 | Based on in vitro observations in scrapie-infected neuroblastoma cells, quinacrine has recently been proposed as a treatment for Creutzfeldt-Jakob disease (CJD), including a new variant CJD which is linked to contamination of food by the bovine spongiform encephalopathy (BSE) agent.
The present study investigated possi... | [
{
"id": "T2",
"label": "Treatment",
"start": 72,
"end": 82,
"text": "quinacrine",
"spans": [
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"start": 72,
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"id": "T3",
"label": "Generic_Prion",
"start": 129,
"end": 154,
"text": "Creutz... |
prion_0294 | Thalamic degenerations or dementias are poorly understood conditions.
The familial forms are (1) selective thalamic degenerations and (2) thalamic degenerations associated with multiple system atrophy.
Selective thalamic degenerations share clinical and pathologic features with fatal familial insomnia, an autosomal dom... | [
{
"id": "T24",
"label": "Anatomic_location",
"start": 0,
"end": 8,
"text": "Thalamic",
"spans": [
{
"start": 0,
"end": 8
}
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"is_discontinuous": null
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{
"id": "T23",
"label": "Differential_Diagnosis",
"start": 0,
"end": 22,
"text... |
prion_0326 | A conformational change of the prion protein is responsible for a class of neurodegenerative diseases called the transmissible spongiform encephalopathies that include mad cow disease and the human afflictions kuru and Creutzfeldt-Jakob disease.
Despite the attention given to these diseases, the normal function of the ... | [
{
"id": "T15",
"label": "Differential_Diagnosis",
"start": 75,
"end": 101,
"text": "neurodegenerative diseases",
"spans": [
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"start": 75,
"end": 101
}
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"is_discontinuous": null
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{
"id": "T3",
"label": "Generic_Prion",
"start": 113,
... |
prion_0341 | Sudden onset neurological syndromes are almost always vascular but there is a wide range of causes of subacute onset neurological syndromes.
Most diagnoses will become clear from clinical assessment and, depending on presentation, computed tomography or magnetic resonance imaging of the brain or spine and cerebrospinal... | [
{
"id": "T2",
"label": "Symptom",
"start": 13,
"end": 35,
"text": "neurological syndromes",
"spans": [
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"start": 13,
"end": 35
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"is_discontinuous": null
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{
"id": "T9",
"label": "Symptom",
"start": 117,
"end": 139,
"text": "ne... |
prion_0343 | BACKGROUND: There has been concern that children with variant Creutzfeldt-Jakob disease (vCJD) might be misdiagnosed as cases of Alpers' syndrome, as a spongiform degeneration of the brain is seen in both conditions.
OBJECTIVE: To report a national prospective surveillance study of children with progressive intellectua... | [
{
"id": "T2",
"label": "vCJD",
"start": 54,
"end": 87,
"text": "variant Creutzfeldt-Jakob disease",
"spans": [
{
"start": 54,
"end": 87
}
],
"is_discontinuous": null
},
{
"id": "T3",
"label": "vCJD",
"start": 89,
"end": 93,
"text": ... |
prion_0359 | OBJECTIVES: The most common familial early onset dementia mutations are found in the genes involved in Alzheimer's disease; the amyloid precursor protein (APP) and the presenilin 1 and 2 (PSEN1 and 2) genes; the prion protein gene (PRNP) may be involved.
METHODS: Following identification of a two-octapeptide repeat ins... | [
{
"id": "T25",
"label": "Differential_Diagnosis",
"start": 28,
"end": 57,
"text": "familial early onset dementia",
"spans": [
{
"start": 28,
"end": 57
}
],
"is_discontinuous": null
},
{
"id": "T1",
"label": "Differential_Diagnosis",
"start"... |
prion_0455 | OBJECTIVE: To investigate whether phosphorylated tau protein (tau-pT181) is increased in variant Creutzfeldt-Jakob disease (vCJD) and if the tau-pT181/tau protein ratio is useful for distinguishing between patients with and without CJD.
METHODS: CSF tau protein and tau-pT181 were measured in 50 patients with sporadic C... | [
{
"id": "T5",
"label": "vCJD",
"start": 89,
"end": 122,
"text": "variant Creutzfeldt-Jakob disease",
"spans": [
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"start": 89,
"end": 122
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],
"is_discontinuous": null
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{
"id": "T6",
"label": "vCJD",
"start": 124,
"end": 128,
"tex... |
prion_0473 | We report the case of a 28 year old man who had received a cadaverous dura mater graft after a traumatic open skull fracture with tearing of the dura at the age of 5 years.
A clinical suspicion of Creutzfeldt-Jakob disease (CJD) was confirmed by a brain biopsy 5 months prior to death and by autopsy, thus warranting the... | [
{
"id": "T1",
"label": "Age",
"start": 24,
"end": 35,
"text": "28 year old",
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"start": 24,
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"is_discontinuous": null
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{
"id": "T15",
"label": "Treatment",
"start": 48,
"end": 86,
"text": "received a cadav... |
prion_0486 | Between 1970 and 2003, seven cases of human dura mater-associated Creutzfeldt-Jakob disease (CJD) were identified in the UK.
Furthermore, we identified a case of CJD in a porcine dura graft recipient.
The mean incubation period of the human dura mater cases was 93 (range 45-177) months.
The clinico-pathological feature... | [
{
"id": "T1",
"label": "Duration",
"start": 0,
"end": 21,
"text": "Between 1970 and 2003",
"spans": [
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"start": 0,
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{
"id": "T3",
"label": "iCJD",
"start": 38,
"end": 91,
"text": "human dur... |
prion_0504 | An autopsy case of Creutzfeldt-Jakob disease with Kuru-like neuropathological changes which revealed clinically extrapyramidal, pyramidal and psychic symptoms is presented in this report.
On microscopic examination, status spongiosus, neuronal degeneration, proliferation of hypertrophic astrocytes and numerous plaques ... | [
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"label": "Autopsy",
"start": 3,
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"id": "T2",
"label": "Generic_Prion",
"start": 19,
"end": 44,
"text": "Creutzfeldt-Jak... |
prion_0506 | The case of a patient 53 years old that had a picture of cortical impairment and pyramidal disfunction, leading in 6 months to acinetic mutism is reported.
The histopathology lead to the diagnostic of Creutzeldt-Jakob disease, with neuronal loss, gliosis and status spongiosus.
The electron-microscopic examination showe... | [
{
"id": "T1",
"label": "Age",
"start": 22,
"end": 34,
"text": "53 years old",
"spans": [
{
"start": 22,
"end": 34
}
],
"is_discontinuous": null
},
{
"id": "T2",
"label": "Symptom",
"start": 57,
"end": 76,
"text": "cortical impairmen... |
prion_0508 | The clinico-pathological features of 4 cases of Creutzfeldt-Jakob disease, a transmissible virus dementia, are reported.
The onset of the disease varied between 54 and 81 years of age: the course is dramatic and the demise occurs 1-4 months after the onset of symptoms.
The clinical picture includes mental deterioration... | [
{
"id": "T2",
"label": "Generic_Prion",
"start": 48,
"end": 73,
"text": "Creutzfeldt-Jakob disease",
"spans": [
{
"start": 48,
"end": 73
}
],
"is_discontinuous": null
},
{
"id": "T1",
"label": "Time_point",
"start": 125,
"end": 145,
... |
prion_0509 | A case of Creutzfeldt-Jakob disease treated with amantadine showed considerable initial improvement, followed by a period of almost five years during which the patient remained in a relatively stable condition until he died accidentally.
The diagnosis was confirmed histologically. | [
{
"id": "T1",
"label": "Generic_Prion",
"start": 10,
"end": 35,
"text": "Creutzfeldt-Jakob disease",
"spans": [
{
"start": 10,
"end": 35
}
],
"is_discontinuous": null
},
{
"id": "T2",
"label": "Treatment",
"start": 49,
"end": 59,
"t... |
End of preview. Expand in Data Studio
PrionNER
This repository accompanies the paper "PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature" and provides a data-only Hugging Face release of PrionNER.
PrionNER is a named entity recognition dataset for prion disease biomedical literature. This release contains canonical train/test splits, fine-grained and coarse-grained annotations, and multiple synchronized data views derived from the same document set.
Dataset Summary
- Total documents: 317
- Train documents: 247
- Test documents: 70
- Fine-grained schema: 31 defined labels, 30 observed in the released data
- Coarse-grained schema: 15 labels
- Fine/coarse entity count: 4,655 train and 1,650 test
- Discontinuous entities: 97 train and 34 test
The fine-grained schema defines VPSPr, but that label does not appear in the current released splits.
Configurations
This dataset card defines two main configurations for loading with datasets:
fine: fine-grained JSON documents withtrainandtestsplitscoarse: coarse-grained JSON documents withtrainandtestsplits
Example:
from datasets import load_dataset
fine = load_dataset("daotuanan/PrionNER", "fine")
coarse = load_dataset("daotuanan/PrionNER", "coarse")
The repository also includes auxiliary release files:
data/raw/: original BRAT source pairsdata/raw_text/: text-only filesdata/fine/brat/anddata/coarse/brat/: BRAT exportsdata/fine/conll/anddata/coarse/conll/: CoNLL exportsmetadata/: schema files, BRAT config, and summary metadata
Data Format
Each JSON document includes:
doc_id: document identifiertext: full document textentities: list of entity annotations
Each entity includes:
id: original BRAT entity IDlabel: entity typestart,end: document-level character offsetstext: entity surface formspans: one or more span objectsis_discontinuous: present when the entity spans multiple non-contiguous segments
Licensing and Rights
This Hugging Face repository uses license: other because it contains mixed-rights data.
- The PrionNER annotation layer and project-authored metadata are intended to be released under
CC BY 4.0, to the extent the repository maintainers hold the necessary rights in those materials. - The underlying article titles, abstracts, and other source text are included publicly in this repository, but they are not blanket-relicensed by the project.
- Please review
LICENSE,DATA_LICENSE.md, andTHIRD_PARTY_RIGHTS.mdbefore redistributing the source text.
Provenance
Some released text may be derived from PubMed or MEDLINE records. Where PubMed- or MEDLINE-derived material is used, please acknowledge the U.S. National Library of Medicine as the source of the bibliographic data and do not imply endorsement by NLM or the U.S. Government.
Citation
If you use PrionNER, please cite the repository and the associated paper:
- "PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature"
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