MedINST: Meta Dataset of Biomedical Instructions
Paper • 2410.13458 • Published • 7
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You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Stochastic models
Stochasticity inevitably emerges when molecular components are present at low cellular concentrations (McAdams & Arkin, 1997; Kierzek et al., 2001). This physical phenomenon generates noise in synthetic and natural circuits (Paulsson, 2004; Mettetal et al., 2006), and its consequences over the phenoty... | [cellular <Cell>] [cell <Cell>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Comparison of image (CAS 200) and flow cytometry determined DNA content of paraffin-embedded Hodgkin's disease tissue.
To assess the reliability of DNA estimation using image cytometry, deparaffinized lymph nodes from 70 patients with Hodgkin's disease were examined and the results obtained were compared with those fro... | [Hodgkin's disease tissue <Tissue>] [lymph nodes <Multi-tissue_structure>] [cell <Cell>] [nuclear <Cellular_component>] [nuclei <Cellular_component>] [lymphocytes <Cell>] [Benign lymph nodes <Pathological_formation>] [cells <Cell>] [lymphocyte <Cell>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Model of how estrogen induces DNA damage. Estrogen enters the cell and is bound by the ER. The dimeric ER-estrogen complex enters the nucleus and induces AID expression. This leads to an increase in mutations and translocations, and potentially cancer
| [cell <Cell>] [nucleus <Cellular_component>] [cancer <Pathological_formation>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | A pancreatic beta -cell-specific enhancer in the human PDX-1 gene is regulated by hepatocyte nuclear factor 3beta (HNF-3beta ), HNF-1alpha, and SPs transcription factors.
The PDX-1 transcription factor plays a key role in pancreas development. Although expressed in all cells at the early stages, in the adult it is main... | [pancreatic beta -cell <Cell>] [pancreas <Organ>] [cells <Cell>] [beta-cell <Cell>] [beta-cells <Cell>] [beta- <Cell>] [non-beta-cells <Cell>] [beta-cell <Cell>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Background
Over the past decades, extensive comparative mapping research has been performed in the plant family Solanaceae. The recent identification of a large set of single-copy conserved orthologous (COSII) markers has greatly accelerated comparative mapping studies among major solanaceous species including tomato, ... | [chromosomal <Cellular_component>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Cognitive function and number of teeth in a community-dwelling elderly population without dementia.
Although the number of sound or decayed teeth has been reported to be associated with cognitive function in elderly populations with dementia, little is known about this association in elderly populations without dementi... | [teeth <Organ>] [teeth <Organ>] [teeth <Organ>] [teeth <Organ>] [blood <Organism_substance>] [blood <Organism_substance>] [teeth <Organ>] [teeth <Organ>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Dynorphin is contained within hippocampal mossy fibers: immunochemical alterations after kainic acid administration and colchicine-induced neurotoxicity.
Antisera raised against synthetic dynorphin or [Leu5]enkephalin demonstrate immunostaining in hippocampal mossy fibers and in dentate granule cells. However, dynorphi... | [hippocampal mossy fibers <Tissue>] [sera <Organism_substance>] [hippocampal mossy fibers <Tissue>] [dentate granule cells <Cell>] [Intrahippocampal <Multi-tissue_structure>] [hippocampus <Multi-tissue_structure>] [Intraventricularly <Multi-tissue_structure>] [CA3-4 pyramidal cells <Cell>] [mossy fibers <Tissue>] [hipp... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Lack of developmental and reproductive toxicity of 2,3,3',4, 4'-pentachlorobiphenyl (PCB 105) in ring-necked pheasants.
Mono-ortho PCBs are global contaminants of wildlife with the potential to produce toxicity by an aryl hydrocarbon receptor (AhR)-mediated mechanism. To determine the potency of 2,3,3',4, 4'-pentachlor... | [egg <Developing_anatomical_structure>] [egg <Developing_anatomical_structure>] [egg <Developing_anatomical_structure>] [Embryo <Developing_anatomical_structure>] [body <Organism_subdivision>] [heart <Organ>] [liver <Organ>] [body <Organism_subdivision>] [liver <Organ>] [heart <Organ>] [beak <Organism_subdivision>] [li... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | [The clinical and laboratory features of acute promyelocytic leukemia: an analysis of 513 cases].
OBJECTIVE:
To investigate the clinical and laboratory features of acute promyelocytic leukemia (APL).
METHODS:
513 APL patients in the last two decades were retrospectively analyzed in this research. We investigated the cl... | [WBC <Cell>] [promyelocyte <Cell>] [blood <Organism_substance>] [chromosome <Cellular_component>] [chromosome <Cellular_component>] [WBC <Cell>] [WBC <Cell>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Novel mechanism for the impairment of cell proliferation in HIV-1 infection.
The synthesis of ribonucleotides is essential to cell proliferation. Defects in the relevant metabolic pathways have been demonstrated in stimulated T cells from AIDS patients and are associated with lymphocyte necrotic death. Here, Margarita ... | [cell <Cell>] [cell <Cell>] [T cells <Cell>] [lymphocyte <Cell>] [cells <Cell>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Conservative treatment of endometriosis: the effects of limited surgery and hormonal pseudopregnancy.
This study compares the effects of limited surgery or hormonal pseudopregnancy, or a combination of these two, upon fertility and the need for subsequent surgery with respect to the extent of the disease at the time of... | [uterus <Organ>] [tubes <Multi-tissue_structure>] [ovaries <Organ>] [ovaries <Organ>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Imaging techniques for the assessment of body composition.
Three imaging methods, ultrasound imaging (UI), computer-assisted axial tomography (CAT) and magnetic resonance imaging (MRI), are widely used in medicine. Their application to the assessment of body composition in nutrition research is still being explored and... | [body <Organism_subdivision>] [body <Organism_subdivision>] [bone <Organ>] [muscle <Organ>] [adipose tissue <Tissue>] [tissue <Tissue>] [abdominal adipose tissue <Tissue>] [subcutaneous adipose tissue <Tissue>] [body <Organism_subdivision>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Effects of buffer properties on cyclodextrin glucanotransferase reactions and cyclodextrin production from raw sago (Cycas revoluta) starch.
Results from the present study have shown that the ionic species of buffers, pH values and reaction temperature can affect the enzyme unit activities and product specificity of To... | [starch <Organism_substance>] [starch <Organism_substance>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Influences on the pharmacokinetics of oxycodone: a multicentre cross-sectional study in 439 adult cancer patients.
OBJECTIVE:
Oxycodone is widely used for the treatment of cancer pain, but little is known of its pharmacokinetics in cancer pain patients. The aim of this study was to explore the relationships between ord... | [cancer <Pathological_formation>] [cancer <Pathological_formation>] [cancer <Pathological_formation>] [serum <Organism_substance>] [cancer <Pathological_formation>] [cancer <Pathological_formation>] [body <Organism_subdivision>] [glomerular <Multi-tissue_structure>] [serum <Organism_substance>] [serum <Organism_substan... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Ca2+ Dependence of Slob57 Modulation of the Voltage Dependence of Activation of dSlo
Ca2+ plays a fundamental role in regulating the dSlo response to membrane depolarization. One of the three known Ca2+ binding sites (Xia et al., 2002; Bao et al., 2002; Zeng et al., 2005b), known as the calcium bowl (Schreiber and Salk... | [membrane <Cellular_component>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Sciatic nerve repair by microgrooved nerve conduits made of chitosan-gold nanocomposites.
BACKGROUND:
To better direct the repair of peripheral nerve after injury, an implant consisting of a multicomponent micropatterned conduit seeded with NSC was designed.
METHODS:
The mechanical properties of the chi-Au nanocomposit... | [Sciatic nerve <Multi-tissue_structure>] [nerve <Multi-tissue_structure>] [peripheral nerve <Multi-tissue_structure>] [conduit <Multi-tissue_structure>] [NSC <Cell>] [cell <Cell>] [NSC <Cell>] [glial cell line C6 <Cell>] [cell <Cell>] [NSC <Cell>] [sciatic nerve <Multi-tissue_structure>] [cell <Cell>] [NSC <Cell>] [cel... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Prognostic significance of TRAIL signaling molecules in stage II and III colorectal cancer.
PURPOSE:
We previously found that cellular FLICE-inhibitory protein (c-FLIP), caspase 8, and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor 2 (DR5) are major regulators of cell viability and chemotherap... | [stage II and III colorectal cancer <Pathological_formation>] [cell <Cell>] [colorectal cancer <Pathological_formation>] [tissues <Tissue>] [stage II and III colorectal cancer <Pathological_formation>] [Tissue <Tissue>] [normal <Tissue>] [tumor tissue <Tissue>] [Colorectal tumors <Pathological_formation>] [normal tissu... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | The right eye of a 50-year-old patient with severe hypertension at the first visit. (a) Fundus photograph shows serous retinal detachment. The optic disc is pale at the temporal side. (b) Optical coherence tomography (OCT) shows retinal detachment involving the fovea and cystic change of inner retina. (c) Early phase i... | [eye <Organ>] [retinal <Multi-tissue_structure>] [retinal <Multi-tissue_structure>] [inner retina <Multi-tissue_structure>] [macular <Tissue>] [retinal <Multi-tissue_structure>] [cystoid edema <Pathological_formation>] [macula <Tissue>] [retinal artery <Tissue>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | 5.
Conclusion
RLs are new actors in animal and plant defense and their low toxicity and biodegradability make them promising molecules to be used against pathogens. In this respect, there are some clues now available for the success of RL applications in greenhouses to fight phytopathogens. A better understanding of RL... | [skin <Organ>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Defective biliary copper excretion in Wilson's disease: the role of caeruloplasmin.
Previous studies have failed to explain the link between copper accumulation and abnormal caeruloplasmin expression in Wilson's disease. Furthermore, despite the isolation of a candidate gene for Wilson's disease, which predicts a defec... | [plasma <Organism_substance>] [liver <Organ>] [bile <Organism_substance>] [liver <Organ>] [bile <Organism_substance>] [serum <Organism_substance>] [bile <Organism_substance>] [liver <Organ>] [bile <Organism_substance>] [plasma <Organism_substance>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Introduction
Tea (Camellia sinensis L.) is one of the most widely consumed beverages in the world. (-)-Epigallocatechin-3-O-gallate (EGCG), which is the major green tea catechin present in the leaves, is believed to the compound most responsible for the health benefits attributed to tea. EGCG was reported to have antio... | [leaves <Organ>] [cancer <Pathological_formation>] [blood <Organism_substance>] [cancer <Pathological_formation>] [cell-surface <Cellular_component>] [cell surface <Cellular_component>] [cell surface <Cellular_component>] [tumor cells <Cell>] [tumor <Pathological_formation>] [cancer <Pathological_formation>] [tumor cel... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Phase II trial with D-Trp-6-LH-RH in prostatic carcinoma: comparison with other hormonal agents.
Various approaches to hormonal treatment of prostate carcinoma are discussed. Eighty-one patients with prostatic carcinoma, eight with stage B, nine with stage C, and 64 with stage D disease, were treated subcutaneously dai... | [prostatic carcinoma <Pathological_formation>] [prostate carcinoma <Pathological_formation>] [prostatic carcinoma <Pathological_formation>] [prostatic carcinoma <Pathological_formation>] [serum <Organism_substance>] [serum <Organism_substance>] [bone <Organ>] [bone <Organ>] [Prostatic <Organ>] [transabdominal <Organism... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Results
In the established adult rat NSC culture, FGF-2 promotes self-renewal by increasing proliferation and inhibiting spontaneous differentiation of adult NSCs, accompanied with activation of MAPK and PLC pathways. Using a molecular genetic approach, we demonstrate that activation of FGF receptor 1 (FGFR1), largely ... | [NSC <Cell>] [NSCs <Cell>] [cytoplasmic <Organism_substance>] [NSC <Cell>] [NSC <Cell>] [NSC <Cell>] [neuronal <Cell>] [oligodendroglial <Cell>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Identification of NAB1, a repressor of NGFI-A- and Krox20-mediated transcription.
NGFI-A (also called Egr1, Zif268, or Krox24) and the closely related proteins Krox20, NGFI-C, and Egr3 are zinc-finger transcription factors encoded by immediate-early genes which are induced by a wide variety of extracellular stimuli. NG... | [extracellular <Immaterial_anatomical_entity>] [cell <Cell>] [macrophage <Cell>] [synaptic <Cellular_component>] [peripheral nerve <Multi-tissue_structure>] [cellular <Cell>] [nuclear <Cellular_component>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | [Epidemiology of respiratory allergy in children].
Epidemiology of paediatric respiratory allergic disorders allows the approach to causal and preventive risk factors by studying groups or sub groups of children in different locations and under different conditions. This is, however, complicated by the lack of consensu... | [respiratory <Anatomical_system>] [respiratory <Anatomical_system>] [skin <Organ>] [airway <Multi-tissue_structure>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | INTRODUCTION
For several years now, virtual microscopy has been utilized in medical teaching, research, proficiency testing, American Board of Pathology examinations, pathology meetings and conferences, and quality assurance programs. In diagnostic practice, it is most widely and routinely used in image analysis. Some ... | [gastrointestinal <Organism_subdivision>] [GI <Organism_subdivision>] [liver <Organ>] [liver <Organ>] [GI <Organism_subdivision>] [GI <Organism_subdivision>] [liver <Organ>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Results
Here we include data obtained from active, oscillatory brain slices as well as from recordings during cortical slow oscillations in anesthetized animals. All recordings included in this study were obtained from the visual cortex of the ferret (in vitro), cat (in vivo) and from barrel cortex of the rat (in vivo)... | [brain slices <Multi-tissue_structure>] [cortical <Multi-tissue_structure>] [visual cortex <Multi-tissue_structure>] [barrel cortex <Multi-tissue_structure>] [neurons <Cell>] [cortical slices <Multi-tissue_structure>] [neurons <Cell>] [visual cortex <Multi-tissue_structure>] [neurons <Cell>] [barrel cortex <Multi-tissu... |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Authors' contributions
OK and MG analyzed and interpreted the patient data regarding his hospitalization. SP and PK performed the coronary angiography, and were the major contributors in writing the manuscript. All authors read and approved the final manuscript.
| [coronary <Multi-tissue_structure>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | Detection of total assist and sucking points based on the pulsatility of a continuous flow artificial heart: in vivo evaluation.
Our novel control strategy for a continuous flow artificial heart by detecting the total assist and sucking points based on pump pulsatility was evaluated in acute animal experiments using be... | [left ventricular <Multi-tissue_structure>] [LV <Multi-tissue_structure>] [LV <Multi-tissue_structure>] [coronary arteries <Multi-tissue_structure>] [LV <Multi-tissue_structure>] [LV <Multi-tissue_structure>] [heart <Organ>] |
You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdiv... | [Histophysiology and histopathology of the adrenals in experimental hypokinesia].
In experiments on male rats in the course of 3-month hypokinesia phasic changes were observed in the relative adrenal gland weight, in the volume of the cell nuclei of the glomerular, fasicular zones and the medulla, in the activity of th... | [adrenals <Organ>] [adrenal gland <Organ>] [cell nuclei <Cellular_component>] [glomerular <Multi-tissue_structure>] [fasicular zones <Multi-tissue_structure>] [medulla <Multi-tissue_structure>] [cortical <Multi-tissue_structure>] [medullary layer <Multi-tissue_structure>] [adrenal glands <Organ>] |
This repository contains the data of the paper MedINST: Meta Dataset of Biomedical Instructions.
Citation
@inproceedings{han-etal-2024-medinst,
title = "{M}ed{INST}: Meta Dataset of Biomedical Instructions",
author = "Han, Wenhan and
Fang, Meng and
Zhang, Zihan and
Yin, Yu and
Song, Zirui and
Chen, Ling and
Pechenizkiy, Mykola and
Chen, Qingyu",
editor = "Al-Onaizan, Yaser and
Bansal, Mohit and
Chen, Yun-Nung",
booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2024",
month = nov,
year = "2024",
address = "Miami, Florida, USA",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2024.findings-emnlp.482",
pages = "8221--8240",
}
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