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Brain Stem

The brain stem is a crucial part of the central nervous system, connecting the cerebrum to the spinal cord and regulating vital functions such as breathing, heart rate, and blood pressure.
This region is composed of the midbrain, pons, and medulla oblongata, each with specialized roles in sensory processing, motor control, and autonomic regulation.
Researchers studying the brain stem face the challenge of reproducibility and accuracy in their experiments, as the complex anatomy and functions of this area require careful methodological approaches.
PubCompare.ai offers an AI-driven platform to help researchers easily locate the best protocols from published literature, preprints, and patents, leverageing intelligent comparisons to identify the most relibale and effective methods for brain stem studies.
This tool can take your research to new heights, maximizing the reproducibility and accuracy of your brain stem investigations.

Most cited protocols related to «Brain Stem»

1
Diagnostic Criteria for Autoimmune Encephalitis

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Publication 2016
Anti-N-Methyl-D-Aspartate Receptor Encephalitis Autoantibodies Brain Stem Consciousness Diagnosis Encephalitis Hashimoto's encephalitis Limbic Encephalitis Memory Neurons Symptom Assessment
2
Polysome Immunoprecipitation and RNA Extraction

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Publication 2008
1,2-dihexadecyl-sn-glycero-3-phosphocholine Alabaster austin Brain Stem Buffers Cells Cerebellum Chloroform Cholinergic Agents Cold Temperature Cycloheximide Deoxyribonucleases Digestion Dithiothreitol Endoribonucleases Ethanol G-substrate Goat HEPES inhibitors Isopropyl Alcohol Lipids Magnesium Chloride Mice, Laboratory Mice, Transgenic Motor Neurons Nonidet P-40 Polyribosomes Protease Inhibitors Purkinje Cells Ribosomal RNA RNA, Messenger Sodium Acetate Sodium Chloride Striatum, Corpus Teflon Tissues trizol
3
Automated Cortical Thickness Extraction Pipeline

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Publication 2017
Ankylosis Ants Brain Brain Stem Cerebellum Cerebrospinal Fluid Cortex, Cerebral Cranium CREB3L1 protein, human Dementia Embarc Genetic Heterogeneity Gray Matter Hybrids Reconstructive Surgical Procedures Tissues White Matter
4
Amyloid PET Imaging Data Analysis Protocols
PiB and florbetapir image data were analyzed using 2 processing streams. The PET-template analysis method was described in a separate study (10 (link)). This method was applied to the raw and unsmoothed datasets. Briefly, image data were spatially normalized to standard atlas coordinates in Talairach space using statistical parametric mapping software (11 ). Mean tracer retention was calculated for 6 predefined target cortical regions of interest (medial orbital frontal, temporal, parietal, anterior cingulate, posterior cingulate, and precuneus) that resulted from a statistical contrast of AD patients and cognitively normal subjects (1 (link)).
The Freesurfer method for quantifying cortical Aβ was applied to the unsmoothed and smoothed datasets. This method was described in detail elsewhere (2 (link),12 (link)) and online (13 ). Structural 1.5-T or 3-T MRI scans (T1-weighted images) were used to define cortical regions of interest and the cerebellar reference region. In general, 2 structural MRI scans were acquired at each visit across several years of follow-up, with the result that several MR images were available for each subject. For processing the PiB images, we chose the T1 scans acquired concurrently with (or closest in time to) the first PiB scan; and for the florbetapir processing, we chose the T1 scans acquired concurrently with (or closest in time to) the florbetapir scan. Structural MR images were segmented and parceled into individual cortical regions with Freesurfer (version 4.5.0; surfer.nmr.mgh.harvard.edu/) and subsequently used to extract mean PiB and florbetapir cortical retention ratios from gray matter within lateral and medial frontal, anterior and posterior cingulate, lateral parietal, and lateral temporal regions.
To examine several reference regions, the unscaled cortical means for each analysis method were divided by mean retention in the following 3 reference regions: brain stem–pons, whole cerebellum (white and gray matter), and cerebellar gray matter, yielding 3 cortical retention ratios for each preprocessing method. Because Freesurfer creates a brain stem, but not pons, region as part of its automated processing stream, the brain stem was used for the Free-surfer processing analysis method and the pons was used for the PET-template processing method.
To summarize, for each of 3 PET sessions (2 PiB scans and 1 florbetapir scan), every subject had cortical retention ratios for 2 levels of processing and 2 analysis methods (raw and unsmoothed for the PET-template method and unsmoothed and smoothed for the Freesurfer method), using 3 reference regions (brain stem–pons, whole cerebellum, cerebellar gray matter), resulting in 36 mean cortical retention ratios per subject that were compared in subsequent statistical analyses.
Landau S.M., Breault C., Joshi A.D., Pontecorvo M., Mathis C.A., Jagust W.J, & Mintun M.A. (2012). Amyloid-β Imaging with Pittsburgh Compound B and Florbetapir: Comparing Radiotracers and Quantification Methods. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 54(1), 70-77.
Publication 2012
Brain Stem Cerebellar Gray Matter Cerebellum Cortex, Cerebral florbetapir Gray Matter Gyrus, Anterior Cingulate MRI Scans Patients Pons Posterior Cingulate Cortex Precuneus Radionuclide Imaging Retention (Psychology) Temporal Lobe
5
Neuroimaging Markers of Cerebrovascular Disease
All MRIs were assessed blinded to clinical information by one experienced neuroradiologist for the presence, location, and size of the recent symptomatic infarct and any other vascular lesions. A recent infarct was defined as a hyperintense area on DWI with corresponding reduced signal on the apparent diffusion coefficient image, with or without increased signal on FLAIR or T2-weighted imaging, that corresponded with a typical vascular territory.18 Recent small subcortical (lacunar) infarcts were defined as rounded or ovoid lesions with signal characteristics as above, >3- but <20-mm diameter, in the basal ganglia, internal capsule, centrum semiovale, or brainstem and carefully distinguished from WMH.1 (link) Cortical infarcts were defined as infarcts involving cortical ± adjacent subcortical tissue, or large (>2-cm) striatocapsular/subcortical lesions.14 (link) Lacunes were defined as rounded or ovoid lesions, >3- and <20-mm diameter, in the basal ganglia, internal capsule, centrum semiovale, or brainstem, of CSF signal intensity on T2 and FLAIR, generally with a hyperintense rim on FLAIR and no increased signal on DWI.14 (link) Microbleeds were defined as small (<5 mm), homogeneous, round foci of low signal intensity on gradient echo images in cerebellum, brainstem, basal ganglia, white matter, or cortico-subcortical junction, differentiated from vessel flow voids and mineral depositions in the globi pallidi.14 (link) Deep and periventricular WMH were both coded according to the Fazekas scale from 0 to 3.19 (link) We defined PVS as small (<3 mm) punctate (if perpendicular) and linear (if longitudinal to the plane of scan) hyperintensities on T2 images in the basal ganglia or centrum semiovale, and they were rated on a previously described, validated semiquantitative scale from 0 to 4.7 (link) Cerebral atrophy was classified for both deep (enlargement of the ventricles) and superficial (enlargement of the sulci) components on a 4-point scale (absent, mild, moderate, severe) in study 1, and on a modified 6-point version of the same scale in study 2.20 (link) The atrophy grade is determined by comparison with templates indicating normal to atrophied brains obtained in research into normal subjects on our scanner.20 (link) To merge the data from both studies, we condensed study 2's version to 4 categories (1 absent, 2–3 mild, 4 moderate, 5–6 severe). The intraclass correlation coefficient for WMH intraobserver rating (100 scans) was 0.96. The intrarater κ for PVS (50 scans) was 0.80 to 0.90 (unpublished data), for lacunes was 0.85 (unpublished data), and for microbleeds was 0.68 to 0.78.21 (link)
Staals J., Makin S.D., Doubal F.N., Dennis M.S, & Wardlaw J.M. (2014). Stroke subtype, vascular risk factors, and total MRI brain small-vessel disease burden. Neurology, 83(14), 1228-1234.
Publication 2014
Basal Ganglia Blood Vessel Brain Brain Stem Cerebellum Cortex, Cerebral Diffusion ECHO protocol Globus Pallidus Heart Ventricle Hypertrophy Infarction Infarction, Lacunar Internal Capsule Magnetic Resonance Imaging Minerals Radionuclide Imaging Tissues Urination White Matter

Most recents protocols related to «Brain Stem»

1
Fetal Brain Structure Segmentation and Volumetric Analysis

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Publication 2023
Basal Ganglia Brain Stem Care, Prenatal Cell Nucleus Cerebellum Cerebral Hemispheres Cortex, Cerebral Gray Matter Heart Ventricle Neurologists Ventricle, Lateral Ventricles, Fourth Ventricles, Third Vermis, Cerebellar White Matter
2
Dissection of Avian Brainstem Regions
According to the previous studies on avian species and a chick brain atlas (Kuenzel and Masson, 1988 ; Kang et al., 2009 (link); Kang et al., 2020 (link)), two major 5-HTergic regions in the brainstem, DRN and CRN, and VTA regions were dissected in a cryostat microtome. The dimensions of the dissected section are as follows: 2.5–3 mm (W) x 1–1.5 mm (H) x 2.5–3.0 mm (L) for DRN; 2–2.5 mm (W) x 1–1.2 mm (H) x 2.5–3.0 mm (L) for CRN; and 3–3.5 mm (W) x 2–3 mm (H) x 1–1.2 mm (L) for VTA. The thickness (W, H, and L) of the dissected brain tissue block was proportionally increased from young birds to older birds based on the brain size and structure. Inside the cryostat, the brain areas shown as rectangles were dissected from each flattened brain section using a scalpel handle and blade (#11) and were quickly transferred to TRIzol reagent and then stored at -80°C until total RNA extraction.
Kang S.W., Christensen K.D., Kidd Jr M.T., Orlowski S.K, & Clark J. (2023). Effects of a variable light intensity lighting program on the welfare and performance of commercial broiler chickens. Frontiers in Physiology, 14, 1059055.
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Publication 2023
Aves Brain Brain Stem Microtomy Tissues trizol
3
Comprehensive Stroke Risk Assessment
In this study, clinical data were collected from the enrolled patients, including demographics (age and sex); vascular risk factors (hypertension, diabetes mellitus, and ischemic heart disease); baseline blood pressure [systolic blood pressure (SBP) and diastolic blood pressure (DBP)]; Trial of Org 10 172 in Acute Stroke Treatment (TOAST) [large-artery atherosclerosis, cardioembolism, small-vessel occlusion, acute stroke of other determined etiology, stroke of undetermined etiology]; stroke severity (SS) [defined as mild stroke according to the National Institutes of Health Stroke Scale (NIHSS) scores of ≤ 8, moderate-to-severe stroke according to NIHSS scores of ≥9; all assessments completed on admission]; magnetic resonance imaging (MRI) features [stroke distribution (SD; anterior circulation, posterior circulation, and anterior/posterior circulation), side of hemisphere (SOH; left, right, and bilateral), number of stroke lesions (NOSs; single and multiple stroke lesions), site of stroke lesions (SOSs; cortical, cortico-subcortical, subcortical, brainstem, and cerebellum)]; laboratory tests [total cholesterol, triglycerides, low-density lipoprotein (LDL), fasting blood glucose (FBG), homocysteine (HCY), uric acid (UA), fibrinogen (FIB), myoglobin (MB), C-reactive protein (CRP), D-dimer brain natriuretic peptide (BNP), HBALC, neuron-specific enolase (NSE), and S-100β levels], treatment regimen [intravenous thrombolysis, arterial thrombolysis, antiplatelet, anticoagulation, statin, and proton pump inhibitor therapy (PPI)]; and stroke comorbidities [dysphagia and stroke-associated pneumonia (SAP)].
Wang K., Gu L., Liu W., Xu C., Yin C., Liu H., Rong L., Li W, & Wei X. (2023). The predictors of death within 1 year in acute ischemic stroke patients based on machine learning. Frontiers in Neurology, 14, 1092534.
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Publication 2023
Acute Cerebrovascular Accidents Arteries Atherosclerosis Blood Glucose Blood Pressure Blood Vessel Brain Stem Cerebellum Cerebrovascular Accident Cholesterol Cortex, Cerebral C Reactive Protein Deglutition Disorders Dental Occlusion Diabetes Mellitus fibrin fragment D Fibrinogen Fibrinolytic Agents gamma-Enolase High Blood Pressures Homocysteine Hydroxymethylglutaryl-CoA Reductase Inhibitors Low-Density Lipoproteins Myocardial Ischemia Myoglobin Nesiritide Patients Pneumonia Pressure, Diastolic Proton Pump Inhibitors Systolic Pressure Therapeutics Treatment Protocols Triglycerides Uric Acid
4
Fluorescent Labeling of Brainstem Neurons
Mice were first deeply anesthetized with a combination of ketamine (100 mg/kg) and xylazine (10 mg/kg), then transcardially perfused with PBS, followed by ice-cold 4% paraformaldehyde (PFA). After removing the cerebral cortex, the brainstem was left in the skull and postfixed in the same fixative overnight at 4°C. Parasagittal or coronal sections, 40–50 μm thick, of the CN were cut with a vibratome (Leica 1000S).
Free floating sections were collected, permeabilized, blocked with 3% BSA, and incubated with primary anti-GFP antibody (rabbit, Abcam catalog #ab290, 1:500) overnight on a shaker at 4°C to preserve the fluorescent signal of CeFP of the hVOS probe in TRAP-labeled neurons. In some experiments, sections were double stained with anti-tubulin β-III antibody (TUBB3, mouse, BioLegend catalog #801202, 1:500), as a neuronal marker. Sections were then incubated with fluorescent-dye conjugated secondary antibodies for 2 h (Alexa 568 anti-rabbit, Abcam catalog #ab175692, 1:500; Alexa 488 anti-mouse, 1:500, ThermoFisher Scientific catalog #A21202) and counterstained with DAPI for 10 min at room temperature. Images were acquired with a confocal microscope (Nikon A1RS) and processed with ImageJ.
Ma Y., Shu W.C., Lin L., Cao X.J., Oertel D., Smith P.H, & Jackson M.B. (2023). Imaging Voltage Globally and in Isofrequency Lamina in Slices of Mouse Ventral Cochlear Nucleus. eNeuro, 10(3), ENEURO.0465-22.2023.
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Publication 2023
alexa 568 anti-H-2 antibodies Antibodies, Anti-Idiotypic Brain Stem Cold Temperature Cortex, Cerebral Cranium DAPI Fixatives Fluorescent Dyes Fluorescent Probes Ketamine Mice, House Microscopy, Confocal Neurons paraform Rabbits TUBB3 protein, human Tubulin Xylazine
5
Ultrastructural Analysis of Brain Capillaries
Another subgroup of SHR-S, SHR-T, Wistar-S, and Wistar-T received, after the functional measurements, an overdose of ketamine + xylazine. Immediately after the respiratory arrest, the thorax was opened and the left ventricle cannulated for sterile saline perfusion (∼30 mL/min, Daigger pump, Vernon Hills IL United States) followed by modified Karnovsky solution (2.5% glutaraldehyde +2% paraformaldehyde in 0.1 M PBS, pH 7.3). Brain was removed and placed on a coronal brain matrix (72–5029, Harvard Apparatus) to obtain hypothalamic and brainstem slices. PVN, NTS, and RVLM nuclei were microdissected with the aid of a magnifying lens, using as anatomic markers the third ventricle and optic chiasma, the central canal and 4th ventricle, and, the nucleus ambiguous, raphe obscurus and inferior olive, respectively. The nuclei were immersed in a 2.5% glutaraldehyde solution for 2 h, washed in PBS and post-fixed in a 2% osmium tetroxide solution for 2 h at 4°C. Tissues were then stained overnight with uranyl acetate, dehydrated in 60% up to 100% ethanol series and immersed in pure resin. Semi-thin slices (400 nm, ultra-microtome Leica EMUC6) were obtained, placed in glass slides and stained with Toluidine Blue in order to select adequate areas for further processing. Ultra-thin slices (60 nm) were obtained with diamond knife, contrasted with 4% uranyl acetate and 0.4% lead acetate and disposed in 200 copper mesh screens.
Transverse sections of PVN, NTS, and RVLM capillaries of the 4 experimental groups were acquired in a transmission electron microscope (FEI Tecnai G20, 200 KV) and analyzed by a blind observer using the ImageJ software. The following parameters were analyzed in 9–11 capillaries/area/rat, 3 rats/experimental group: luminal and abluminal perimeter, lumen diameter, area of the endothelial cell, thickness of the basement membrane, pericytes’ coverage of capillaries, extension of capillary border between adjacent endothelial cells, the occurrence/extension of tight junctions, and, the counting of transcellular vesicles/capillary. To avoid the inclusion of non-transcytotic vesicles such as lysosomes, endosomes, peroxisomes, only the vesicles being formed at the luminal, and abluminal membranes were counted. Vesicle counting was expressed as number/capillary. Using the zoom to expand acquired images, the whole extension of capillaries was analyzed.
Candido V.B., Perego S.M., Ceroni A., Metzger M., Colquhoun A, & Michelini L.C. (2023). Trained hypertensive rats exhibit decreased transcellular vesicle trafficking, increased tight junctions’ density, restored blood-brain barrier permeability and normalized autonomic control of the circulation. Frontiers in Physiology, 14, 1069485.
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Publication 2023
Brain Brain Stem Capillaries Cell Nucleus Chest Copper Diamond Drug Overdose Endosomes Endothelial Cells Ethanol Glutaral Hypothalamus Ketamine lead acetate Left Ventricles Lens, Crystalline Lysosomes Membrane, Basement Microtomy Nucleus Raphe Obscurus Olivary Nucleus Optic Chiasms Osmium Tetroxide paraform Perfusion Pericytes Perimetry Peroxisome Phenobarbital Pulp Canals Rattus norvegicus Resins, Plant Respiratory Rate Saline Solution Sterility, Reproductive Tight Junctions Tissue, Membrane Tissues Tolonium Chloride Transcytosis Transmission Electron Microscopy uranyl acetate Ventricles, Fourth Ventricles, Third Visually Impaired Persons Xylazine

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1
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