The largest database of trusted experimental protocols
> Anatomy > Body Part > Lamina 3

Lamina 3

Lamina 3 is a key component of the cerebral cortex, playing a crucial role in sensory processing and information integration.
This layer, located between the superficial and deeper cortical layers, is known for its unique neuronal circuitry and connectivity patterns.
Researchers can leverage PubCompare.ai's AI-powered platform to easily locate and compare protocols related to Lamina 3 from a wide range of literature, pre-prints, and patents.
This streamlined process helps identify the most relevant and effective protocols, optimizing research efforts and driving scientific discoveries forward.

Most cited protocols related to «Lamina 3»

Manual segmentations of the 6 cortical layers were created on 51 regions of the cortex, distributed across 13 of the original histological BigBrain sections rescanned at a higher in-plan resolution of 5 μm (Fig 2). These regions were chosen to give a distribution of examples demonstrating a variety of cytoarchitectures, a variety of rostrocaudal locations, in both gyri and sulci, from sections where the cortex was sectioned tangentially.
Layers were segmented according to the following criteria. Layer I, the molecular layer, is relatively cell sparse with few neurons and glia. Layer II, the external granular layer, is a much denser band of small granular cells. Layer III, the external pyramidal layer, is characterized by large pyramidal neurons that become more densely packed toward its lower extent. Layer IV, the internal granular layer (usually referred to simply as the “granular layer”), generally contains only granular neurons, bounded at its lower extent by pyramidal neurons of layer V. Layer V, the internal pyramidal layer, contains large but relatively sparse pyramidal neurons, whereas layer VI, the multiform layer, has a lower density of pyramidal neurons [1 ]. Alongside association areas with such typical neocortical laminar structure, samples from the primary visual and motor cortices were specifically included as they exhibit unique laminar characteristics.
Segmentations were verified by expert anatomists: SB, NPG, and KZ. This resolution is sufficient to distinguish individual cell bodies, a prerequisite to analyze their distribution pattern in cortical layers and to delineate the layers. Averaged across all training examples, layer classes contributed to profiles as follows: background/cerebrospinal fluid (CSF): 14.6%, layer I: 7.5%, layer II: 5.6%, layer III: 20.8%, layer IV: 5.5%, layer V: 14.8%, layer VI: 17.8%, white matter: 13.4%. For the cortical layers, these values represent an approximate relative thickness.
Manual segmentations were then coregistered to the full aligned 3D BigBrain space. The manually drawn layers were used to create corresponding pial and white surfaces. These cortical boundaries were extended beyond layer VI and beyond the pial surface between 0.25 mm and 0.75 mm so as to match the variability of cortical extent in the test profile data set. Training profiles were created by sampling raw, smoothed, and manually segmented data, generating thousands of profiles per sample. Each pixel in the labeled data had a class value of 0 to 7, in which pixels superficial to the pial surface were set to 0, followed by layers numbered 1 to 6, and white matter was classed as 7. This 1D profile-based approach greatly expanded the training data set from 51 labeled 2D samples to over 500,000 profiles. Coregistered manually annotated data are available to download at ftp://bigbrain.loris.ca/BigBrainRelease.2015/Layer_Segmentation/Manual_Annotations/.
Full text: Click here
Publication 2020
Anatomists Cell Body Cells Cerebrospinal Fluid Cortex, Cerebral Genus Loris Lamina 3 Motor Cortex Neocortical External Granular Layer Neuroglia Neurons Neutrophil Band Cells Pyramidal Cells White Matter

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2019
ARID1A protein, human Biological Assay Buffers Cells DNA, A-Form DNA, Single-Stranded DNA Replication Fluorescence Kymography Lamina 3 Microscopy, Confocal Movement Polystyrenes Proteins Radionuclide Imaging Streptavidin TRAP1 protein, human
To analyse AFSM accumulation and glial activation in the grey matter (GFAP‐positive astrocytes + CD68‐positive microglia), markers of oligodendrocyte precursors (Olig2 and NG2) in the white matter and CGRP‐positive fibres in laminae III‐IV of the dorsal horn of the spinal cord, semiautomated thresholding image analysis was performed using Image‐Pro Premier (Media Cybernetics) [17]. This involved collecting slide‐scanned images at 10× magnification from each animal followed by demarcation of regions of interest. Images were subsequently analysed using Image‐Pro Premier (Media Cybernetics) using an appropriate threshold that selected the foreground immunoreactivity above background. Due to the density of interneurons in laminae I‐III of the dorsal horn [20, 21, 22], image densitometry for the average pixel luminance data was gathered for those antigens that showed a higher density of staining (calbindin, calretinin and parvalbumin) and for other antigens with higher staining densities (CGRP, Substance P). Slide‐scanned images at 10x magnification were collected, followed by collecting the mean luminance data across all pixels from regions of interest delineated using StereoInvestigator (MBF Bioscience).
Publication 2020
Animals Antigens Astrocytes Calbindins Calretinin Densitometry Fibrosis Glial Fibrillary Acidic Protein Gray Matter Interneurons Lamina 3 Lamina 4 Microglia Neuroglia OLIG2 protein, human Oligodendrocyte Precursor Cells Parvalbumins Posterior Horn of Spinal Cord Substance P White Matter
MitoSox Red (Molecular Probes, Eugene, OR) was dissolved in a 1:1 mixture of dimethylsulfoxide (DMSO) and saline to a final concentration of 33 μM. Under isoflurane anesthesia, 10 μl of MitoSox was injected intrathecally by using a direct transcutaneous intrathecal injection method described previously. Approximately 23 hrs after MitoSox injection, mice received an i.d. injection of either capsaicin (0.5 %, 25 μl) or the same volume of vehicle on both the plantar and dorsal surfaces of the left hind foot. Mice remained under 1.5 % isoflurane anesthesia for 30 min to suppress any side effects induced by capsaicin. Mice were perfused through the aorta with saline followed by fixative containing 4% paraformaldehyde 1 hr after capsaicin injection and the L4-L5 spinal cord segments were removed. The cord was postfixed 4-15 hr in the perfusion fixative, equilibrated in 30% sucrose, cryosectioned at 30 μm, and mounted on gelatin coated slides. The sections were examined under a fluorescent microscope with a rhodamine filter. Two different regions of the dorsal horn were photographed from 10 randomly selected sections from each animal: the lateral part of laminae I -II and laminae III-V. Photographs were taken with a Q-Imaging Retiga 2000R digital camera attached to an Olympus BX50 microscope using a 63x oil objective lens and saved as digital image files. The number of MitoSox positive cellular profiles with distinctive nuclei (dark oval shaped space surrounded by red granules) was counted from these pictures.
Publication 2009
Anesthesia Animals Aorta Capsaicin Cell Nucleus Cone-Rod Dystrophy 2 Cytoplasmic Granules Fingers Fixatives Foot Gelatins Intrathecal Injection Isoflurane Lamina 1 Lamina 3 Lens, Crystalline Mice, House Microscopy MitoSOX Molecular Probes paraform Perfusion Posterior Horn of Spinal Cord Rhodamine Saline Solution Spinal Cord Sucrose Sulfoxide, Dimethyl
Rapid cooling and laser warming were performed as described by Khosla et al.6 (link), with small modifications as shown in Figure 2. Instead of a zebrafish embryo, microliter-sized droplets with varying CPA and GNR concentrations were pipetted onto the 3.0 × 2.0 × 0.08 mm blade of a modified cryotop (Fig. 6a). A specially designed automated system was used to rapidly cool the droplets by plunging them into liquid nitrogen for at least 10 seconds to allow for equilibration to liquid nitrogen temperature (Fig. S4). For rewarming, a 1064nm Nd: YAG laser (iWeld 980 Series, 120 joule, LaserStar Technologies, FL, USA) was used to provide a high energy singular millisecond pulse. This laser is equipped with a stereomicroscope with an eyepiece crosshair reticule to allow for visualization and alignment of the specimen within the laser chamber, along with a phototube to record high speed video. Once the jig raises the cryotop into the laser’s focus, the laser is automatically fired. The energy provided by a single pulse can be varied by changing the input voltage and pulse time. A laser calibration table was generated using a laser power meter (Nova II, Ophir, Jerusalem, Israel) to determine the amount of energy in joules produced by the laser at a given voltage and pulse time (See Figure S3).
This entire process of cooling and laser warming droplets is captured by the camera. There are two distinct time points in the video which are used to observe ice formation during this process. The first is “prewarming” wherein the droplet is quickly raised into the laser’s focus from the liquid nitrogen; this transition takes less than 0.3s. For our purposes, a vitrified droplet appears transparent without any white spots, whereas ice formation in the droplet appears white or cloudy (either partially or completely). For example, a vitrified 1µL droplet of 2M PG and 1M Trehalose can be seen in Fig. 6d, and a crystalized 1µL droplet of 2M PG can be seen in Fig. 6e.
The second observation point is “post-warming,” wherein the droplet is seen immediately after the laser is fired. It should be noted that the video recording during the millisecond(s) of laser warming is blocked by a protective filter due to possible damage to the camera. Our physical definition of success is that the droplet remains clear, i.e. without the appearance of ice post laser warming. A first warming failure mode we term crystallization exists when the droplet shows ice (white spots) due to underheating because the laser energy was too low to completely rewarm the droplet to its melting temperature. A second failure mode exists if the droplet disappears or get damaged if the laser energy exceeds the rewarming threshold. Examples of all three cases can be seen in Figures 7ac. For each laser warming case, the voltage and pulse width were varied until there was no ice formation within the droplet during rewarming (n=5). For example, a laser pulse with voltage of 250V and pulse width of 1.6ms successfully rewarmed a vitrified 1µL droplet with 2M PG, 1M Trehalose and 1.26×1017 nps/m3 GNR. This technique was used to obtain the laser energy conditions for physical success at different GNR concentrations, CPA concentrations, and droplet volumes.
Publication 2018
Crystallization Embryo Exanthema Lamina 3 Nitrogen Physical Examination Pulse Rate Substantia Gelatinosa Trehalose Vision YAG Lasers Zebrafish

Most recents protocols related to «Lamina 3»

Aerospace structures have employed 3D woven composites in a variety of applications, such as fan blades in the CFM International LEAP (Leading Edge Aviation Propulsion) engine (SAFRAN and GE) [15 ].
The fan is the first rotating element in contact with the air at the entrance of a turbojet engine. It consists of a number of blades arranged on a hub and rotating at the same speed as the rotor. Aircraft fan blades are manufactured using 3D fiber reinforced composites [16 ]. To demonstrate our methodology based on an offline/online strategy, we used numerical simulations of damaged blades to construct an offline database. The literature on numerical modeling of 3D woven composites reveals that several noteworthy investigations have been conducted in the past 20 years [17 (link)].
The foreign object damage panel (FOD panel) used in our case study is a representative substructure of the fan blade chord of dimensions 800 × 350 × 50 mm 3 as shown in Figure 2 and it is used in a V&V (verification and validation) process by the engine OEM (original equipment manufacturer) to evaluate the designed and manufactured hybrid material regarding bird strike and its induced damage. The FOD panel is considered in the European project MORPHO (H2020 EU Project) [18 ].
Full text: Click here
Publication 2023
Aves Europeans Fibrosis Foreign Bodies Hybrids Lamina 3 safran
A standardized procedure was used for constructing the specimens of all four different blocks/groups.
The blocks were inspected for defects such as air bubbles or external voids by visual examination. The blocks were sectioned with the Isomet low-speed saw (Buehler, 11-1280-160, USA), wafering diamond blade 102 mm diameter × 0.3 mm (Buehler, 11-4254, series 15 LC diamond, USA), and lubricant oil (Buehler, Isocut fluid, 11-1193-032, 11-1193-128, USA). The 40 × 45 × 15 mm block was sectioned using a perpendicular holder into two identical specimens, each with the dimensions of 35 × 30 × 6 mm, as shown in Figure 3.
The edges of each block were discarded, while the remaining portion of the rectangular specimens was sectioned further with the help of the Isomet cutting machine calipers. The caliper dimension was adjusted to 2.4 mm, taking into consideration the disc thickness (every two sections from the starting point measured 1 mm in thickness). The specimens were sectioned to obtain the final 15 samples of each of the four provisional restorative materials, Figure 4. The final samples had dimensions of 25 × 2 × 2 mm. A total of 60 specimens were obtained from all four groups of provisional restorative materials.
The 60 specimens were washed under running water and air-dried. The final selection included 10 per group. The specimens chosen were required to have perfect dimensions and did not show any defect under the stereomicroscope.
Full text: Click here
Publication 2023
Diamond Lamina 3 Urination
Fixed SC sections were sliced using a cryostat (Leica CM3050) into 30 μm transverse sections (4 series). The contralateral side was identified with a small cut in the ventral horn. Free-floating sections were stored at −20 °C in a cryoprotectant solution of 30% (m/v) sucrose dissolved in phosphate buffer 0.1 M and 30% (v/v) ethylene glycol, until analysis.
Immunofluorescence staining for ionized calcium binding adaptor molecule 1 (Iba-1) was performed to assess microglial activation. Briefly, one series of SC sections of each animal was washed in 0.1 M PBS, treated with 1% sodium borohydride in PBS for 30 min, and further washed in PBS and in PBS with 0.3% of Triton X-100 (PBST). Then, the sections were incubated for 2 h with a blocking solution containing 0.1 M glycine and 10% normal horse serum (NHS, Gibco, Cat. No. 16050130, Auckland, New Zealand) in PBST to minimize background staining, and incubated for 2 overnights at 4 °C with a rabbit anti-Iba-1 primary antibody (1:1000; Fujifilm Wako, Cat. No. 019-19741, Neuss, Germany) diluted in PBST with 2% NHS. Sections were subsequently washed in PBST and incubated for 1 h with Alexa Fluor-594 donkey anti-rabbit secondary antibody (1:1000; Invitrogen, Cat. No. A21207, Waltham, MA, USA). Finally, after repeated washing with PBST and PBS, sections were mounted on gelatin-coated slides and coverslipped with Prolong Gold antifade mounting reagent with DAPI (Invitrogen Ltd., Cat. No. P36941). Negative controls were performed by omitting the incubation with the primary antibody.
Images of the immunofluorescence reactions were acquired with 2.5 × and 10 × objectives, using a fluorescence microscope (Axio Imager.Z1, Zeiss), through an AxioCam MRm digital camera with AxioVision 4.8.2 software (Carl Zeiss MicroImaging GmbH, Oberkochen, Germany), under the same image acquisition settings. Iba-1 fluorescent intensity was determined in images captured with a 10 × objective, using the open-source software Fiji [47 (link)] in a blinded manner. Images were first converted to 8-bit grayscale and mean grey values were automatically measured within a rectangular region of fixed dimensions (266 × 159 µM) comprising the medial two-thirds of the dorsal horn (laminae I-III) [48 (link)]. Both ipsilateral and contralateral sides were evaluated, and the average ipsilateral/contralateral ratio was calculated to normalize the data. Sections severely damaged in the region of interest were not analyzed and only animals with a minimum of 5 sections available were included in the statistical analysis.
Full text: Click here
Publication 2023
Alexa594 Animals anti-c antibody Antibodies, Anti-Idiotypic Buffers Calcium, Dietary Cryoprotective Agents DAPI Equus asinus Equus caballus Fingers Fluorescent Antibody Technique Gelatins Glycine Glycol, Ethylene Gold Horns Immunoglobulins Lamina 3 Microglia Microscopy, Fluorescence Phosphates Posterior Horn of Spinal Cord Rabbits Serum sodium borohydride Sucrose Triton X-100
The FDA blood pump is a centrifugal pump with a rotor diameter of 52 mm and four rounded blades 3 mm high and 3 mm wide. The diameter D of the inlet section and outlet section of the FDA blood pump is 12 mm. As shown in Figure 1a, the FDA blood pump model was set as Model 1, the position of the inlet was inlet-1, and the length L1 of the inlet was 336 mm, i.e., 28D. To study the influence of inlet position, we truncated the inlet section of the FDA blood pump model and set it as Model 2 (as shown in Figure 1b). Its cut-off position was inlet-2, and the length L2 of the remaining was 36 mm, i.e., 3D. The red dotted line in the figure was the center line from the position plane of inlet (i.e., inlet-1 and inlet-2) to the top plane of the guide-cone, indicating the length of the inlet section of Model 1 and Model 2, which were 28D and 3D respectively. Model 1 and Model 2 represented the extracorporeal blood pump with external loop pipe and the intracorporal blood pump directly connected to the end of the heart respectively. We extended the outlet section of the two models to 203.5 mm to ensure full blood development. Because of the adverse pressure gradient in the diffuser, the position of “Line-d” (see Figure 1c) is likely to cause flow phenomena such as flow separation and transition. Therefore, the flow here is sensitive to the numerical schemes and turbulence models, and can test the capability of numerical schemes in particular.
PIV tests of the FDA blood pump were carried out [10 (link),11 (link)]. The average velocity distributions and pressure heads were tested for six operating conditions, including flow rates from 2.5 L/min to 7 L/min and rotational speeds from 2500 rpm to 3500 rpm. The experimental velocity was taken from 45° of the first quadrant of the impeller and from the line-d of the diffuser in a plane with Z = 6.8 mm (as shown in Figure 1c). The CFD data mentioned in the subsequent results section were also extracted from these lines and compared with the experimental results.
Full text: Click here
Publication 2023
BLOOD Head Heart Hematologic Tests Lamina 3 Pressure Retinal Cone Venous Catheter, Central
Under isoflurane anesthesia, a 3-mm longitudinal incision was made in the skin and fascia of the right hind paw of a mouse using a No. 23 scalpel blade from 3 mm from the proximal end of the heel to the toe. Next, with the use of a monopolar electrosurgery unit (at 50 W; Vetroson® V-10; Summit Hill Laboratories, NJ, USA) with a dispersive electrode pad placed under the mouse's body, a 3-mm longitudinal incision was made on the plantaris muscle, as previously described [18 (link)]. Electrocautery was performed while maintaining coagulation and hemostasis of the incision during dissection. The skin was stitched with two mattress sutures of 7-0 nylon. In sham operated mice, the plantaris muscle was exposed without the incision, and the skin was stitched with a simple interrupted suture of 7-0 nylon.
Full text: Click here
Publication 2023
Anesthesia Coagulation, Blood Diathermy Dissection Electrocoagulation Fascia Heel Hemostasis Human Body Isoflurane Lamina 3 Mice, House Nylons Plantaris Muscle Skin Sutures

Top products related to «Lamina 3»

Sourced in United States
Image-Pro Premier is a powerful image analysis software designed for a wide range of applications. It provides advanced tools for image processing, measurement, and quantification. The software's core function is to enable users to efficiently analyze and extract valuable information from digital images.
Sourced in United States, Canada, Japan, Germany
StereoInvestigator is a software tool designed for quantitative analysis of microscopic samples. It provides a comprehensive platform for stereological data collection and analysis, allowing researchers to obtain precise measurements and estimates of various biological parameters from microscopic images.
Sourced in United States, China, United Kingdom, Germany, Japan, Canada, Australia, Italy, Switzerland, France, Spain
MitoSOX Red is a fluorogenic dye designed to measure superoxide in the mitochondria of live cells. It is readily oxidized by superoxide but not by other reactive oxygen species. The oxidized product is highly fluorescent, allowing for the detection and quantification of mitochondrial superoxide.
Sourced in United States
The CapSure Macro LCM Caps are a specialized laboratory equipment designed for laser capture microdissection (LCM) applications. These caps are used to capture and isolate specific cells or tissue sections from a sample for further analysis.
Sourced in United States
AutoDock Tools 1.5.6 is a molecular docking software package. It allows users to perform automated docking of ligands (small molecules) to protein receptors. The software provides a graphical user interface for preparing input files, running docking calculations, and analyzing the results.
Sourced in United Kingdom
Exponent version 4.0.13.0 is a software product developed by Stable Micro Systems. It is a data analysis and visualization tool designed to work with their line of lab equipment. The software enables users to collect, analyze, and present data from various experiments and tests performed with Stable Micro Systems' instrumentation.
Sourced in Germany, United States, Italy, Switzerland, United Kingdom
The Axiovert 25 is an inverted microscope designed for routine laboratory use. It provides basic functionality for observation and documentation of biological samples.
Sourced in Germany, United States, Japan, Canada, United Kingdom, Switzerland, France, Italy, China, Denmark, Australia, Austria, Slovakia, Morocco
The LSM 700 is a versatile laser scanning microscope designed for high-resolution imaging of samples. It provides precise control over the illumination and detection of fluorescent signals, enabling detailed analysis of biological specimens.
Sourced in United Kingdom, United States
The Texture Analyzer TA.HD Plus is a versatile instrument designed to measure the physical properties and textural characteristics of a wide range of materials. It is capable of performing various tests, including compression, tensile, shear, and puncture tests, to quantify the mechanical and textural properties of samples. The instrument features a robust design and advanced software for data acquisition and analysis.
Sourced in United States, United Kingdom, Germany, Japan, France, Canada, Switzerland, Sweden, Italy, China, Australia, Austria, Ireland, Norway, Belgium, Spain, Denmark
HBSS (Hank's Balanced Salt Solution) is a salt-based buffer solution commonly used in cell culture and biological research applications. It provides a balanced ionic environment to maintain the pH and osmotic pressure of cell cultures. The solution contains various inorganic salts, including calcium, magnesium, and potassium, as well as glucose, to support cell viability and homeostasis.

More about "Lamina 3"

Lamina 3, a critical component of the cerebral cortex, plays a pivotal role in sensory processing and information integration.
This middle layer, situated between the superficial and deeper cortical strata, is renowned for its unique neuronal circuitry and connectivity patterns.
Researchers can leverage the AI-powered platform of PubCompare.ai to easily locate and compare protocols related to Lamina 3 from a wide range of literature, pre-prints, and patents, streamlining the research process and driving scientific discoveries forward.
Explore the intricate workings of Lamina 3 and its importance in the cortical hierarchy.
Delve into the diverse neuronal populations, including pyramidal cells, interneurons, and specialized subtypes, that contribute to the layer's complex functionality.
Understand how Lamina 3 integrates sensory inputs, processes information, and facilitates higher-order cognitive processes.
Utilize cutting-edge tools and software to study Lamina 3 in-depth.
Leverage Image-Pro Premier for advanced image analysis, StereoInvestigator for 3D reconstruction and quantification, and MitoSOX Red for mitochondrial function assessment.
Employ CapSure Macro LCM Caps for precise cell isolation, AutoDock Tools 1.5.6 for molecular docking simulations, and Exponent version 4.0.13.0 for comprehensive data analysis.
Visualize Lamina 3 using Axiovert 25 and LSM 700 microscopy systems, and measure its mechanical properties with the Texture Analyzer TA.HD Plus.
Explore the wealth of protocols and studies related to Lamina 3, curated and compared by the AI-powered PubCompare.ai platform.
Identify the most relevant and effective methodologies, optimize your research efforts, and drive your scientific discoveries to new heights.
Harness the power of PubCompare.ai to streamline your Lamina 3 investigations and unlock the secrets of this pivotal cortical layer.