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Brain

The brain is a complex and fascinating organ that serves as the control center of the body.
It is responsible for a wide range of functions, including cognition, emotion, movement, and sensory perception.
The brain is composed of billions of interconnected neurons that work together to process information and coordinate the body's activities.
Researchers in the field of brain science are constantly working to unravel the mysteries of this remarkable organ, exploring its anatomy, physiology, and the ways in which it can be affected by disease, injury, and environmental factors.
Whether you're interested in the neurobiology of learning and memory, the neural basis of psychopathology, or the potential of brain-computer interfaces, the study of the brain offers endless possibiliites for discovery and advancement.
Dive into the worlld of brain research and unlock the secrets of this remarkable organ.

Most cited protocols related to «Brain»

1
Functional MRI Preprocessing Workflow

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Publication 2011
bis(tri-n-hexylsiloxy)(2,3-naphthalocyaninato)silicon Brain fMRI Head Movements Movement Radionuclide Imaging Rage
2
Optimizing Eddy Current Correction for Diffusion MRI Data
For several of the data sets, the diffusion gradients are duplicated for opposing PE-directions. This offers a way to assess the performance of eddy and also to compare it to a commonly used existing method (eddy_correct in FSL) that uses FLIRT (Jenkinson and Smith, 2001 (link)), a 12-dof affine transformation and correlation ratio as a cost-function to register the diffusion weighted images to a b = 0 image. Two images acquired with the same diffusion gradient will have the same contrast and any difference between them should be due to differences in distortions and/or measurement error (noise). We therefore ran eddy separately on the data with the two different PE-directions and then calculated the sum-of-squared differences for paired diffusion weighted images.
Data acquired with different PE-directions also differ with respect to different susceptibility-induced distortions and if not corrected these would dominate any comparison between the images. We therefore used RGM and pairs of b = 0 (where there will be no eddy current-induced distortions) with different PE-directions to estimate the susceptibility-induced off-resonance field and applied that to the images using spline-interpolation and Jacobian modulation (see section Resampling the images). These “susceptibility-only corrected” pairs were the baseline against which the eddy and eddy_correct methods were compared. The eddy_correct method was modified to use spline interpolation and also to be able to incorporate the susceptibility-field from RGM so as to allow for a single resampling into a space corrected for susceptibility, eddy currents and subject movement in the same way that eddy does.
A series of tests was run on the FMRIB (data sets A and B ) and the early HCP data ( C ) to evaluate different settings for the options in eddy. As described above these tests were performed by running eddy separately on the A → P and the P → A (or L → R and R → L in the case of the HCP 3 T data ( C )) data and then compared pairwise to assess how well the correction worked. These settings were
Estimation of GP hyperparameters There are several different options for determining the hyperparameters for the Gaussian process that model the diffusion signal. These are maximum marginal likelihood (MML), leave-one-out cross validation (CV) and Geissers's surrogate predictive probability (GPP). For each method data was extracted from 1000 random brain voxels and used for the estimation. Note that this random voxel selection potentially introduces a run-to-run variability to the eddy results, but which can be turned off by specifying a seed at the command level.
Q-space smoothing The GP can be seen as a smoothing operation in Q-space. We tested different levels of increased smoothing by multiplying the error-variance estimates (hyperparameter of the GP) by values ranging from 1 (no additional smoothing) to 10.
Spatial smoothing Data and predictions were smoothed with a Gaussian filter with FWHM ranging from 0 to 5 mm. N.B. that the filtering is applied only during the estimation phase and not to the final resampled results.
EC model Different models for the EC-induced fields corresponding to first (four parameters), second (ten parameters) and third (20 parameters) order polynomials were tested. See Appendix A for a complete description of the different models.
Second level modeling The EC-parameters were fitted to a first or second order polynomial at the end of each iteration.
Joint modeling of multi-shell data When having multi-shell data one can either correct each shell independently or one can model (and correct) them all simultaneously. The latter option is potentially better because the Gaussian process is able to use data from one shell when making predictions about another shell (Andersson and Sotiropoulos, 2015 ). To test that, we corrected the HCP 3 T data ( C ) for each shell individually and also jointly for all four shells.
Andersson J.L, & Sotiropoulos S.N. (2016). An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. Neuroimage, 125, 1063-1078.
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Publication 2016
Brain Diffusion Joints Movement Susceptibility, Disease Vibration
3
Systematic Characterization of Mouse Brain
All experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Allen Institute for Brain Science in accordance with NIH guidelines. All characterization was done using adult mice around ages P56 or older. The mice that were characterized were in a mixed genetic background, containing 50–75% C57BL/6 background and the remainders of 129 or other backgrounds from the various Cre lines. For systematic characterization of fluorescent proteins either by their native fluorescence or IHC, perfused brains were cryosectioned using a tape transfer technique, sections were then DAPI stained directly or following antibody staining, and images were captured using automated fluorescent microscopy. Microtome sections of 100-μm thickness from perfused brains were used for confocal imaging of fluorescently labeled cells. For systematic characterization of gene expression by colorimetric ISH or DFISH, the Allen Institute established pipelines for tissue processing, probe hybridization, image capture and data processing were utilized. Informatics signal identification, mapping, and quantification used the Allen Mouse Brain Atlas spatial mapping platform24 (link), 29 . In this pipeline, image series are preprocessed (white-balanced and cropped), then registered to a three-dimensional informatics reference atlas of the C57BL/6J mouse brain28 . This registration enables data to be displayed in 2D sections or reconstructed 3D volumes.
Madisen L., Zwingman T.A., Sunkin S.M., Oh S.W., Zariwala H.A., Gu H., Ng L.L., Palmiter R.D., Hawrylycz M.J., Jones A.R., Lein E.S, & Zeng H. (2009). A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nature neuroscience, 13(1), 133-140.
Publication 2009
Acid Hybridizations, Nucleic Adult Brain Cells Colorimetry DAPI Fluorescence Gene Expression Genetic Background Immunoglobulins Institutional Animal Care and Use Committees Mice, Inbred C57BL Mice, Laboratory Microscopy Microtomy Proteins Tissues
4
Robust Functional Connectivity Analysis

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Publication 2011
Brain derivatives Head Heart Ventricle Human Body Muscle Rigidity Neurons White Matter
5
Benchmarking RNA-seq Expression Profiles
As an example of real RNA-seq data with known expression profiles, data generated by the SEQC Project (2 (link)) was used. Two particular FASTQ files were used, one generated from sequencing of Human Brain Reference RNA (HBRR) and one from Universal Human Reference RNA (UHRR). Each file contains 15 million 100 bp read-pairs and was generated from an Illumina HiSeq sequencer.
The SEQC Project includes expression values measured by TaqMan RT-PCR for slightly over 1000 genes for both HBRR and UHRR. 958 of these TaqMan validated genes were found to have matched symbols with genes in the RNA-seq data. The TaqMan RT-PCR expression values are available from the seqc Bioconductor package.
Liao Y., Smyth G.K, & Shi W. (2019). The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research, 47(8), e47.
Publication 2019
Brain Genes Homo sapiens Reverse Transcriptase Polymerase Chain Reaction RNA-Seq

Most recents protocols related to «Brain»

1
Xenon Liposome Protects Astrocytes
Not available on PMC !

Example 5

Human brain astrocytes play a key role in maintaining nerve cell function and survival against oxidative stress. Exposure of cultured human brain astrocytes to H2O2 causes significant damages to the cells, and caused them to release large amounts of LDH. However, pretreatment of the brain cells with Xe-ELIP reagents markedly reduced LDH release (FIG. 15), indicating a protective effect of Xe-ELIP on the brain cells injured by the oxidative stress. No or little protective effect was found in the cells treated with ELIP alone or control media (FIG. 15).

US11872312B2. Neuroprotective liposome compositions and methods for treatment of stroke (2024-01-16). The Board of Regents of The University of Texas System [US]. Inventors: Shao-Ling Huang [US], Melvin E. Klegerman [US], Yong-Jian Geng [US], Hyunggun Kim [US], David D. McPherson [US].
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Patent 2024
Astrocytes Brain Cells Cytotoxin Homo sapiens Neurons Oxidative Stress Peroxide, Hydrogen
2
Evaluating Tucaresol and Checkpoint Inhibitors in Xenograft Models
Not available on PMC !

Example 7

Five groups including tucaresol, tucaresol plus PD-1 or PD-L1 antibody, tucaresol plus CTLA-4 antibody, CTLA-4 antibody plus PD-1 or PD-L1 antibody, and tucaresol plus plinabulin are tested to determine their effect in an animal xenograft model.

The combined treatment with tucaresol and the checkpoint inhibitor(s) is tested in comparison with the treatment with tucaresol alone, the treatment with checkpoint inhibitor alone, or combination of checkpoint inhibitors. The tests are performed using seven to ten-week old athymic (nu/nu) mice that were injected subcutaneously with human tumor cell lines (of either solid or liquid tumor origin, for example of breast, lung, colon, brain, liver, leukemia, myeloma, lymphoma, sarcoma, pancreatic or renal origin). Six to ten testing groups are prepared, and each group includes 10 mice.

Each treatment starts at tumor size between 40-150 mm3 and continues until Day 24-56, when the animals are necropsied. To determine the efficacy of each treatment, the following data are collected: mortality; the body weight of the mice assessed twice weekly both prior to treatments; the rate of tumor growth as determined by the tumor size measurement (twice every week); the tumor growth index; overall survival rate; the tumor weight at necropsy; and the time required to increase tumor size 10 fold.

US11857522B2. Compositions containing tucaresol or its analogs (2024-01-02). BeyondSpring Pharmaceuticals, Inc. [US]. Inventors: Ramon Mohanlal [US], Lan Huang [US], George Kenneth Lloyd [US].
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Patent 2024
Animal Model Animals Autopsy Body Weight Brain Breast CD274 protein, human Cell Cycle Checkpoints Cell Line, Tumor Colon Combined Modality Therapy CTLA4 protein, human Genes, Neoplasm GZMB protein, human Heterografts Homo sapiens Immunoglobulins inhibitors Kidney Leukemia Liver Lung Lymphoma Mice, Nude Multiple Myeloma Mus Neoplasms Pancreas plinabulin Sarcoma Thymic aplasia tucaresol
3
In Vivo Imaging of Soft Tissue Infection
Not available on PMC !

Example 4

Initial in vivo studies focused on soft tissue models of MSSA infection. This included a mouse thigh infection model and rat triceps model. FIG. 2 shows data for the accumulation of [18F]F-PABA in the triceps of an infected rat. Fifty μL of 109 CFU of Newman S. aureus BHI culture was injected into the right triceps of a rat. After 10-15 hr the rats were imaged following iv administration of 0.8-1.2 mCi of [18F]F-PABA. The images clearly show the accumulation of radioactivity in the right but not the left triceps. In addition to monitoring the time course of [18F]F-PABA biodistribution, we also quantified tracer levels by postmortem ex vivo counting. While the [18F]F-PABA distributed to all tissues and organs with the exception of the brain, significant tracer accumulation was only observed in the right triceps, as well as the kidney, bladder and GI tracts due to tracer clearance. At 60 min tracer levels were 5.4× higher in the infected right triceps compared to the uninfected left triceps. This compares favorably with other tracers.

US11857352B2. Positron imaging tomography imaging agent composition and method for bacterial infection (2024-01-02). The Research Foundation for the State University of New York [US]. Inventors: Peter Tonge [US], Zhuo Zhang [US], Peter Smith-Jones [US], Li Liu [US], Hui Wang [US].
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Patent 2024
4-Aminobenzoic Acid Autopsy Brain Gastrointestinal Tract Infection Kidney Mus Radioactivity Rattus Thigh Tissues Urinary Bladder
4
Sepsis Modeling in Mice Using N. meningitidis Strains
Not available on PMC !

Example 7

Sepsis modeling was performed as described by Gorringe A. R., Reddin, K. M., Voet P. and Poolman J. T. (Methods Mol. Med. 66, 241 (Jan. 1, 2001)) and Johswich, K. O. et al. (Infect. Immun. 80, 2346 (Jul. 1, 2012)). Groups of 6 eight-week-old C57BL/6 mice (Charles River Laboratories) were inoculated via intraperitoneal injection with N. meningitidis strain B16B6, B16B6 Δtbpb, or B16B6 Δnmb0313 (N=2 independent experiments). To prepare inoculums, bacterial strains for infection were grown overnight on GC agar, resuspended and then grown for 4 h in 10 ml of Brain Heart Infusion (BHI) medium at 37° C. with shaking. Cultures were adjusted such that each final 500 μl inoculum contained 1×106 colony forming units and 10 mg human holo-transferrin. Mice were monitored at least every 12 h starting 48 h before infection to 48 h after infection for changes in weight, clinical symptoms and bacteremia. Mice were scored on a scale of 0-2 based on the severity of the following clinical symptoms: grooming, posture, appearance of eyes and nose, breathing, dehydration, diarrhea, unprovoked behavior, and provoked behavior. Animals reaching endpoint criteria were humanely euthanized. Animal experiments were conducted in accordance with the Animal Ethics Review Committee of the University of Toronto.

FIG. 7 shows the results obtained. FIG. 7A shows a solid phase binding assay consisting of N.men cells fixed with paraformaldehyde (PFA) or lysed with SDS and were spotted onto nitrocellulose and probed with α-TbpB antibodies. ΔSLAM/tn5 refers to the original strain of SLAM deficient cells obtained through transposon insertion. ΔSLAM describes the knockout of SLAM in Neisseria meningitidis obtained by replacing the SLAM ORF with a kanamycin resistance cassette. FIG. 7B shows a Proteinase K digestion assay showing the degradation of TbpB, LbpB and fHbp only when Nm cells are SLAM deficient (ΔSLAM). Nm cells expressing individual SLPs alone and with SLAM were incubated with proteinase K and Western blots were used to detect levels of all three SLPs levels with and without protease digestion (−/+). Flow cytometry was used to confirm that ΔSLAM cells could not display TbpB (FIG. 7C) or fHbp (FIG. 7D) on the cell surface. Antibodies against TbpB and fHbp were used to bind surface exposed SLPs followed by incubation with a α-Rabbit antibody linked to phycoerythrin to provide fluorescence. The mean fluorescent intensity (MFI) of each sample was measured using the FL2 detector of a BD FACS Calibur. The signal obtained from wildtype cells was set to 100% for comparison with signals from knockout cells. Error bars represent the standard error of the mean (SEM) from three experiments. Shown in FIG. 7E are the results of mice infections with various strains. Mice were infected via intraperitoneal injection with 1×106 CFU of wildtype N. meningitidis strain B16B6, B16B6 with a knockout of TbpB (ΔtbpB), or B16B6 with a knockout of nmb0313 Δslam and monitored for survival and disease symptoms every 12 h starting 48 hr pre-infection to 48 h post-infection and additionally monitored at 3 hr post-infection. Statistical differences in survival were assessed by a Mantel-Cox log rank test (GraphPad Prism 5) (*p<0.05, n.s. not significant). These results show a marked reduction in post-infection mortality in mice infected with the knockout of nmb0313 Δslam strain.

US11872275B2. SLAM polynucleotides and polypeptides and uses thereof (2024-01-16). ENGINEERED ANTIGENS INC. [CA]. Inventors: Trevor F. Moraes [CA], Christine Chieh-Lin Lai [CA], Yogesh Hooda [CA], Andrew Judd [CA], Anthony B. Schryvers [CA], Scott D. Gray-Owen [CA].
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Patent 2024
Agar Animals Antibodies Bacteremia Bacterial Infections Biological Assay Brain Cells Cultured Cells Dehydration Diarrhea Digestion Endopeptidase K Eye Flow Cytometry Fluorescence Genes Heart Homo sapiens Immunoglobulins Infection Injections, Intraperitoneal Jumping Genes Kanamycin Resistance Mice, Inbred C57BL Mus Neisseria Neisseria meningitidis Nitrocellulose Nose paraform Peptide Hydrolases Phycoerythrin prisma Rabbits Rivers Sepsis Strains Transferrin Virulence Western Blot
5
Recombinant Antigen Production from cDNA Libraries
Not available on PMC !

Example 2

Five cDNA libraries that had been produced from different human, tissues (foetal brain, intestine, lung, liver and T-cells) were used for the production, of the recombinant antigens. All cDNAs were expressed in E. coli under the transcriptional control of the lactose-inducible promoter. The resultant proteins carry, at their amino terminus, an additional sequence for a hexahistidine purification tag (His6 tag), Target, antigens which were not present, in the cDNA library were produced by chemical synthesis (Life Technologies) and cloned into the expression vector pQE30-NST, which already codes an amino-terminal His6 tag.

Following recombinant expression of the proteins, these were isolated in denaturising conditions and purified by means of metal affinity chromatography (IMAC). The proteins were lyophilised and stored set −20° C. until further use (http://www.lifesciences.sourceboioscience.com).

US11860162B2. Marker sequences for diagnosing and stratifying SLE patients (2024-01-02). Oncimmune Germany GmbH [DE]. Inventors: Angelika Luking [DE], Peter Schulz-Knappe [DE], Carmen Theek [DE], Petra Budde [DE], Anna Telaar [DE].
Full text: Click here
Patent 2024
Antigens Brain cDNA Library Chromatography, Affinity Cloning Vectors DNA, Complementary Escherichia coli Fetus His-His-His-His-His-His his6 tag Homo sapiens imidazole-4-acetic acid Intestines Lactose Liver Lung Metals Proteins Recombinant Proteins T-Lymphocyte Tissues Transcription, Genetic

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More about "Brain"

The human brain is a remarkable and complex organ that serves as the central control center of the body.
Encompassing a vast network of interconnected neurons, the brain is responsible for a diverse array of functions, including cognition, emotion, movement, and sensory perception.
Researchers in the field of neuroscience continuously work to unravel the mysteries of this fascinating organ, exploring its anatomy, physiology, and the ways in which it can be affected by disease, injury, and environmental factors.
Whether you're interested in the neurobiology of learning and memory, the neural basis of psychopathology, or the potential of brain-computer interfaces, the study of the brain offers endless possibilities for discovery and advancement.
From the use of TRIzol reagent for RNA extraction to the application of MATLAB for data analysis, researchers have a wealth of tools and techniques at their disposal to further our understanding of this remarkable organ.
Dive into the world of brain research and unlock the secrets of this remarkable CNS (central nervous system) structure.
Leverage the power of AI-driven platforms like PubCompare.ai to optimize your research protocols, identify the best products and reagents (such as FBS, RNeasy Mini Kit, and Penicillin/streptomycin), and improve the reproducibility of your experiments.
Experience the power of cutting-edge technologies and unlock new frontiers in the study of the human brain.
Explore the wonders of the VT1000S and VT1200S cryostats, which enable precise tissue sectioning for histological analysis, and discover the benefits of Vectashield for fluorescent microscopy.
Embark on a journey of discovery and uncover the remarkable secrets of this truly fascinatign organ.