SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
Immune Tolerance
This crucial mechanism helps the body maintain balance and avoid autoimmune disorders.
Researchers can leverage PubCompare.ai's cutting-edge AI tools to streamline their immune tolerance research, rapidly identifying the best protocols from literature, preprints, and patents.
With intelligent comparisons, scientists can pinpoint the optimal approaches to accelerate their discoveries and unlock new insights into this vital physiological process.
Most cited protocols related to «Immune Tolerance»
The large and rapidly growing protein sequence databases provide a wealth of information for the identification of protein-coding transcript. We derive another three features from parsing the output of BLASTX (16 (link)) search (using the transcript as query, E-value cutoff 1e-10) against UniProt Reference Clusters (UniRef90) which was developed as a nonredundant protein database with a 90% sequence identity threshold (17 (link)). First, a true protein-coding transcript is likely to have more hits with known proteins than a non-coding transcript does. Thus we extract the NUMBER OF HITS as a feature. Second, for a true protein-coding transcript the hits are also likely to have higher quality; i.e. the HSPs (High-scoring Segment Pairs) overall tend to have lower E-value. Thus we define feature HIT SCORE as follows:
where Eij is the E-value of the j-th HSP in frame i, Si measures the average quality of the HSPs in frame i and HIT SCORE is the average of Si across three frames. The higher the HIT SCORE, the better the overall quality of the hits and the more likely the transcript is protein-coding. Thirdly, for a true protein-coding transcript most of the hits are likely to reside within one frame, whereas for a true non-coding transcript, even if it matches certain known protein sequence segments by chance, these chance hits are likely to scatter in any of the three frames. Thus, we define feature FRAME SCORE to measure the distribution of the HSPs among three reading frames:
The higher the FRAME SCORE, the more concentrated the hits are and the more likely the transcript is protein-coding.
We incorporate these six features into a support vector machine (SVM) machine learning classifier (18 ). Mapping the input features onto a high-dimensional feature space via a proper kernel function, SVM constructs a classification hyper-plane (maximum margin hyper-plane) to separate the transformed data (18 ). Known for its high accuracy and good performance, SVM is a widely used classification tool in bioinformatics analysis such as microarray-based cancer classification (19 (link),20 (link)), prediction of protein function (21 (link),22 (link)) and prediction of subcellular localization (23 (link),24 (link)). We employed the LIBSVM package (25 ) to train a SVM model using the standard radial basis function kernel (RBF kernel). The C and gamma parameters were determined by grid-search in the training dataset. We trained the SVM model using the same training data set as CONC used (13 (link)), containing 5610 protein-coding cDNAs and 2670 noncoding RNAs.
data acquisition, Thermo RAW files were processed using
a series of software tools that were developed in-house. First the
RAW files were converted to mzXML using a custom version of ReAdW.exe
(
had been modified to export ion accumulation times and FT peak noise.
During this initial processing we also corrected any erroneous assignments
of monoisotopic m/z. Using Sequest,24 (link) MS2 spectra were searched against the human
UniProt database (downloaded on 08/02/2011), supplemented with the
sequences of common contaminating proteins such as trypsin. This forward
database was followed by a decoy component, which included all target
protein sequences in reversed order.
Searches were performed
using a 50 ppm precursor ion tolerance.25 (link) When searching Orbitrap MS2 data, we used 0.02 Th fragment ion tolerance.
The fragment ion tolerance was set to 1.0 Th when searching ITMS2
data. Only peptide sequences with both termini consistent with the
protease specificity of LysC were considered in the database search,
and up to two missed cleavages were accepted. TMT tags on lysine residues
and peptide N-termini (+ 229.162932 Da) and carbamidomethylation of
cysteine residues (+ 57.02146 Da) were set as static modifications,
while oxidation of methionine residues (+ 15.99492 Da) was treated
as a variable modification. An MS2 spectral assignment false discovery
rate of less than 1% was achieved by applying the target-decoy strategy.26 (link) Filtering was performed using linear discriminant
analysis as described previously27 (link) to create
one composite score from the following peptide ion and MS2 spectra
properties: Sequest parameters XCorr and unique ΔCn, peptide
length and charge state, and precursor ion mass accuracy. The resulting
discriminant scores were used to sort peptides prior to filtering
to a 1% FDR, and the probability that each peptide-spectral-match
was correct was calculated using the posterior error histogram.
Following spectral assignment, peptides were assembled into proteins
and proteins were further filtered based on the combined probabilities
of their constituent peptides to a final FDR of 1%. In cases of redundancy,
shared peptides were assigned to the protein sequence with the most
matching peptides, thus adhering to principles of parsimony.28
Most recents protocols related to «Immune Tolerance»
Example 1
Variety 18GG0453L has shown uniformity and stability for all traits, as described in the following variety description information. The variety has been increased with continued observation for uniformity.
Table 1 provides data on morphological, agronomic, and quality traits for 18GG0453L. When preparing the detailed phenotypic information, plants of the new 18GG0453L variety were observed while being grown using conventional agronomic practices.
Example 4
Testing to evaluate hard water tolerance of exemplary formulations of a high-foaming, higher alkaline chlorinated cleaner (with and without PSO) was conducted to determine the impact of the PSO on hard water tolerance. The evaluated formulations are shown below in Table 8 wherein alkaline cleaning compositions including hydroxide alkalinity sources were combined with the PSO adducts and compared to the formulations without the PSO adducts (Control).
The hardness tolerance testing of the EXP 9 formulation and the control were conducted using 1% solutions in water with varying degrees of synthetic hardness created by adding various amounts of dissolved CaCl2) and MgCl2 to a combination of deionized water and NaHCO3. Once the solutions reached 140° F. they were removed from the heat and let stand for 30 minutes. A failure was characterized by the presence of visible flocculent after the 30 minutes, whereas a passing evaluation was characterized by the absence of visible flocculent after the 30 minutes. The results are shown in Table 9.
As shown in Table 10, the exemplary high-foaming formulation (EXP 9) according to the invention containing the PSO adducts had increased hard water tolerance over cleaning compositions not containing the PSO adducts.
The inventions being thus described, it will be obvious that the same may be varied in many ways. Such variations are not to be regarded as a departure from the spirit and scope of the inventions and all such modifications are intended to be included within the scope of the following claims.
Example 15
Diet Induced Obese (DIO) mice were purchased from Charles River and administrated by s.c. route with GLP1R agonist or GLP1R/GCGR dual agonist. Mouse body weight and food intake were monitored daily for 2 weeks, and followed before (5 days in total) and during treatment (5-weeks in total). After 5 weeks, mice were sacrificed and visceral fat mass were taken out and weighed.
Dose dependent weight loss induced by mTA4 or mTA37 (see Table 6) is shown in
Example 1
Trial consisted of 2 treatment regimens with Imazamox applications at approximately the preflood stage with rates of 0.5×, 1×, 2×, or 4×, either alone or 2 weeks following application of 1× Imazethapyr.
Summary:
The results of this trial indicates that RiceTec (RT) IMI hybrids show high levels of tolerance to Imazamox herbicide. No injury was observed in any of the RT IMI hybrids in any treatment. However, injury was observed in the single trait mutant lines. This was expected, because it is known that the G654E mutation only confers a weak level of tolerance to IMI herbicides. Due to the trial being conducted in the greenhouse during the difficult winter season the injury response may not have shown exactly as that of an optimal field trial, but given the consistency of response across all treatments the data indicates that RT IMI hybrids have equal or higher levels of tolerance to Imazamox than current commercial IMI hybrids.
Example 2
Trial:
single herbicide application at the 3-4 leaf stage using the half-step log sprayer at rates from 16× to 1/128×.
Plot Images 3 Weeks Post Application.
Summary:
Top products related to «Immune Tolerance»
More about "Immune Tolerance"
This crucial mechanism helps the body maintain balance and avoid autoimmune disorders.
Researchers can leverage cutting-edge AI tools like PubCompare.ai to streamline their immune tolerance research, rapidly identifying the best protocols from literature, preprints, and patents.
With intelligent comparisons, scientists can pinpoint the optimal approaches to accelerate their discoveries and unlock new insights into this vital physiological process.
Immune tolerance is closely related to other key biological concepts and tools used in research.
Proteome Discoverer and Mascot are software platforms used for protein identification and quantification, which can provide valuable insights into the molecular mechanisms underlying immune tolerance.
Humulin R is a form of insulin used to manage diabetes, a condition that can be impacted by immune system dysfunction.
D-glucose, the primary sugar molecule in the body, also plays a crucial role in immune system regulation and metabolic processes.
By leveraging the power of AI-driven platforms like PubCompare.ai, researchers can enhance their understanding of immune tolerance and accelerate their discoveries.
These tools enable rapid identification of the best protocols from a vast array of literature, preprints, and patents, helping scientists pinpoint the optimal approaches to advance their research.
With Mascot 2.4 and Proteome Discoverer 2.2, researchers can further analyze and quantify the proteins and molecules involved in immune tolerance, unlocking new insights and accelerating their progress.