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Homo sapiens

Homo sapiens, the modern human species, is the subject of diverse research across fields such as evolutionary biology, anthropology, and medicine.
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Most cited protocols related to «Homo sapiens»

Reads were aligned using the TopHat2 aligner [65 (link)], and assigned to genes using the summarizeOverlaps function of the GenomicRanges package [60 (link)]. The sequence read archive fastq files of the Pickrell et al. [17 (link)] dataset (accession number [SRA:SRP001540]) were aligned to the Homo sapiens reference sequence GRCh37 downloaded in March 2013 from Illumina iGenomes. Reads were counted in the genes defined by the Ensembl GTF file, release 70, contained in the Illumina iGenome. The sequence read archive fastq files of the Bottomly et al. [16 (link)] dataset (accession number [SRA:SRP004777]) were aligned to the Mus musculus reference sequence NCBIM37 downloaded in March 2013 from Illumina iGenomes. Reads were counted in the genes defined by the Ensembl GTF file, release 66, contained in the Illumina iGenome.
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Publication 2014
Genes Homo sapiens Mice, House
MACS is implemented in Python and freely available with an open source Artistic License at [16 ]. It runs from the command line and takes the following parameters: -t for treatment file (ChIP tags, this is the ONLY required parameter for MACS) and -c for control file containing mapped tags; --format for input file format in BED or ELAND (output) format (default BED); --name for name of the run (for example, FoxA1, default NA); --gsize for mappable genome size to calculate λBG from tag count (default 2.7G bp, approximately the mappable human genome size); --tsize for tag size (default 25); --bw for bandwidth, which is half of the estimated sonication size (default 300); --pvalue for p-value cutoff to call peaks (default 1e-5); --mfold for high-confidence fold-enrichment to find model peaks for MACS modeling (default 32); --diag for generating the table to evaluate sequence saturation (default off).
In addition, the user has the option to shift tags by an arbitrary number (--shiftsize) without the MACS model (--nomodel), to use a global lambda (--nolambda) to call peaks, and to show debugging and warning messages (--verbose). If a user has replicate files for ChIP or control, it is recommended to concatenate all replicates into one input file. The output includes one BED file containing the peak chromosome coordinates, and one xls file containing the genome coordinates, summit, p-value, fold_enrichment and FDR (if control is available) of each peak. For FoxA1 ChIP-Seq in MCF7 cells with 3.9 million and 5.2 million ChIP and control tags, respectively, it takes MACS 15 seconds to model the ChIP-DNA size distribution and less than 3 minutes to detect peaks on a 2 GHz CPU Linux computer with 2 GB of RAM. Figure S6 in Additional data file 1 illustrates the whole process with a flow chart.
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Publication 2008
Chromatin Immunoprecipitation Sequencing Chromosomes DNA Chips FOXA1 protein, human Genome Homo sapiens MCF-7 Cells Neoplasm Metastasis Python
To promote the analysis of eQTL results across a wide range of human tissues, the NIH funded five centers to develop improved methods for statistical analysis. Investigators funded through this RFA form an analysis consortium that will provide innovative approaches to analyses of GTEx data and other similar datasets. Investigators also collaborate with the LDACC to perform data quality assessment/quality control before release into dbGaP. The initial GTEx Consortium publications, anticipated in 2013, will include genome-wide analysis of cis- and trans-eQTLs, allele-specific expression, splicing quantitative trait loci, and a comparison of array and RNA-Seq based gene expression results.
Publication 2013
Alleles Gene Expression Genome Homo sapiens Quantitative Trait Loci RNA-Seq Tissues
The 16S rRNA gene amplicon data from human vaginal samples in [19 (link)] (2.13M paired-end Illumina Miseq reads in 157 samples) and from mouse feces in [17 (link)] (3.65M paired-end Illumina Miseq reads in 362 samples) were analyzed with the DADA2 pipeline outlined above. First the demultiplexed fastq files were filtered and trimmed in the same manner as the test datasets. Each sample was dereplicated, a portion of the dataset was used to estimate the error parameters, and dada() was applied to the full pooled dataset using those inferred error parameters. isBimeraDenovo() was used to remove chimeras.
For the human vaginal samples, output sequences that appeared in at least two samples and at least 0.3% of the total reads were taxonomically identified by BLAST. Further analysis focused on the six L. crispatus sequence variants identified by this procedure.
Publication 2016
Chimera Feces Genes Genetic Diversity Homo sapiens Mice, House RNA, Ribosomal, 16S Vagina

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Publication 2019
Cells Chromium Gene Expression Genes Genes, vif Germ Cells Homo sapiens Human Body Mitochondrial Inheritance PBMC Peripheral Blood Mononuclear Cells Single-Cell RNA-Seq XCL1 protein, human

Most recents protocols related to «Homo sapiens»

Example 14

The ability of anti-PD-L1 antibodies to modulate immune responsiveness was assessed using a mixed lymphocyte reaction (MLR). With this assay, the effects anti-PD-L1 antibodies on cell activation and the production of IL-2 were measured. The MLR was performed by culturing 105 purified human CD4+ cells from one donor with 104 monocyte derived dendritic cells prepared from another donor. To prepare the dendritic cells, purified monocytes were cultured with GM-CSF (1,000 U/ml) and IL-4 (500 U/ml) for seven days. Anti-PD-L1 or control antibodies were added to the allogeneic MLR cultures at 10 μg/ml unless stated otherwise. Parallel plates were set up to allow collection of supernatants at day 3 and at day 5 to measure IL-2 using a commercial ELISA kit (Biolegend). The antibodies used were the disclosed H6B1L, RSA1, RA3, RC5, SH1E2, SH1E4, SH1B11, and SH1C8 as compared to prior disclosed antibodies 10A5 (Bristol-Myers-Squibb/Medarex) and YW243.55S70 (Roche/Genentech) that were obtained via in-house production from prior-disclosed antibody sequences (U.S. Patent Application 2009/0055944 and U.S. Patent Application US 2010/0203056; the disclosure of which are incorporated by reference herein).

Production of IL-2 was enhanced by the addition of the anti-PD-L1 antibodies.

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Patent 2024
Anti-Antibodies Antibodies Antigens Binding Proteins Biological Assay CD274 protein, human Cells Dendritic Cells Enzyme-Linked Immunosorbent Assay Granulocyte-Macrophage Colony-Stimulating Factor Homo sapiens Immunoglobulins Lymphocyte Culture Test, Mixed Monocytes Tissue Donors

Example 3

Human primary sebocytes (Zenbio, RTP, NC) were plated at confluence on 96 well Scintiplates and allowed to adhere overnight. Cells were treated with the SCD1 inhibitor Compound A prepared in media containing the LXR agonist and insulin and cultured overnight. The DGAT inhibitor A922500 (2 μM) was included as a positive control. The following day 14C-acetate was added to each well and the plate was gently mixed. Cells were placed in the incubator at 37° C. for 4 hours total. After 2 hours of incubation the Cell Titer Blue (CTB) assay was started, 10 μl of CTB reagent was added to each well and incubated for the remaining 2 hours at 37° C. Following the 4 hour incubation, the RFU was determined using the SpectraMax Gemini EM under the following parameters: 560ex/590em with a 570 cutoff, top read. The medium was removed and cells were washed 3× with PBS. All of the PBS was removed from the wells and the plates were allowed to air dry. The plate was read in the MicroBeta TriLux counter and data was analyzed as CPM and normalized to CTB readout. Data is shown in FIG. 2.

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Patent 2024
Acetate Biological Assay Cells Homo sapiens Insulin N,N,N-triethyl-11-(4-methyl-2-oxo-2H-chromen-7-yloxy)-11-oxoundecan-1-aminium bromide Psychological Inhibition
Not available on PMC !

Example 10

This example provides in vitro IC50 data for the blocking of the interaction between recombinant human PD-1 (PD-1-Fc Chimera; Sino Biologics) and human PD-L1 expressed CHO cells by anti-PD-L1 antibody G12. Here, CHO cells expressing PD-L1 were pre-incubated with G12 prior to the addition of rhPD-1-Fc chimeric protein. After incubation and washing, PD-1 binding to cell surface expressed PD-L1 was detected using an Alexa-Fluor 647 tagged anti-PD-1 antibody by flow cytometry (Intellicyt HTFC; FL-4H). This example shows that anti-PD-L1 monoclonal antibody G12 was able to inhibit efficiently the binding of PD-1 to PD-L1 expressed on the surface of CHO cells.

Results: As shown in FIG. 8 and Table 4, the IC50 for blocking of the PD-1/PD-L1 cellular interaction by G12 is 1.76E-09 M. Data was collected on the Intellicyt HTFC flow cytometer, processed using FlowJo software, and analyzed and plotted in Graph Pad Prizm using non-linear regression fit. Data points are shown as the median fluorescence detected in the FL-4H channel+/−Std Error.

TABLE 4
G12
Inhibition of PD-1/PD-L1CHO-PD-L1/1.76E−09
Interaction IC50 (M)rhPD-1-Fc

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Patent 2024
Alexa Fluor 647 Antibodies, Anti-Idiotypic Antigens Binding Proteins Biological Factors CD274 protein, human Cell Communication Cells Chimera CHO Cells Flow Cytometry Fluorescence Homo sapiens Immunoglobulins isononanoyl oxybenzene sulfonate Monoclonal Antibodies Proteins Psychological Inhibition

Example 12

As a proof of concept, the patient population of this study is patients that (1) have moderate to severe ulcerative colitis, regardless of extent, and (2) have had an insufficient response to a previous treatment, e.g., a conventional therapy (e.g., 5-ASA, corticosteroid, and/or immunosuppressant) or a FDA-approved treatment. In this placebo-controlled eight-week study, patients are randomized. All patient undergo a colonoscopy at the start of the study (baseline) and at week 8. Patients enrolled in the study are assessed for clinical status of disease by stool frequency, rectal bleeding, abdominal pain, physician's global assessment, and biomarker levels such as fecal calprotectin and hsCRP. The primary endpoint is a shift in endoscopy scores from Baseline to Week 8. Secondary and exploratory endpoints include safety and tolerability, change in rectal bleeding score, change in abdominal pain score, change in stool frequency, change in partial Mayo score, change in Mayo score, proportion of subjects achieving endoscopy remission, proportion of subjects achieving clinical remission, change in histology score, change in biomarkers of disease such as fecal calprotectin and hsCRP, level of adalimumab in the blood/tissue/stool, change in cytokine levels (e.g., TNFα, IL-6) in the blood and tissue.

FIG. 72 describes an exemplary process of what would occur in clinical practice, and when, where, and how the ingestible device will be used. Briefly, a patient displays symptoms of ulcerative colitis, including but not limited to: diarrhea, bloody stool, abdominal pain, high c-reactive protein (CRP), and/or high fecal calprotectin. A patient may or may not have undergone a colonoscopy with diagnosis of ulcerative colitis at this time. The patient's primary care physician refers the patient. The patient undergoes a colonoscopy with a biopsy, CT scan, and/or MRI. Based on this testing, the patient is diagnosed with ulcerative colitis. Most patients are diagnosed with ulcerative colitis by colonoscopy with biopsy. The severity based on clinical symptoms and endoscopic appearance, and the extent, based on the area of involvement on colonoscopy with or without CT/MRI is documented. Treatment is determined based on diagnosis, severity and extent.

For example, treatment for a patient that is diagnosed with ulcerative colitis is an ingestible device programmed to release a single bolus of a therapeutic agent, e.g., 40 mg adalimumab, in the cecum or proximal to the cecum. Prior to administration of the treatment, the patient is fasted overnight and is allowed to drink clear fluids. Four hours after swallowing the ingestible device, the patient can resume a normal diet. An ingestible device is swallowed at the same time each day. The ingestible device is not recovered.

In some embodiments, there may be two different ingestible devices: one including an induction dose (first 8 to 12 weeks) and a different ingestible device including a different dose or a different dosing interval.

In some examples, the ingestible device can include a mapping tool, which can be used after 8 to 12 weeks of induction therapy, to assess the response status (e.g., based on one or more of the following: drug level, drug antibody level, biomarker level, and mucosal healing status). Depending on the response status determined by the mapping tool, a subject may continue to receive an induction regimen or maintenance regimen of adalimumab.

In different clinical studies, the patients may be diagnosed with Crohn's disease and the ingestible devices (including adalimumab) can be programmed to release adalimumab in the cecum, or in both the cecum and transverse colon.

In different clinical studies, the patients may be diagnosed with illeocolonic Crohn's disease and the ingestible devices (including adalimumab) can be programmed to release adalimumab in the late jejunum or in the jejunum and transverse colon.

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Patent 2024
Abdominal Pain Adalimumab Adrenal Cortex Hormones Biological Markers Biopsy BLOOD Cecum Colonoscopy C Reactive Protein Crohn Disease Cytokine Diarrhea Diet Endoscopy Endoscopy, Gastrointestinal Feces Homo sapiens Immunoglobulins Immunosuppressive Agents Jejunum Leukocyte L1 Antigen Complex Medical Devices Mesalamine Mucous Membrane Neoadjuvant Therapy Patient Care Management Patients Pharmaceutical Preparations Placebos Primary Care Physicians Safety Therapeutics Tissues Transverse Colon Treatment Protocols Tumor Necrosis Factor-alpha Ulcerative Colitis X-Ray Computed Tomography

Example 8

Human subcutaneous pre-adipocytes (Zenbio (RTP, NC, U.S.A.)) were received pre-plated in white-walled 96-well plates. A schematic description of the protocol used for examining the effects of Compound A on lipid accumulation in differentiating human adipocytes is shown in FIG. 9. Upon arrival of cells (Day 1) 150 μL media in the wells was replaced with adipocyte differentiation media (Zenbio (RTP, NC, U.S.A.)). The following day media was replaced as described for Day 1. Media was subsequently replaced as described every two to three days. On Day 6, 150 μL of the adipocyte differentiation media was replaced with vehicle (0.1% DMSO), or the SCD1 inhibitors at the concentrations indicated. After two days (Day 8) 150 μL media was replaced with 150 μL adipocyte maintenance media containing vehicle (0.1% DMSO) or the SCD1 inhibitors at the concentrations indicated as described above. Following a further four days of incubation (Day 12) cells were stained with AdipoRed™ (Lonza Bioscience (Walkersville, MD, U.S.A.)) according to the manufacturer's instructions. Cytotoxicity following incubation of adipocytes with Compound A was determined in separate wells, not used for Adipored™ staining, and was measured using CellTiter-Glo® (Promega (Madison, WI)) according to the manufacturer's instructions. Following a 10 min room temperature incubation the luminescence measured as relative light units (RLU) was determined in a luminescent plate reader. For adipocytes treated with concentrations of 1.2-100 nM Compound A for 6 days, cell viability as determined by RLU following CellTiter-Glo® remained greater than 75% of the value obtained with vehicle-treated adipocytes. The RLU dropped to 72% of vehicle in adipocytes treated with 1 μM Compound A (data not shown). These findings indicate that the decrease in lipid accumulation in the differentiating primary human adipocytes following Compound A treatment is not associated with cytotoxicity at least up to 100 nM Compound A.

Calculation of the IC50 for inhibition of triglyceride accumulation in human adipocytes was determined by non-linear regression analysis of the RFU, using a variable slope, 4-parameter fit (GraphPad PRISM®). FIG. 10 Shows the reduction in lipid accumulation following treatment of differentiating primary human adipocytes with 100 nM Compound A and analogs Compounds B, D, E, G and H for six days. FIG. 11 shows a representative study comparing the concentration-dependent reduction in lipid accumulation with Compounds A, G and H. Compound D was tested at 5 μM only. The relative IC50 values for Compound A, G and H in this study were 9.3 nM, 24.2 nM and 56 nM respectively.

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Patent 2024
Adipocytes Cells Cell Survival Cytotoxin Homo sapiens inhibitors Light Lipids Luminescence prisma Promega Psychological Inhibition Sulfoxide, Dimethyl Triglycerides

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L-glutamine is an amino acid that is commonly used as a dietary supplement and in cell culture media. It serves as a source of nitrogen and supports cellular growth and metabolism.

More about "Homo sapiens"

Homo sapiens, the modern human species, is the subject of extensive research across diverse fields, including evolutionary biology, anthropology, and medicine.
This research often involves the use of various cell culture media and reagents, such as Fetal Bovine Serum (FBS), Dulbecco's Modified Eagle's Medium (DMEM), Penicillin/Streptomycin, RPMI 1640 medium, Lipofectamine 2000, and TRIzol reagent.
These tools and materials play a crucial role in maintaining and manipulating human cell lines, which are essential for understanding the biology and behavior of Homo sapiens.
Researchers studying the modern human species can leverage PubCompare.ai's innovative AI-driven platform to enhance the reproducibility and accuracy of their investigations.
This platform simplifies the identification and comparison of relevant protocols from literature, preprints, and patents, allowing researchers to easily locate the best protocols and products to optimize their Homo sapiens research workflow and drive meaningful discoveries.
By utilizing PubCompare.ai's tool, researchers can streamline their processes, improve the overall quality and impact of their Homo sapiens investigations, and uncover new insights into the complex and fascinating world of the modern human species.
The platform's AI-driven comparisons and recommendations can help researchers navigate the wealth of information available and identify the most effective protocols and products to advance their research goals.