Science topic

Breast Cancer - Science topic

Breast cancer (malignant breast neoplasm) is a type of cancer originating from breast tissue, most commonly from the inner lining of milk ducts or the lobules that supply the ducts with milk.
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Germany, Sweden or Los Angeles, USA
Breast cancer survivors with bone metastasis
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There is the BOMET trial that just finished recruitment. It is the 2nd trial of the same Author from Turky who presented data on primary surgery for stage 4 breast cancer 4 years ago at ASCO
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Can anyone please suggest a detailed protocol for tumor sample collection from breast cancer patients? What necessary precautions should be taken?
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We had experience of working with oncosurgeon. The most important thing we had to deal with was the timing. Sometimes, our fellow had to wait for a tissue more than 12hrs. We don't have -80 fridges at tissue collection site and don't have that much facilities. For tissue sample preservation, RNALater is a blessing for us. Part of the tumor tissues was kept for pathological tests and the rest was given to us for molecular analysis. Tissue sample was stored in RNALater containing tube immediately after collection, transported to lab in an icebox, and stored at -20C.
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I was planning to evaluate the protein expression profile of a gene of my interest, in breast cancer patients. Does anyone know if such dataset ( like we use TCGA datasets to examine mRNA expression )exists?
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Hi Sir,
You can check gene expression at protein level using Human Protein Atlas (https://www.proteinatlas.org). Also, NCI Proteomic Data Commons can be explored (https://pdc.cancer.gov/pdc/)
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We need to recognise the best way to monitor the breast cancer development
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Tumor markers, also called serum markers are substances found at higher-than-normal levels in the blood of cancer patients. Serum biomarkers are especially appealing for the potential to detect disease progression or response to treatment.
In breast cancer care, three tumor markers -- cancer antigen 15-3 (CA 15-3), cancer antigen 27.29 (CA 27.29), and carcinoembryonic antigen (CEA) -- have been used to help monitor metastatic breast cancer.
National Comprehensive Cancer Network (NCCN) and American Society of Clinical Oncology (ASCO) guidelines recommend serial monitoring of CEA, CA 15-3, and/or CA 27-29 in metastatic disease; particularly, an elevation of 20% to 30% in any of these markers in addition to clinical exam can indicate treatment failure.
National Academy of Clinical Biochemistry (NACB), and European Group on Tumor Markers (EGTM) recommend measuring CEA, CA 15-3, and CA 27-29 for postoperative surveillance, even without evidence of progression.
The EGTM alone recommends preoperative measurement of CEA or CA 15-3/CA 27-29 in combination with established factors to aid in determining prognosis.
Best.
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Do ERAS protocol apply to simple and modified radical mastectomy or just in cases of reconstruction?
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Haddadi Saïd , true for reconstruction, can this extend or be extended to only simple mastectomy or radical one ,without rec?
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I need to use BCDR mammography database (http://bcdr.inegi.up.pt/patient/list). But it includes 4 different mammogram images (LMLO,RMLO,LCC,RCC) for each patient. I am confused with those images. I need to detect microcalcifications on mammograms. Which image do I need to use for this purpose?
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Where we can download the BCDR mammo database (especially the Digital part of the collection) ? No one seems to answer from the official site. Anyone who can provide a download link?
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I am pursuing research in breast cancer, where I need MCF-10 A cell line, however unable to get it due to funds restriction. Can anyone suggest an alternative cell line to that of MCF-10A.
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thank you.
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This question is spurred by the different effects of BRCA1/2 vs. PARP.
Thanks in advance for insights.
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DNA repair pathways are involved in maintaining genetic stability and, in this respect, repair factors are to be considered as tumor suppressors. This applies to the BRCA1/2 genes, for which inherited mutations in one allele predispose to cancer. There is no paradox in the fact that PARP inactivation leads to the death of BRCA-deficient tumor cells. In this case where homologous recombination is impaired, cell survival relies on PARP-dependent backup repair processes. Apparently, here, PARP promotes tumor development but even in non-tumor HR-deficient cells, survival would depend on PARP. We just take advantage of this synthetic lethality phenomenon due to HR deficiency to kill cancer cells.
Anyway PARP functions are not restricted to DNA repair and it is possible that in some peculiar circumstances PARP may rather promote tumorigenesis.
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Hello everyone,
I am looking for gene expression data for affected/metastatic and unaffected/non-metastatic lymph nodes in breast cancer patients to find whether our two genes under question are differentially expressed between them.
Does anybody have any idea where I can find such a database? I have already searched GEO and TCGA.
Best regards,
Mehdi Montazer
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Ellen A G Chernoff Dear Professor Chernoff, thank you so much for the advice. I did not know about these tools. I will check them.
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Dear All, I am going to detect MMP2 and MMP9 in different cancer cell lines after drug treatment, like breast cancer and lung cancer. However, I cannot get bands in western blot using both cell lysate and culture medium. I guess the antibodies did not work so I just bought new ones. The question is do MMPs difficult to detect by WB and how can I improve this? I also find someone use zymography to detect MMPs, is it a better way or not? Thanks in advance!
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Hello Gongli Cai
There are techniques that have been developed to detect and identify MMPs in various samples. Enzyme linked immunosorbent assay (ELISA) and Western blot require the use of antibodies targeted to the MMP of interest.
I would suggest you use gel zymography which is extensively used to detect MMPs in many cell types and tissues as well as in most bodily fluids.
You may follow the protocol described in the article attached below.
Best.
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I struggled to find a paper related to any research using C12 Ceramide as a bioactive lipid to enhance the toxicity against breast cancer cells.
I'm going to incorporate C12 Ceramide in liposome and lipid nanocapsules but there is a lack of research that studied even Free C12 Ceramide (the mechanism, therapeutic dosage that affects cells, etc.)
I ended up with found only 1 paper ( ) and I need more literature references to help my research.
I really appreciate it if you could suggest other papers related to the C12 Ceramide study.
Thank you very much.
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Hi all,
I am going to try 3D culture (on top) with MCF10A cells. I am planning to start with matrigel and regular cell culture dishes and then perform confocal microscopy. Can anyone help me with the following points-
1. What should be the cell density of stable MCF10A cells (transfected and drug-selected) to seed on top of matrigel (according to dish size)?
2. After seeding how can I exactly observe acini formation? Do I need a specifically featured microscope? Or regular microscopes are fine?
3. If acini are formed (I hope positively), how acini are to be detached from matrigel? should I grow the cells on coverslips? Or how am I supposed to transfer the acini onto the slides?
Thanks in advance,
Swarnali
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Thank you Susan C Hubchak for your useful reply. I'll definitely try like you said.
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Dear: Does infection with Covid 19 stimulate cancer cells, especially breast cancer? Is there any research in this field?
One of the women, at the age of more than fifty-five years, had a fracture of the spine, and it was later revealed as a result of the diagnosis that she had breast cancer, and it developed towards the lymph nodes and then the spine. Is there research in this area and what is the relationship of cancer to broken bones of the back vertebrae? Is there a cure for such injuries?
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I'm passionate in oncology research. I did bachelor in Zoology and now pursuing MPhil Molecular Biology and Biotechnology and working on cancer genetics. I am greatly interested to do PhD in cancer research from a world renowned institute but I think with this profile I would get a position in top ranked institute for PhD. Should I go for another master from a renowned foreign institute with major in oncology?
Thanks
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If you ate well grounded in the course of your MPhil Molecular Biology and Biotechnology, there may not be need to go for another MSc in Molecular Biology and Biotechnology
I advice you proceed to doing PhD in Molecular Biology and Biotechnology except you know within yourself that you not well grounded enough and this depends on how truthfully you have evaluated your competence
Best wishes
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The age cut-off for screening for breast cancer in Australia was increased from 69 years to 74 years in 2013. In this assessment, you are asked to design an observational study that will examine if:
  • · Breast cancer screening leads to reduced mortality from breast cancer among women aged 70 to 74 years;
  • · Breast cancer screening leads to reduced mortality from any cause aged 70 to 74 years.
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Oh, it's great to hear you from sir Robert Boer. I already cited your work multiple times.
Well, I adopted case-control and also cited some limitations of it from your paper.
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Dear All
I have stained breast cancer cells from culture with Ki67 after treatment. However, some cells express Ki67 very strongly, some cells have fade staining and almost all cells have a different background staining. In that case, should I check the percentage of positive cells/all cells? But then I will discard the differential expression levels. And if I quantify signal intensity levels, then first I will need to remove background from each image and that may alter the Ki67 signal levels also.
I would be very happy to have your suggestions.
Many thanks in advance!
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K. Sujathan Thank you very much!
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How to develop the basic algorithm for confocal microwave image reconstruction algorithm in Matlab. Anynone can share the code for head imaging or breast cancer.
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Hello. Did you get the code?
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I am looking for surface temperature data of infected breast cancer patients for early detection of breast cancer.
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Kindly see also the following useful RG link:
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I used an IHC staining for Pan-cytokeratin to test for metastasis from breast to brain. I am not sure if the only cells found in brain that are stained brown-ish are the tumor cells from breast cancer that metastasized or could be any other type of cell already present in the brain?
Thanks!
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Sorry for the late response. I would like to correlate with H&E. Can you please share that? Thanks
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If someone can explain to me how long serum starvation condition suitable for compare to control and TGF beta induction with appropriate TGF beta concentration especially MCF-7 & T47D cells . Thanks for your thoughts and information you might provide!
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normally people starve at low concentration 0.2% serum for 12h or sometimes 24h
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Hi!
Let me give some background information, I was planning to demonstrate non-inferiority of one breast cancer diagnositic tool to mammogram. The question is: should I use specificity and selectivity to calculate the sample size for positive and negative group. The formulae I used is in the figure below, and I just put specificity (or selectivity) of my tool and mammogram in as Pc and Pt, where D is the difference of Pc and Pt and delta is the non-inferiority margin.
So my understanding is this formula is indended for proportions (e.g. cure rate of treatment), not the specificity and selectivity.
Can anyone provide any help on this?
Thank you!
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I will respond to this question in french. in my thesis, the sratician calculate the "taille échantillonale" en se basant sur les résultats de la sensibilité (Se) et de la specificité (Sp) retrouvés dans la littérature médicale.
nSe= 4 x Se x (1-Se)/i×i
nSp= 4 x Sp x (1-Sp)/ixi
N= nSe+nSp
i étant la précision que l'on souhaite obtenir. Elle varie de 5 à 10%.
Good luck.
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I'm looking for any publicly available RNA-seq data sets related to all sub-types of breast cancers to presearch for thesis project, thank you all...
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Thanks Saubhik Sengupta...
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Researchers have discovered that breast cancer cells are more likely to jump into the blood when people are resting. The revelation is relevant because cancer is at its deadliest when a tumour’s cells worm their way into the bloodstream and travel to a new location in the body to set up shop — a process called metastasis. It doesn’t mean that people with breast cancer should avoid sleep — that’s bad for you. But it does give clinicians a better understanding of how to track these rogue cells. “The first lesson for me is that the time of day you take a blood sample can give you misleading information”, says cancer biologist Chi Van Dang...
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All the method of detection of breast cancer.
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Thank you
@Malcolm Nobre
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I am working on expressional profiling of microRNA in breast cancer patients and struggling to calculate fold change between two groups.
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You can assess the normality of your data's distribution using skewness and kurtosis tests.
If your data fit the assumptions of the appropriate parametric test (for example: https://www.statology.org/t-test-assumptions/), then you probably should use that test. You can always substitute a non-parametric test for a parametric test, but you typically will lose some statistical power. However, if your data violate the assumptions of the parametric you will need to use the non-parametric test.
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Hello,
I'm newly working with MDA-MB 231 cells. I have sub-cultured cells using 4. 0 mL L-15 media with 10% FBS in a T-25 culture flask. The cells have incubated them incubator at 37°C, with (0 % CO2, recommended company for L-15 media). After the 48 incubations, I checked the cells under the microscope, and the cells were dead. I checked the flask also, and some of the white precipitated parts were attached to the flask. For reference, I have attached the cells Images. This is the 4th time I face this issue and I cannot figure out why. I would appreciate any suggestions/tips on what I might be doing wrong. Thanks in advance!
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hi,
the white layer on the flask is debris of dying cells. Are you sure, that the flasks are Tissue culture grade/ coated for adhesion cell culture? For me it looks like an attachment issue and all non-suspension cells die fast in the wrong type of bolltes
Sven
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we are working on breast cancer and mmp9 and il8 as metastatic markers . we want to know about the details of breast malignancies with positivity with these metastatic markers in developing countries
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Both collagenases and cytokines are mistakenly regarded as facilitators of metastatic spread of tumors. Tumor cell itself has the remnants of gene regulation and the adjacent tissues are partners in the upregulation of estrogen signaling and DNA restoration in tumors. Collagenases help the arrival of cytokines and other mediators aiming the restoration of the genomic machinery in tumors and self directed death. Cytokines activate aromatase enzyme for stimulation of estrogen synthesis, while an increased estrogen level silences inflammation and improve DNA stability even in tumor cells. In conclusion; there is no parallelism between the activity of collageneses or cytokunes and tumor spread.
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My research is about micro RNA in breast cancer and I have to publish the research in an SCI or extended SCI journal. Would you please suggest journals that can response in real-time with logical prices?
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Concerning cancer research, Journal of Oncology and International Journal of Molecular Science provide good possibilities for publication of innovative works.
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I have been trying to proliferate cells for almost 4 weeks culturing 4T1 cells in RPMI 1640 medium supplemented as recommended by the ATCC (10% FBS, 5% antibiotic).
Started with a frozen vial (passage # 4).
Cells are not growing at all. I even increased FBS to 20% and have been changing medium every 2-3 days, passing cells 1:2 and can't see any sign that cells are getting off stationary phase.
Any recommendations?
I will appreciate your input. Thank you
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Giuliana D Noratto came across a question and answer typically not same but somehow linked to your question so felt like sharing the answer and you can see how Dr S J Malik https://www.researchgate.net/post/Problem_with_4T1_Tumor_Model_Development-Can_anyone_help
This is for your refernce
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We are trying to design Mesoporous Silica Nanoparticles for breast cancer treatment by PhotoDynamic Therapy.
And we are challenging with a question that Which ligand should we add onto the particle for attaching only breast cancer cells when the particles are added into the tumor cells directly by the vaccine (intra-tumoral injection).
Our ligand choice is Anti-HER2 antibody, HA.
We try to research that it is a good choice for us.
#Ligand #HyaluronicAcid #DrugDelivery #BreastCancer #PhotodynamicTherapy #SilicaNanoParticles #Ligand #Antibody #IntraTumoralInjection
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If you administrated your nanoparticles locally (intrtumor injection) , I think you needn't design the specificities or targeted strategies of your drug delivery. Because from tumor biology perspectives, the aggressive cancer cells are always infiltrating into surrounding microenvironment with some physical or immune barriers. Therefore, even if you treated the cancer cells by monoantibodies, you can't kill the tumor totally.
However, if your delivery strategies are intravenous injection, tageted therapy is the most important principle that you must take into considerations. So, in this context, my suggestions are that what kind of tumor you are goning to treat decides what antibodies you are attaching. As is known to all, breast cancer has less than three kinds: ER+, HER2+, and trible negative (luminal). I suggest you could widen your antibody choices for HER2+ breast cancers. Do the nanoparticles have a good ability to load Antibodies? What's the relationship between your breast cancer cells with your mesoporous NPs, drugs, and Antibodies? ...
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I have some apoptotic proteins identified from breast cancer datasets. I have a general queres in my mind.
1) How does apoptotic proteins function in cancer cells?
2) Would inhibiting an upregulated apoptotic protein would be feasible via molecular docking if we are aiming for a therapeutic alternative?
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Dear Dr Sing,
To find the function of proteins you can use uniprot database or genecard.
Before molecular docking, you should check the druggability of your protein by pockdrug. By molecular docking and MD you can find best compounds
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Traditionally, we have performed surgery first, followed by chemotherapy for breast cancer. Neoadjuvant treatment was limited to patients with contraindications to surgery. However, according to the latest ASCO guidelines (1), only patients with T1aN0 and T1bN0 HER2-positive disease should not be routinely offered neoadjuvant therapy. Should we now reverse our therapeutic approach?
1. Korde, L. A., Somerfield, M. R., Carey, L. A., Crews, J. R., Denduluri, N., Hwang, E. S., Khan, S. A., Loibl, S., Morris, E. A., Perez, A., Regan, M. M., Spears, P. A., Sudheendra, P. K., Symmans, W. F., Yung, R. L., Harvey, B. E., & Hershman, D. L. (2021). Neoadjuvant chemotherapy, endocrine therapy, and targeted therapy for breast cancer: ASCO Guideline. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 39(13), 1485-1505. https://doi.org/10.1200/JCO.20.03399
Translated with www.DeepL.com/Translator (free version)
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Yes, neoadjuvant systemic therapy is now considered standard practice for following subsets of breast cancer patients:
1. Inflammatory breast cancer
2. cT4 disease
3. cN2 or cN3 disease
4. Operable breast cancer with triple negative or HER2 +ve molecular subtype with cT2/N+ or higher disease stage
5. Large primary tumor relative to breast size, or when cN+ likely to become cN0 with neoadjuvant systemic therapy to facilitate breast conservation
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on a tight budget with little experience in studying cancer in mice which method should we pursue for successful implatation of MCF-7 cancer cells on mice
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The most recommended method is to use estradiol pellet to support growth of MCF7 cells, but implanting cells with materigel can work (though low tumor formation rate) which is more cost effective.
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More women in the U.S. are choosing to have their breasts removed for early cancers instead of breast-conserving procedures that deliver equal results, according to a new study.
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There are biological, ethical, legal and personal factors influence the treatment decisions of pregnancy associated breast cancer, but, which one is the most important factor?
1. What is the most important factor influencing the treatment of pregnancy associated breast cancer?
2. What are examples of personal factors (religion, family, personal beliefs) that could influence treatment when dealing with these cases?
3. Who do you believe has the right to make the final decision about the treatment the pregnant woman with breast cancer is going to receive?
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In my opinion informed patient decision would be the most important thing.
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I started my literature exploring HSI and i found out breast cancer to be an interesting area to work on . Since i am new to this technology and lots of research has been going on worldwide i want to explore what are the challenges still needs attention in HSI for breast cancer or in general for any other cancer
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To control direct tumor response after introducting drug chemothrapy or target thearapy.
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As the title says I am an engineer and happen to be working in the cancer domain specifically TNBC. I am working on a research project where I am trying to understand the signaling pathways activated in TNBC stem cells, due to my limited knowledge in this field I am having difficulties finding answers to some probably very dumb questions which I have listed below. Your answers and feedback are greatly appreciated.
  1. Do breast cancer stem cells (BCSC) vary in terms of what signaling pathways are activated or inhibited based on the kind of breast cancer e.g. TNBC, HER2+, Luminal A, or Luminal B ? Essentially when we talk of BCSC do we need to specify what kind of BCSC is it from a TNBC tumor or Her2+ Tumor, etc?
  2. Say a patient has HER2+ Breast Cancer, can some breast cancer cells evolve into TNBC after a point? I am trying to find out if a patient can have both HER2+ and TNBC, i.e. some Breast cancer cells exhibit HER2+ molecular signatures while the rest exhibit TNBC signatures.
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TNBC, HER2+ are different sub-types with different signaling pathways (though most pathways in all cancers are common). Since they are 2 different subtypes based on the presence or absence of different protein/receptors their signaling mechanism will be different.
when you talk about BCSC you need to specify the source, which is important.
the patient can have low HER2+ and TNBC (is another emerging sub-type within TNBC and have a low level of HER2+), so it is possible.
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I'm looking for breast cancer CTC detection strategies
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Liquid biopsy techniques can provide real-time information regarding patient staging (metastatic vs. nonmetastatic) and the molecular profile of the tumor. Moreover, liquid biopsies can be repeated with the desired frequency for close monitoring of progress and treatment
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I am looking forward to explore / validate the role of a drug in breast cancer treatment particularly in the absence of mismatch repair proteins via in-silico analysis. Picking random DNA could not serve the purpose. Is there anyone who can suggest about the selection of DNA sequence / structure... the DNA needed shouldn't be more then 12 to 14 nucleotides and should be specific to that particular protein.
I am trying to dock the drug with DNA (with or without MMR proteins).
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if you are looking for nucleotide sequence... plz go to protein database .. if you want normal sequence ... if you want mutated then OMIM or other ... and wanna compare , i think BLAST is the best tool for comparison
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I am an engineer trying to understand breast cancer stem cells. I understand breast cancer can be classified according to its molecular signatures e.g. HER2+ or TNBC. Do these classifications apply to breast cancer stem cells? Are there stem cells that belong to TNBC specifically or do we talk about stem cells more generally across the various kinds of breast cancers.
Thanks.
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Human breast cancer includes a highly diverse set of diseases and is classified in to at least 6 distinct clinically-relevant molecular subgroups - luminal A, luminal B, HER2+/ER-, basal-like, normal breast-like, and the most recently recognized claudin-low. It is clear that at the molecular level, each breast cancer subtype displays distinct gene expression profiles, and exhibits significant differences in response to therapy and patient outcome
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We have been using the Celigo to count and measure the size of breast cancer cell mammospheres and we are having issues getting accurate results. The machine tends to break up large mammospheres into 3-4 pieces and count them individually, while also counting a bunch of smaller individual mammospheres as 1, and also counting things that are just single cells near each other.
I have played with the settings numerous times and have worked with a technical person from Nexcelom and cannot get the settings to work for us. I was wondering if anyone had any luck using the Celigo for these purposes? I have tried analyzing the mammospheres using the Colony setting and the Tumorsphere setting.
Thank you in advance for any insight.
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So I will preface this by saying I work for a completely different company just so that is clear but I've run into a few groups with a similar problem and it seems like the software itself needs some adjustments. This is likely a back end fix/code rewrite that Nexcelom and companies like it need to do, to make the systems work more effectively across a variety of assays and cell types.
On that note Jennifer, depending on how often you and your team run these assays (mammospheres, colony, organoid, etc) there are other systems which are more dedicated to the task are doing (ie counting and sizing), the GelCount being the one I know. Not suggesting this is a fix for your problem but just a different solution. All the best.
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can we treat breast cancer with vitamin d?
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Also see the following useful link for more insight.
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We want to know if one protein can be used as a breast cancer biomarker or not. So we'll have to compare normal and patients, and our question is whether we can get samples from patients who received chemotherapy before?
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thank you for answring my quesion dear Dr Erum Zafar
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Hello,
I am conducting studies to look at inertial focusing of MCF-7 cells in spiral microfluidic channels. Recently, it has been reported that deformability plays an important role in cell-based focusing. To derive the cellular model of deformability (rigidity in my case), I am treating MCF-7 breast cancer cells with Glutaraldehyde (Sigma-Aldrich, 50 wt% in water). Protocol can be found in this paper:
The authors in the paper worked on Jurkat cells. I am wondering if anyone has tested Glutaraldehyde on MCF-7 cells? If so, would you mind sharing the optimal concentration at which these cells show maximum rigidity? I tried 0.1% (V/V) which was the maximum concentration reported in the paper but found no significant effect on focusing.
Any help here would be greatly appreciated.
Best
Ani
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Hi,
I don't know for MCF7 specifically, but the concentration used for different cell types are quite similar:
0.01% for CH27 result in half-max. stiffness increase: DOI:
  • 10.13140/RG.2.1.2911.8961
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I am trying to do segmentation for breast cancer organoids to see the difference of HER2 surface expression between the cells after IF staining. In order to do the segmentation I would stain the cytoplasm and us it as segmentation marker. any ideas?
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aside from pcr, what other test could i do to measure the changes of circadian clocks / rythmn in a give time.
if possible please provide a journal
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You can use real-time luminometry to study changes in gene expression. The investigators generated luciferase reporter systems to track BMAL1 and PER2 expression in real time.
Please refer to the research article attached for the detailed protocol.
Good Luck.
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I'm working on DMBA induced breast cancer in mice. What should be the histological, molecular or some other tests needs to perform to establish the anticancer and apoptotic activity of the natural product against DMBA induced breast cancer in mice?
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اسباب كثيرة ينبغي عليك البحث عنها
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I have two anticancer drugs that are used to have a concentration of drug A (1 mg/kg) and drug (5 mg/kg) from literature. I need to combine these two drugs and load them in a nanoparticle for i.v. injection in 4T1-bearing BALB/c mice.
My questions are:
1) At which concentration I need to adjust these drugs in the combination?
2) how to decide the injection periods?
3) how to decide the injection volume?
Thanks.
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Dear Majdi,
Even if you are going to start at 1:5 ratios of the two drugs when you prepare the NP, you most likely won't end up with a final ratio of 1:5 encapsulated. Thus you will need to optimize the protocol to produce the final NP with a ratio of 1:5 encapsulated. Then simply you inject an equilavent dose of drugs.
For example, if for free drugs you will use 1 and 5 mg/kg respectively, you will have to inject the same dose with the nano ( a concentration of nano that has 1mg/kg of drug 1 and 5mg/kg of drug 2). For this, it is critical to produce the nano with 1:5 final ratio.
I hope this helps.
Regards
Francesco
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We have performed human whole-genome sequencing of 100 Bangladeshi samples using NovaSeq6000 and analyzed the data using Basespace. Now I got some results for breast cancer 28 genes list along with other genes which have been assembled in an excel file. Anybody can help me regarding how I should go further to come up with good findings? Which software and pipeline we can use for the analyses. My target is to find a novel gene that is responsible for breast cancer disease. For this, we are seeking an experienced person's guideline. Interested person can give me a mail to shahinaakterbcsir2021@gmail.com
Thank you very much.
Dr. Shahina Akter
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Hello,
I have formalin-fixed paraffin-embedded samples of breast cancer and I want to extract RNA from them. I tried several times with the RNeasy FFPE Qiagen extraction kit, but I usually get low RNA concentration (~10-20), and also the 260/280 ratio never reaches 2.0. Moreove, the 260/230 ratio is usually ~0.8.
I really don know what am I doing worng? So please if anyone could help I will be grateful.
I tried to cut my samples by a microtome and tried to use a scalpel and there is no difference.
thank you.
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Hi Manar Serageldin,
I've been facing the same problem too but with a different kit called Macherey-Nagel Total RNA Isolation from FFPE. I was trying to extract RNA from formalin-fixed paraffin-embedded samples of colorectal cancer. For the first few attempts in extracting RNA from the FFPE tissue, I followed exactly what the protocols say, where it stated to incubate the FFPE with proteinase K in the lyse step for only 15 mins which gave me very low RNA concentration (~10-40), and also the 260/280 ratio. However, after troubleshooting I got to know that we can optimize the duration of incubation from 15 mins up to 3 hours with proteinase K (overnight digestion can also be done, but up to 3 hours is the optimal digestion time) depending on the size and thickness of samples and also by looking at the portion of the undigested sample. So I started to incubate my samples for approximately 2 hours and I managed to get a high amount of RNA concentration (~500-1500). However, for the 260/280 ratio, the best I have gotten to date is 1.9. Maybe you should try to increase the washing steps to get a good ratio of 260/280 and 260/230.
I hope this helps.
All the best to you.
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I have two treatments:1, breast cancer patients treated with drug A. 2, Breast cancer patients treated with Drug A+B. Each patient is either sensitive or resistant to drug A or Drug A+B. That means I have four groups in all. I want to extract the differential genes that related with drug B. My hepothesis is: if a patients is sensitive to Drug A but resistant to Drug A+B, then Drug B is the reason that cause the resistant. And if Drug A is resistant to Drug A+B, but sensitive to Drug B, then Drug B is the reason that cause sensisive. My quesion is how to design the compare matirx? what kind of statistic method should I use? thanks in advance!
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Dear Yongzi
I am not sure that your conclusions can be accepted without further experiments.
For example,
do cells express MDR proteins,
or the drugs are weak bases that can be easily ionized
or what chemical interactions occur between the drugs.
Answering these questions should precede the statistical representation.
Kind regards.
Tomas
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I have performed human whole-genome sequencing using NovaSeq6000 and analyzed the data using Basespace. Now I got some results for breast cancer 28 genes list which has been assembled in an excel file. Anybody can help me regarding how I should go further to come up with good findings? Which software I can use for the analyses. My target is to find a novel gene that is responsible for breast cancer disease.
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Hello Shahina Akter I am not sure what you are asking Since baseSpace gave you the final vcf and list of breast cancer mutations detected! I assume you want to focus on identifying mutations in BC gene unidentified samples. If you are looking for novel genes, then match the mutations you found in known BC genes to the samples and exclude these samples as cause identified and focus on the samples without a known cause. Prioritize the detected variants in those samples based on consequence (nonsense mutations first, missense second) utilize mutation prediction software to help you with these since some are harmless, and exclude common missense variants of frequencies more than 0.05 in genome databases (genome AD, 1000 genome project). Then when you have a shortlist, go through literature to identify functions of these genes or whether they were reported before in sporadic reports. Good luck.
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I have only been able to find one phospho-ER alpha S294 antibody from Abcam (https://www.abcam.com/estrogen-receptor-alpha-phospho-s294-antibody-bui-1-37-ab207602.html) but it is only validated for use in Western Blots. I would be very grateful if anyone had more information on this.
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For specified products like S294 antibody only from Abcam, I suggested contacting Cell signalling or Thermo Fischer technical support for the UK area. They are fast response using email.
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Hello!
I am creating a meta-analysis based on hazard ratios given for breast cancer incidence in BRCA1/2 carriers. Would this be fixed or random-effects? I am creating a forest plot using RevMan and after reading the examples for each type I am still confused!
Thanks in advance!
Carrie OH
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Agree with Gordon here -- fixed-effect models are typically not adequate (see https://www.meta-analysis.com/downloads/M-a_f_e_v_r_e_sv.pdf)
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If there is, I need info on
-The effectiveness of these ultrasound method compare to palpation.
-Where I can get the equipment and few suggestion.
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There are a few vendors, but here is an option. https://sonovol.com/
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I want to start research in a new aspect, anti cancer drugs especially drugs used in breast cancer. I think to begin with a research to but me on the way, my core to involve in pharmacogenomic and pharmacogenetic, but I don't know which point could i start with.
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Hello,
I have an interest in nanomedicine and am currently studying Breast Cancer (BC) so I would recommend starting with the following paper:
Di Wu, M. S., Xue, H. Y., & Wong, H. L. (2017). Nanomedicine applications in the treatment of breast cancer: current state of the art. International journal of nanomedicine, 12, 5879.
One of the most common medications used for BC treatment and probably the most effective so far is Doxorubicin. Perhaps this might be a better starting point before branching out.
I hope this helps!
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Hi,
What cell density will be good to generate breast cancer in BALB/C mice? I am planning to use serum-free culture medium to suspend the cells for injection. Please recommend the best suggestion.
Thanks
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Hello,
For aggressive cell lines, I recommend 100 000 to 200 000 cells to be injected subcutaneously to induce tumor in BALB/c mice.
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Hello!
My SR with meta-analysis will be looking at risk-reducing salpingo oophorectomy on ovarian/peritoneal/falloptian tube cancer risks, as well as risk-reduction mastectomy on breast cancer risks in BRCA2+ carriers.
For the inclusion criteria, am I allowed to include people who previously had breast cancer in my search for the ovarian cancer risk-reducing salpingo-oophorectomy data and people who never had breast cancer before for the breast cancer mastectomy data?
Meaning, am I allowed to have two types of inclusion criteria in one SR as I have two study types being analyzed, or must it only contain people with/without breast cancer? The unifying factor is that all participants are BRCA2+ carriers and are women.
I hope this makes sense!!
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Before trying to give a tentative answer, I would like to ask: What is your research question / are your research questions? And a bit nitpicky: Allowed by who?
My impression is that you have two quite distinct research questions:
- What is the effect on ovarian cancer of salpingo-oophorectomy in women who are BRCA2+ and have a history of breast cancer?
- What is the effect on breast cancer of mastectomy in women who are BRCA2+ without a history of breast cancer?
I expect that you will find no trials that address both questions at the same time, and even if they do, they will very likely report on the two questions separately.
Whether you say that you do one SLR or two does not seem to matter substantially, therefore I would say: call it what you think is best.
Doing one or two meta-analyses of course does make a substantial difference. I see no reason why you would want to put both those questions into one meta-analysis but maybe you do. E.g. is there any provider interested in the result of that one meta-analysis? (I can’t imagine that any patient has that interest, if only because no-one patient can have both a history of breast cancer and not have that.)
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The prevailing theory is that cancerous tumors reflect a form of cellular natural selection, where random mutations confer evolutionary advantages to tumor cells. These survival benefits accumulate over time, eventually empowering tumor cells to outcompete healthy cells and defeat the immune system.
Given this theory, one expects a correlation between cell division rate and cancer rate -- tissues with the highest number of cell divisions should show the highest incidence of cancer (environmental and hereditary factors notwithstanding).
However, few papers seem to verify this assumption, or even document cell division rates and lifetime cell divisions among different tissues.
These are the two best papers so far:
However, the same senior author leads both papers, and the papers seem to omit the most common cancer types, breast and prostrate. Furthermore, the methodology seems fragile as they conducted an analysis across different studies that may not have employed uniform methods.
Could anyone recommend more robust or authoritative papers on the subject of cell division rates?
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I wish you Mr Clarence Hu to be a doctor very soon . Best regards.
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Best module for breast cancer induction.
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For Breast cancer induction mice are suitable because of mice are smaller in size and the induction period 3 to 4 month.
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Can you calculate IR and IRR p-values and CI in SPSS without using a regression model such as Poisson? I have calculated the breast cancer incidence for various groups by hand using the breast cancer incidence rates of the entire population of a country as a reference. I have calculated the p-values and CI also by hand, but I would like to check this using an analysis in SPSS. Thank you in advance.
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Hello Rachel Dassen. Well, you could convert your hand calculations into SPSS syntax. But I'm not sure that's what you're asking.
Which method of adjustment are you using, direct or indirect? Can you share the data (including the standard population info) with us?
Why are you opposed to using a regression model if it gives the correct results? HTH.
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Hi,
I will be grateful if any one could give a detailed description on their experience/precautions to be taken with RNA extraction from breast tissue (stored in -80). I am planning to use Qiagen RNeasy mini kit and homogenize the tissue with help of crushing in mortor and pestle with liquid nitrogen followed by homogenizing with lysis buffer. I was wondering the normal breast tissue which is usually with fat, will homogenize in the same way? Any information related to this will be greatly appreciated.
Thanks!
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Qiagen has a RNA extraction kit specifically for tissue with a high lipid content (RNeasy Lipid Tissue Mini Kit) that might help maximize your RNA yield.
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I have designed a training model for the breast cancer dataset using floating-point multipliers and adders (adder tree)by storing patient data and weight value for each feature in BRAM for further processing. Some 20% of data is kept stored in the BRAM for testing. My doubt is how to pass testing data to the trained model. I have calculated the weight value for each feature using python script and which is the same for all patients. Please help me in this regard. If I am following the wrong method please suggest me.
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Thank you sir for your suggestion, My question is how to verify the SVM training model with testing data for FPGA implementation. I have stored testing data in BRAM.
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Hello, I am trying to isolate single cell colonies form MCF-7 breast cancer cells. I didn"t get any colony in my plate. they were edited by CRISPR but the deletion does not affect their growth/survival. Thank you!
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Yes it will work fine, the detailed protocol can be obtained from this link. Best of Luck.
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I'm working on a research that requires strain elastography images. If anyone can provide the source for it that'll be great. Please comment.
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Try searching the imaging database at www.imagingQA.com at the link below :
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Hello,
I am planning on designing an experiment with FISH imaging with a collaborator.
I want to research the sample preparation of breast cancer tumor tissues before I start anything.
Can you recommend me a protocol or literature sources to follow on.
Spatial transciptomics is higly new and I would love to hear hands on experience.
Best
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These links may be of help
1)__ June 2021 paper in Nature / Nature Reviews - Genetics
Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
2)__ 10-X Genomics
A company and not hands on information…
but a decent introduction to the ideas
of spatial transcriptomics
3)__ July 2021 paper in Science
Embryo-scale, single-cell spatial transcriptomics
Access to full paper by one of three science literature groups
or purchase of the full paper
4)__ May 2021 paper in “Frontiers of Cell Biology”
Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
This is the full paper
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Family history is an important risk factor for breast cancer incidence, but the parameters conventionally used to categorize it are based solely on numbers and/or ages of breast cancer cases in the family and take no account of the size and age-structure of the woman’s family. What are your views?
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I think there is a difference between BRCA1 and BRCA2. In general terms between 25-50% or even more. It may depend on the cancer, some are 33%. This one is quite high.
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Dear researchers, I would be appreciated if you answer the following question.
I want to identify genes that are upregulated or downregulated during breast cancer progression based on T-stage. to perform that, I have used differential gene expression analysis between different T stages and a linear regression model.
The consequence is not suitable. The genes that are identified are not completely overexpressed during cancer progression. for example, some of them are upregulated in T4 compared to T2 but downregulated in T3 with a similar comparison to T2.
I have received suggestions to use a multinomial lasso-penalized regression combined by fitting trend models to the data.
I do not have enough information about this method and how to perform it in R. I would be glad if you share your suggestions and experiences about the mentioned issue.
with best regards.
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LabelMe-The Open annotation tool - MIT
LabelMe is a project created by the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) which provides a dataset of digital images with annotations. The dataset is dynamic, free to use, and open to public contribution. The most applicable use of LabelMe is in computer vision research. As of October 31, 2010, LabelMe has 187,240 images, 62,197 annotated images, and 658,992 labeled objects.
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In the LableMe tool, you can select a specific region and annotate it according to your class. But here you have a 200k dataset.
So what I suggest is, you can generate those text files automatically.
  • Eg: You have 2 images, but the region of the class you are annotating is in the same place on both images. So for those images, you only need to generate one text file with that coordinates and then automatically generate those files from an algorithm using the same coordinates.
  • But if the region of class in a separate place, then you have no choice rather manually annotating.
One of my research in a YOLO training dataset, I have used this technique to annotate multiple images.
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These breast cancer cells, dissolved at -80 degrees, did not adhere to the T75 flask in the first 20 hours, what can be done?
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Hello
The cells may be under stress. Did you follow a proper thawing protocol. The cells have to be washed in order to get rid of the freezing medium containing DMSO.
Sometimes, if the cells are not frozen in a proper manner or if there is variation in storage temperature then there could either be loss in cell viability or change in cell behaviour as in this case. Have you checked the cell viability after thawing?
I suggest you culture these cells in a smaller surface area like 6-well plate or T-25 flask so that the cells may come closer to each other and begin to adhere and grow.
Good Luck.
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Breast cancer is highly heterogeneous. Each subtype is unique with respect to immunogenicity and responds differently to immuno therapy.
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Immunogenicity is the ability to induce a humoral and/or cell-mediated adaptive immune response. The tumor neoantigens that are produced because of genomic instability in breast cancer cells, can be recognized by the immune system and induce T-cell responses and antitumor immunity. So, the burden of tumor mutations and the load of neo-epitopes are the two factors that are linked to response to immune checkpoint inhibitors.
Most of the breast tumors are immunologically silent, characterized by the presence of low mutation, neoantigen burden and few effector tumor infiltrating lymphocytes except for the three subtypes namely,
1) Triple negative breast tumors (TNBC) which are unique among breast cancer subtypes having a higher mutational load compared to other subtypes. In addition, higher levels of tumor-associated antigens suggests that immunotherapies are a promising treatment option.
2) High tumor infiltrating lymphocytes (TILs) and programmed cell death-ligand 1 (PD-L1) expression have been found in a considerable proportion of HER2+ breast cancer patients.
3) Estrogen receptor-negative and HER2 positive have also shown evidence of immunogenicity.
Best,
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Some literatures mentioned viral infection-associated breast and lung cancers are possibly involved as pathogens in cancer, because carcinogenesis is a multistep process with several contributing factors. Some viruses like  herpesvirus, polyomavirus, papillomavirus, and retrovirus families definitely associate with breast cancer. 
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The viral cause of sporadic breast cancer (SBC) has been proposed based on an experimental mouse model of breast tumor induced by mouse mammary tumor virus (MMTV), Epstein-Barr virus (EBV), and human papillomavirus (HPV). While some studies have shown viral sequences of MMTV, HPV, and EBV in breast cancer cells, others have failed. Another study suggested that MMTV, HPV, and EBV have a potential role in the development of breast cancer and added more reasons to move forward in the search for a possible viral origin of breast cancer.
Kindly check the following RG link:
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To achieve the goal of personalized medicine it is necessary not only to have agents with defined molecular specificities, but to have minimally invasive biomarker and imaging tests that will identify which patients have the target in their tumor and the patient’s pharmacogenotype. A related objective is to have a way to measure the effect of a drug on its molecular target in the tumor to be able to answer important questions, such as how much drug is required to inhibit the target in a tumor and is there is a benefit to giving more drug or will this only increase toxicity.
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The Oncotype DX portfolio of breast, colon, and prostate cancer tests applies advanced genomic science to reveal the unique biology of a tumor in order to optimize cancer treatment decisions. In breast cancer, the Oncotype DX Breast Recurrence Score test is the only test that has been shown to predict the likelihood of chemotherapy benefit as well as recurrence in invasive breast cancer. Additionally, the Oncotype DX Breast DCIS Score test predicts the likelihood of recurrence in a pre-invasive form of breast cancer called DCIS. In prostate cancer, the Oncotype DX Genomic Prostate Score® test predicts disease aggressiveness and further clarifies the current and future risk of cancer prior to treatment intervention.
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I tried staining MCF7 and MB231 for Vimentin and Cytokeratin antibodies, and surprisingly, I saw both cell lines showed both markers. According to the literature, MB231 is a mesenchymal type cell and MCF7 is luminal, so shouldn't it be that MB231 shows more cells positive for Vimentin as compared to MCF7?
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Hi Rafał Watrowski . Adity Pore was just asking why markers for the hypothetical EMT do not make sense in the 2 cell lines she is looking at.
I agree. The EMT is just a hand waving explanation of how epithelial cells, that are normally sedentary, suddenly become motile and invasive when they are cancerous.
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Dear fellow researchers,
I am studying the risk of breast cancer when using a certain type of medication, compared with never-users of this medication.
When using the Cox model, I have used the time exposed to the medication as the time dependent variable and I have adjusted for age (and other covariates) in the models.
However, age is a much stronger risk factor for developing breast cancer than using this medication. So, I am wondering - should I use age as the time dependent variable instead of exposure time? In that case, it seems strange to me to adjust for exposure time (in this specific model at least), as I am only interested in the risk among all current users, irrespective of exposure time.
Thank you in advance!
Kind regards from Jenny Niemeyer Hultstrand, M.D. PhD at Uppsala University, Sweden.
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good information regarding your question is available on....
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For siRNA transfection of the 4T1 cell line, how is it possible to maintain the cells in the serum-free medium for 48 hours in order to let the previously produced proteins degrade?
In my experience, aggressive metastatic cell lines can not be adapted and cultured in media complemented with less than 4 percent FBS.
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Hello,
Depending on your protein's half life and siRNA efficiency, you don't need to deplete from serum. For instance, I manage to use my siRNA in 10% FBS and for a specific protein (which has a very short half life), after 48h my protein isn't detected by western blot. While others are still detectable but with a much lower expression level (knockdown effect). If this isn't applicable in your case, in my experience, certain cancer cell lines are adaptable, like the BT549. So you might consider also, changing your siRNA protocol to increase efficiency or the cell lines used, or a different adaptation protocol https://www.thermofisher.com/pt/en/home/references/protocols/cell-culture/serum-protocol/adaptation-of-cell-cultures-to-a-serum-free-medium.html