Conf: SfN19 Chicago

Session Type: Poster
Session Number: 340
Session Title: Software Tools: Analysis I
Session Date and Time: 10/21/2019 8:00:00 AM – 10/21/2019 12:00:00 PM
Location/Room: McCormick Place: Hall A

Presentation Time:  10/21/2019 11:00:00 AM –  10/21/2019 12:00:00 PM
Presentation Number:  340.16
Poster Board Number:  CC73
Abstract Control Number: 14195

Poster boards are six feet (1.8 m) wide and four feet (1.2 m) high. More information on preparing your poster, including poster templates, can be found on  Poster templates are provided as guidelines for creating a poster.  Posters are not required to follow a particular format. They should follow requirements for scientific rigor, outlined below. 

Layout (4 column)

  • Title: Prepare a banner for the top of the poster indicating the abstract title, author(s), affiliation(s), and the presentation number. Use lettering at least one-inch high.
  • Illustrations: Design figures for viewing from a distance and use clear, visible graphics and large type. Colors are effective if used sparingly; use dark colors on white or pale backgrounds and light colors on dark backgrounds. Figures should illustrate no more than one or two major points. However, simple figures are unnecessary. Make clear main points, but include detail for the aficionado. Indicate illustration sequences with numbers or letters at least one inch high. (Omit “Fig.” or “Figure.” This is unnecessary and occupies excess space).
  • Text
    • Each figure or table should have a heading of one or two lines in very large type stating the “take-home” message. Provide additional essential information below in a legend set in 16 point or larger type.
    • Minimize narrative. Integrate text that would normally appear in the body (Results and Discussion) of a manuscript in figure legends. Concisely describe not only the content of the figure, but also the derived conclusions. Place brief details of methodology at the end of each legend.
    • Use large type in short, separated paragraphs with unjustified (ragged right) margins. Numbered or bulleted lists are effective ways to convey a series of points. Do not set entire paragraphs in uppercase (all capitals) or boldface type.
    • Place an introduction at the upper left and a conclusion at the lower right, both in large type. It is rarely necessary to post a copy of the abstract.

T. Chen Fong and fMRI+ephys

Neuralink investor

Southern Alberta hall of fame

Order of canada

Simultaneous fMRI and Ephys

Simultaneous FMRI and electrophysiology in the rodent brain.

Ferromagnetic material free probe from neuronexus

ferromagnetic material (iron cobalt nickle)

Small animal MRI

Bruker Biospin 9.4T scan- ner (Bruker Medizintechnik, Karlsruhe, Germany) equipped with an actively shielded gradient coil. A quadrature volume transmitter coil (model: MT0381, inner diameter=86mm) was used for RF excitation. An actively-decoupled surface coil (model: MT0105-20) was placed di

9.4 T 210 ASZ (Varian, Inc. Palo Alto, USA) 

Small animal MRI in uCalgary: experimental imaging center (Jeff Dunn)

Dunn et al 2009: carbon electrode + MRI
Cam Teskey: Jeff Dunn’s collaborator

Correlative measurement study

OptoMRI: light modulated vaso dialation.
fMRI vs ephys agree and disagree
JoVE article on fMRI+glass electrode

Small animal MRI in uAlberta

uoc visit

jorn davidsen. fMRI paper. two network interactions. stability across subject. connect him to dan english.

christph simon. quantum effects in neuroscience. photons in the brain. network. cryptoprotein.

Wilten Nicola. hard drive theory. nature neuroscience paper. two oscillations. interneuron rings.

how to decode information from hippocampus and expose them.

# Committee
David Knudsen, David Park, Ania Harlick, Jo-Anne Brown, Claudia Gomes da Rocha,

# Funding
NIH-CANADA: Participation by Canadian Researchers in the NIH BRAIN Initiative
NSERC Discovery Grant: Aug 1 (intent), Nov 1 (application), instruction
NSERC CREATE Grant: Collaborative research and trainig experience training. $1.65M for 6 years
CFI: Canadian foundation for innovation (Sep 16)
Compute Canada: Nov 8
KECK foundation:
Simon’s foundation

# Equipment
Surgical microscope

# Day 0 schedule

# Day 1 schedule

Talk, lecture (clustering)
meetings with David Knudsen, Jo-Ann Brown, Ania Harlick,
Lunch with students
Richard Frayne

# Day 2 schedule

Group questions: funding. research. impact. teaching. outreach
meetings with Wilten Nicola, Jorn Davidsen
Lunch with David Feder, David Hobil, Ania. Penetrating ground radio
Meetings with Christoph Simon, David Feder, David Hobil

# Day 3 schedule

Breakfast with T. Chen Fong with Jorn Davidsen, Wilten Nicola, David Park @ Calgary Golf & Country Club

Deciding programming language for computational physics course

Matlab vs. Python (Medium)

Python is free, Matlab is well documented and has simulink.

Mathwork’s answer to it

My decision: is Matlab available at UOC? No data

Matlab to python migration guide (Enthought)

I did the tutorial on google colab and very easy to write and run, without having to setup anything. this is how students should do their assignment and projects.

Python with web interface. Offer hosting with herokuapp. how about jupyterhub account for students?

UOC uses desire2learn (linkedin learning) or D2L system. Students can submit .py files (or ipynb files). or through google colab which might be the easiest.

So give them projects in python and run it on google colab.

Mom treatment summary so far


  • antibiotics: ernepenem
  • pain medication: hydromorpho(0.5 mg/day. @22:00). tyrenol.
  • anticoagulation: enoxaparin 40mg/day (@14:00). previously heparin (IV) and Tinzaperin.

#Physiological variables

  • urine (1L/day)
  • stool (2-3x/day)
  • Blood pressure
  • oxygen saturation (above 90%)
  • oxygen suppply (1L/min).
  • Temperature
  • Weight (target 50KG)
  • Pain level
  • Swelling on the legs

#Blood test

  • CBC. hemoglobin.
  • Electrolyte
  • Cretinine (kidney, lower better)

July 27. Treatment plan for mom

Risk factors

  • immuno-compromized condition during chemo
  • flu shot (peaks in November in Alberta)
  • Arterial rupture: low-dose aspirin?

Low-dose aspirin (not recommended, will thin blood too much and risk for hemorrhage)

How you prepare for Chemo (mayo clinic)

How you prepare for chemotherapy depends on which drugs you’ll receive and how they’ll be administered. Your doctor will give you specific instructions to prepare for your chemotherapy treatments. You may need to:

  • Have a device surgically inserted before intravenous chemotherapy. If you’ll be receiving your chemotherapy intravenously — into a vein — your doctor may recommend a device, such as a catheter, port or pump. The catheter or other device is surgically implanted into a large vein, usually in your chest. Chemotherapy drugs can be given through the device.
  • Undergo tests and procedures to make sure your body is ready to receive chemotherapy. Blood tests to check kidney and liver function and heart tests to check for heart health can determine whether your body is ready to begin chemotherapy. If there’s a problem, your doctor may delay your treatment or select a different chemotherapy drug and dosage that’s safer for you.
  • See your dentist. Your doctor may recommend that a dentist check your teeth for signs of infection. Treating existing infections may reduce the risk of complications during chemotherapy treatment, since some chemotherapy may reduce your body’s ability to fight infections.
  • Plan ahead for side effects. Ask your doctor what side effects to expect during and after chemotherapy and make appropriate arrangements. For instance, if your chemotherapy treatment will cause infertility, you may wish to consider your options for preserving your sperm or eggs for future use. If your chemotherapy will cause hair loss, consider planning for a head covering.
  • Make arrangements for help at home and at work. Most chemotherapy treatments are given in an outpatient clinic, which means most people are able to continue working and doing their usual activities during chemotherapy. Your doctor can tell you in general how much the chemotherapy will affect your usual activities, but it’s difficult to predict exactly how you’ll feel.Ask your doctor if you’ll need time off work or help around the house after treatment. Ask your doctor for the details of your chemotherapy treatments so that you can make arrangements for work, children, pets or other commitments.
  • Prepare for your first treatment. Ask your doctor or chemotherapy nurses how to prepare for chemotherapy. It may be helpful to arrive for your first chemotherapy treatment well-rested. You might wish to eat a light meal beforehand in case your chemotherapy medications cause nausea.Have a friend or family member drive you to your first treatment. Most people can drive themselves to and from chemotherapy sessions. But the first time you may find that the medications make you sleepy or cause other side effects that make driving difficult.

What does R-CHOP treat (Healthline)

Three of the drugs in R-CHOP are powerful cytotoxics, which means they kill cells. One is a type of immunotherapy and the last is a steroid, which has shown to have anticancer effects.

Rituximab (Rituxan)

Rituximab is generally used to treat NHL. It’s a monoclonal antibody. It targets a protein called CD20 on the surface of white blood cells called “B cells. Once the drug attaches to the B cells, your immune system attacks and kills them.

Cyclophosphamide (Cytoxan)

This drug can treat a variety of cancers, including lymphoma and cancer of the breast and lung. Cyclophosphamide targets the DNA of cancer cells and signals them to stop dividing.

Doxorubicin hydrochloride (Adriamycin, Rubex)

This drug is an anthracycline that can treat many types of cancer, including breast, lung, and ovarian cancer. Doxorubicin blocks an enzyme cancer cells need to grow and reproduce. It’s bright red color has earned it the nickname “the red devil.”

Vincristine (Oncovin, Vincasar PFS, Vincrex)

Vincristine is an alkaloid that can treat many types of cancer, including advanced-stage breast cancer, lymphomas, and leukemia. It interferes with genes to stop them from replicating. This drug is a vesicant, meaning it can damage tissue and vessels.


This drug is a corticosteroid available under a variety of brand names. Unlike the others, this is an oral medication. It works with your immune system to help reduce:

  • inflammation
  • nausea
  • vomiting
  • allergic reactions
  • low platelet levels, or thrombocytopenia
  • high calcium levels, or hypercalcemia

Together, these drugs create a potent cancer-fighting cocktail.

Ibrutinib + R-CHOP in DLBCL: does age make a difference

Journal of Hematological Oncology
Randomized Phase III Trial of Ibrutinib and Rituximab Plus Cyclophosphamide, Doxorubicin, Vincristine, and Prednisone in Non-Germinal Center B-Cell Diffuse Large B-Cell Lymphoma.

The study did not meet its primary end point in the ITT or ABC population. However, in patients age younger than 60 years, ibrutinib plus R-CHOP improved EFS, PFS, and OS with manageable safety. In patients age 60 years or older, ibrutinib plus R-CHOP was associated with increased toxicity, leading to compromised R-CHOP administration and worse outcomes.

CBC (complete blood count)

Red blood cell countMale: 4.35-5.65 trillion cells/L*
(4.32-5.72 million cells/mcL**)Female: 3.92-5.13 trillion cells/L
(3.90-5.03 million cells/mcL)
HemoglobinMale: 13.2-16.6 grams/dL***
(132-166 grams/L)
Female: 11.6-15 grams/dL
(116-150 grams/L)
HematocritMale: 38.3-48.6 percent
Female: 35.5-44.9 percent
White blood cell count3.4-9.6 billion cells/L
(3,400 to 9,600 cells/mcL)
Platelet countMale: 135-317 billion/L
(135,000 to 317,000/mcL)
Female: 157-371 billion/L

What caused mom’s Arterial hemorrhage (Retroperitoneal bleeding)?

Retroperitoneal bleeding (wiki)

Paper: VTE in DLBCL, Ayyappan et al, Blood Journal, 2015

VTE: Venous Thromboembolic events
DLBCL: Diffuse large B-cell lymphoma

DLBCL patients present a high risk of VTE, with approximately half of all VTE events occurring early in the course of the disease. We were able to identify the presence of bulky disease at diagnosis and the absence of response to first line therapy as risk factors for developing VTE. Te use of anthracycline-containing regimens was protective against VTE, likely because of the increased rates of disease response. Patients with VTE had worsened outcomes, likely a result of the presence of persistent disease, although a direct effect of VTE on long-term outcomes cannot be ruled out. Our results highlight the need for a heightened awareness of the increased risk of VTE in DLBCL patients and the need for prevention strategies.

How to prevent arterial embolism? Healthline article

Luke Rannelli mentioned that it’s not related to DVT (Deep vein Thrombosis) nor Lymphoma. So it has to linked to Heparin administration.

Risk factor: are of advanced age
MRI available @ RGH

How to prevent arterial embolism?


  • statins – used to lower your blood cholesterol levels 
  • anticoagulant medicines- such as warfarin
  • antiplatelet medicines – such as low-dose aspirin or angiotensin-converting enzyme (ACE) inhibitors (used to treat high blood pressure)


  • reduce salt intake
  • eat at least 5 portions of fruit and vegetables and 2 portions of fish per week (1 oily)
  • do a minimum of 30 minutes of moderate exercise such as walking or cycling at least 5 times a week

PAPER: Managing thrombosis in cancer patients

Managing thrombosis in cancer patients

Low‐molecular‐weight heparin (LMWH), when compared with warfarin, has been shown to reduce the risk of recurrent VTE in patients with cancer‐associated thrombosis (CAT),4 and is therefore the standard treatment for acute CAT for the past 15 years. However, the high cost and significant lifestyle burden associated with LMWH have led many clinicians and investigators to wonder whether the direct oral anticoagulants (DOACs) might be a better choice for primary and/or secondary VTE prevention in patients with cancer. 

Based on the aggregate of available evidence, warfarin and other VKA should be a “third choice” for cancer patients, used only in situations where neither a DOAC nor LMWH is feasible.

direct oral anticoagulants :

Direct oral anticoagulants (DOAC)

Four DOACs have been approved for the treatment of DVT and/or PE, including dabigatran, rivaroxaban, apixaban, and edoxaban. All have demonstrated a comparable efficacy and safety to VKA in the cancer subpopulation.37 However, the cancer subpopulation enrolled in these large studies was small and generally had lower risks of both recurrent VTE and hemorrhage when compared with patients enrolled in earlier studies specific to cancer patients (such as CLOT study).38Meta‐analyses have suggested that DOACs and LMWH may have similar efficacy and safety in cancer patients, but these were based on indirect comparisons.3839 A few single‐center cohort studies of rivaroxaban for CAT have yielded encouraging results, but all had significant methodologic limitations.40414243 A recent study explored the use of rivaroxaban in cancer patients with catheter‐related thrombosis also had promising results.44 Overall, these preliminary results are encouraging, but not definitive.

Heparin (blood thinner) vs LMWH (low molecular weight heparin)

Heparin Sodium in 5% Dextrose Injection
Used July 25-26 (stopped ~9AM)
Molecular weight: 1039.9 g/mol

Low molecular weight heparin (wikipedia)
Patients with cancer are at higher risk of venous thromboembolism and LMWHs are used to reduce this risk.[10] The CLOT study, published in 2003, showed that, in patients with malignancy and acute venous thromboembolism, dalteparin was more effective than warfarin in reducing the risk of recurrent embolic events.[11] Use of LMWH in cancer patients for at least the first 3 to 6 months of long-term treatment is recommended in numerous guidelines and is now regarded as a standard of care.[10]

Note (JJJ): Delteparin (Tinzaparin) and Nadroparin are better than Warfarin.

reference: [10] Nishioka J, Goodin S (2007). “Low-molecular-weight heparin in cancer-associated thrombosis: treatment, secondary prevention, and survival”. Journal of Oncology Pharmacy Practice13 (2): 85–97.doi:10.1177/1078155207079169PMID17873108.

LMWH is also the favored treatment for cancer-related blood clots, since it has been shown to be more effective than warfarin (tablet).

LMWH is often used temporarily to help patients transition – or bridge – to long-term oral anticoagulant therapy, most commonly warfarin or Coumadin®. Your doctor will usually add warfarin to your medication schedule, so you take both warfarin and LMWH for several days under careful monitoring. Once your body achieves therapeutic blood levels of warfarin, your doctor will discontinue LMWH injections.

As with UFH, let your doctor know if you are taking aspirin, other non-steroidal anti-inflammatory drugs (NSAIDs) – such as ibuprofen or naproxen – or clopidogrel before starting LMWH treatment, because these drugs increase the risk of bleeding.