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§ construct building in strongyloides
§ electrophysiology of a reflex circuit
§ NURP projects
§ population constraints on individuals
§ so you want to be a drosopholist
§ so you want to be a nemotologist
§§ flight motor control notes
Ache.etal2019
AFD neurons are required for positive thermotaxis
AFD neurons response to heat demonstrates evolutionary adaptation
Ahmed.etal2023a
Ahrens2017
all nematodes share common anatomical features
all neurons within a hemilineage use the same neurotransmitter
allen brain atlas
amphids
an equivalent circuit mathematically models a cell
an ion's water shell contributes to ion channel selectivity
anatomy of wing muscles
antagonistic song exploits narrow tuning of female receptivity circuitry during competitive courtship
antennal mechanosensory and motor center
applying to grad school
ascending histamine neurons participate in flight feedback loop
ascending neurons
ascending neurons tune sensorimotor behaviors
ATR
ATR preparation
autumn 2023 with nico
axon guide
backlinks are the powerhouse of obsidian
Baker.etal2022
banc
beer is the fuel of collective discovery
behavioral entropy is a readout of behavioral repertoire
behaviors adapt to divergent environments despite small, simple nervous systems
Berman.etal2016
Bialek.etal2012
bio robotic research coarsely demonstrate flight cessation with implanted neural stimulations in large insects
Biona report II physiology and biophysics of insect flight
Brezovec.etal2024
Bryant.etal2018
Bryant.etal2022
Cafaro.Rieke2013
Calabrese.Marder2024
Cande.etal2018
capacitance
care work is valued work
Chen.etal2021b
Cheong.etal2024a
cholinergic hemilineages
chordotonal organ
Clark.Abbott2023
Clowney.etal2015
connecting a github pages site to a custom domain
connectome datasets
conservation of nervous system and structure in nematode species
consider transvection when designing fly crosses
considerations for grad school interviews
coordinated activity of the flight power muscles are critical for flight
Cowley.etal2024
CSHL Neurobiology of Drosophila Conference
CSHL Neurobiology of Drosophila poster session I
CSHL Neurobiology of Drosophila poster session II
CSHL Neurobiology of Drosophila Session I talks
CSHL Neurobiology of Drosophila Session II talks
CSHL Neurobiology of Drosophila Session III talks
CSHL Neurobiology of Drosophila Session VII talks
CSHL Neurobiology of Drosophila Session VIII talks
cytological locations of attp landing sites
Dag.etal2023
Demir.Dickson2005
descending neurons
developmental hacking of circuit wiring to study odor encoding in flies
Dickinson.Muijres2016
Ding.etal2019
diphtheria toxin
distributed LC neurons cooperate to encode visual stimuli
DLMn activity drives linear changes in wing beat frequency
DLMns adjust myoplasmic calcium levels to control wing power
DNg02
DNg02 activity increases wing beat amplitude
DNp07
DNp07 elicits visually evoked landing motor patterns during flight
DNp10
DNp10 elicits visually evoked landing motor patterns during flight
dorsal nerve cord
dorsal thalamic neurons in zebrafish are specifically tuned to conspecific fish-like motion
dorsal ventral organization of descending neurons corresponds to motor output
dumit styles of reading
Ehrhardt.etal2023
electrophysiology preparation
EMG electrode parts
employing expansion layer framework to better understand associative learning and memory in drosophila
entropy
entropy is a tool
entropy reduction in low dimensional map reveals stereotyped behaviors
equity in authorship order requires diverging from conventional metric systems
every labeled brain structure falls within a general hierarchy of the central brain
example implementation of maximum entropy model
Experimentally testing and confirming the Albus-Marr expansion layer model in the mushroom body
extracellular saline protocol
FAFB
FANC
female receptivity circuitry
femoral chordotonal organ
flies have 9 spiracles per side
flying insects decouple wings from thorax for steering
foraging in C. elegans depend on organization of 5HT receptors, not their molecular properties
forming a supervisory committee
freezable chaos framework has advantages over traditional synaptic facilitation models
freezable chaos is a novel network model of plasticity
gabaergic hemilineages
Gadagkar.etal2016
general properties of ion channels
genetic toolbox in flies
giant fiber
Glaser.etal2019
glutamatergic hemilineages
Gouwens.Wilson2009
GridTape speeds up EM volume data collection
hemilineages provide a functional and anatomical classification for neurons in the vnc
Hoopfer.etal2015
how I made this site
how I read academic papers
how to ask for feedback
how to backup and timestamp digital lab notebook
how to create application package
how to find genetic drivers for candidate neurons
how to find labeled neurons in the connectome
how to find schools to apply to
how to give feedback
how to keep a lab notebook
how to make fly tethers
how to pull electrodes
how to run jupyter on hpc cluster
how to use marimo
how to use obsidian
how to use rclone to sync remote drives
Hurkey.etal2023
Hutt.etal2023
indirect flight muscle organization
Jadzinsky.Baccus2013
Jiang.etal2022
Johnston's organ neurons
Kappel.etal2022
Kato.etal2015
kir2.1
Klapoetke.etal2017
kyle thieringer
labial and cephalic sensilla
LCs convey specific visual features to the brain
Lehmann.Bartussek2017
Lesser.etal2024
Liboiron.etal2017
limitations to machine learning
Lindsay.etal2017
lipid bilayers are impermeable to ions
literature notes
looming feature detectors convey visual information to VNC for takeoff response
looming stimulus evokes opposite behaviors depending on behavioral state
lore drops
LPLC2
machine learning solves engineering problems
male cMPOA activity represents social fear
male MPOA displays heterogenous activity during male social behaviors
males engage in aggressive behaviors during competitive courtship
Mamiya.etal2018
MANC
Manjila.etal2019
maui setup protocol
maximum entropy model for group dynamics
maximum entropy model lacks free parameters
Mellert.Truman2012
metamorphosis of a note
mimir
model of the entire fly brain connectome accurately predicts sensorimotor transformations
model organisms for studying insect flight
modeling whole fly brain provides a framework to rapidly screen for circuit mechanisms
modular note table
mutual information
Namiki.etal2022
NBLAST
nematode neurons lack action potentials
nematode neuropeptide system is complex
nematode species identified
nematode thermosensory neurons detect temperature changes through guanylate cyclase receptors
nernst equation
nerve ring
network and local serotonin dynamics both influence global brain dynamics
neuromodulation of flight
neurons in the AMMC show preferences to courtship song modes
neurons with stereotyped functions are still context dependent
neurotransmitter predictions in fanc
normative models are concrete ways to predict animal behavior
normative models predict behavior, but do not explain the mechanism
NSB patching guide
nsf grfp evaluation criteria
nsf grfp format guidelines
NSF GRFP resources
obsidian is a powerful and flexible tool
obsidian plugins that i use
octopamine
octopamine activity increases during flight
octopamine gates activity of DNp07
octopamine orchestration hypothesis
P1 neurons
Patella.Wilson2018
pC1 neurons
pC1 neurons coordinate extensive social behavior repertoire
pC1x neurons
PH-miniSOG optogenetically ablates cells
phasmids
phylogeny of nematodes
pick an advisor who is good at science
pick an advisor with good mentorship style
pleurosternal muscles
point spread function protocol
pore theory explains channel selectivity
Pouille.Scanziani2004
proprioception
proprioceptive organs
proprioceptor driver lines
pseudocoelomic body cavity
Randi.etal2023
read papers closely
reading papers quickly
resting membrane potential
resting membrane potential in flies
resting potential is determined by passive channels
Reynolds number
Sadaf.etal2015
Sane2016
scale invariance in group behavior modeling
Schafer2016
serotonergic signaling drives changes in foraging behavior in C. elegans
setting up zotero integration
sexually dimorphic fru isoforms regulate male courtship behaviors
sexually dimorphic gene expression is driven by sex specific splicing of fruitless
shibire
Shiozaki.etal2024
Shiu.etal2023
Simmons.etal2010
social behaviors in fish depend on specifically tuned visual circuits
somatic muscle cells
somatic muscles
spiracles
splayed DLMn firing stabilizes wingbeat frequency
spring 2024 with ari
Steinmetz.etal2019
Sten.etal2023
studying parasitic nematodes improves public health crisis
Suver.etal2012
take literature notes
take meaningful notes
take modular notes
task engagement drives widespread activity in the mouse brain
tax-4 gene
tax-4 gene is required for positive thermotaxis in worms
tergal depressor of the trochanter
the auditory connectome is highly recurrent
the cMPOA-VMHvl circuit gates aggression in male mice
the DLMns compose a minimal flight CPG
the giant fiber receives visual input from LPLC2 driving looming escape behavior
the mechanical power calculation of the indirect flight muscle
the nematode nervous system is simply organized
the pleurosternal muscle tensions the thorax
the thorax mechanically links wings and halteres through oscillations
the three pass approach to read papers
thermosensation overrides chemosensation in parasite migration behavior
thoughts only transmute to knowledge with lore drops
three dopamine neurons in the VNC coordinate wings during flight
tonotopy of the auditory system acts as an array of bandpass filters
Tschida.etal2019
Tuthill.etal2014
Ueda.etal2020a
unsupervised clustering of calcium imaging data
use hub notes to organize projects
use research rabbit to find papers
ventral nerve cord
ventral nerve cord (nematodes)
vertebrate circuit mapping techiques
VonPhilipsborn.etal2011
weak electrical coupling between DLMns favors splayed firing pattern
wedge
Wei.etal2023
Weinreb.etal2024
wing kinematics during flight are constrained by a max power output
wing motor neurons
wings have synchrony during both initiation and cessation of flight
winter 2024 with kailee
worms engage in different migratory behaviors depending on sensory information
worms engage in local search behavior
worms have experience dependent plasticity for temperature navigation
Wu.etal2016
Xu.Chisholm2016
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Sep 03, 2025
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literature notes
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metamorphosis of a note
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Wu.etal2016
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axon guide
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Patella.Wilson2018
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Pouille.Scanziani2004
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Sadaf.etal2015
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Sane2016
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Kato.etal2015
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Lehmann.Bartussek2017
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Lesser.etal2024
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Liboiron.etal2017
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Lindsay.etal2017
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Mamiya.etal2018
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Manjila.etal2019
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Mellert.Truman2012
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Namiki.etal2022
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Dag.etal2023
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Demir.Dickson2005
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Dickinson.Muijres2016
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Ding.etal2019
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Ehrhardt.etal2023
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Gadagkar.etal2016
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Glaser.etal2019
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Gouwens.Wilson2009
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Hoopfer.etal2015
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Hurkey.etal2023
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Bialek.etal2012
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Biona report II physiology and biophysics of insect flight
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Brezovec.etal2024
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Bryant.etal2018
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Bryant.etal2022
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Cafaro.Rieke2013
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Calabrese.Marder2024
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Cande.etal2018
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Chen.etal2021b
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Cheong.etal2024a
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Clark.Abbott2023
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Clowney.etal2015
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Cowley.etal2024
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Ache.etal2019
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Ahmed.etal2023a
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Ahrens2017
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Baker.etal2022
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Berman.etal2016
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