Johns Hopkins Research Data Repository
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Data associated with the publication: The cellular architecture of memory modules in Drosophila supports stochastic input integration
No full textArticle abstract: The ability to associate neutral stimuli with valence information and
to store these associations as memories forms the basis for decision
making. To determine the underlying computational principles, we build
a realistic computational model of a central decision module within
the Drosophila mushroom body (MB), the fly’s center for learning and
memory. Our model combines the electron microscopy-based architecture
of one MB output neuron (MBON-alpha 3), the synaptic connectivity of
its 948 presynaptic Kenyon cells (KCs), and its in vivo membrane
properties obtained from patch-clamp recordings. We show that this
neuron is electrotonically compact and that synaptic input
corresponding to simulated odor input robustly drives its spiking
behavior. Therefore, sparse innervation by KCs can efficiently control
and modulate MBON activity in response to learning with minimal
requirements on the specificity of synaptic localization. This
architecture allows efficient storage of large numbers of memories
using the flexible stochastic connectivity of the circuit.The data-set contains the coding environment and scripts for running the computational model, experimental data for model fitting and all resulting data from computational simulations related to the above mentioned manuscript.
The Fitting.zip file stores the resulting trace from fitting the model in tabular form.
The Raw Experimental Traces for Fitting.zip file stores the experimental traces that were used for model fitting in tabular form. One .csv file per cell with the 35 traces and the corresponding time.
The Simulation_Code.zip file contains the coding environment, simulation scripts and vector data for synapses and model as .py, .swc and .json files.
The thirteen Simulation .zip files store all the raw data in a folder resulting from one specific simulation (.dat and .csv files) in tabular form . A subfolder contains .tif, .pdf, .ps files, for the visualization of the plotted data and in some cases example images of activated regions in the dendritic tree of the neuron.
For example: Simulation 1 - 1 KC Synapses.zip includes all the data resulting from simulated successive activation of each individual KC. Each trial involved the activation of 10 synapses per KC.
amp_PN/soma.dat contains the resulting amplitude of changes in membrane potential at the proximal neurite/soma in mV.
num_alphas.csv contains a matrix of the number of activated synapses per trial.
PN/soma_voltage.csv contains the resulting changes in membrane potential at the proximal neurite/soma over time in mV.
synapse_sites.csv contains the specified numbers of each activated synaptic site during the trial.
time.csv contains the time axis for each trial in ms.
The subfolder Sim1_Figs contains .pdf and .ps of two example images of the activated synapses from trial 1 and trial 948. Other folders also contain files with plots of the corresponding data.
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Federal court case event and coreference data
No full textThis contains much of the intermediate data and final data for the paper “Improved Induction of Narrative Chains via Cross-Document Relations” in StarSem 2022. The raw data came from the federal cases dataset at the excellent Caselaw Access Project (https://case.law) from Harvard’s Law Library
Data associated with the publication: "In our culture, if you quarantine someone, you stigmatize them": Qualitative insights on barriers to observing COVID-19 prevention behaviors in Côte d’Ivoire
No full textWhile vaccines are now authorized for use against the SARS-CoV2 virus, they remain inaccessible for much of the world and widespread hesitancy persists. Ending the COVID-19 pandemic depends on continued prevention behaviors such as mask wearing, distancing, hand hygiene, and limiting large gatherings. Similarly, stigma related to COVID-19 has received little attention from the global south. The Breakthrough ACTION project led by Johns Hopkins Center for Communication Programs conducted a qualitative study in November 2020 in Côte d’Ivoire to explore people’s experience with and perceptions of the COVID-19 pandemic. We conducted 24 focus group discussions and 29 in-depth interviews with members of the general population and health providers which have allowed for the analysis of vaccine perceptions, attitudes and practices related to prevention behaviors, and stigma
Data associated with the publication: The combined influence of polythiophene side chains and electrolyte anions on organic electrochemical transistors
No full textThe data consists of graphs and spreadsheets showing the device response for different combinations of receptor polymers with electrolyte anions in electrochemical transistors. The data are organized according to the manuscript figures that they support. The files are the sources of data used to construct the plots that report the observations and trends in the manuscript
Data associated with the publication: Abundant and Persistent Sulfide-oxidizing Microbial Populations are Responsive to Hypoxia in the Chesapeake Bay
No full textThe number, size and severity of aquatic low oxygen dead-zones are increasing worldwide. Microbial processes in low oxygen environments have important ecosystem-level consequences, such as denitrification, greenhouse gas production and acidification. To identify key microbial processes occurring in low oxygen bottom waters of the Chesapeake Bay, we sequenced both 16S rRNA genes and shotgun metagenomic libraries to determine the identity, functional potential and spatiotemporal distribution of microbial populations in the water column. Unsupervised clustering algorithms grouped samples into three clusters using water chemistry or microbial communities, with extensive overlap of cluster composition between methods. Clusters were strongly differentiated by temperature, salinity, and oxygen. Sulfide-oxidizing microorganisms were found to be enriched in the low-oxygen bottom water and predictive of hypoxic conditions. Metagenome assembled genomes demonstrate that some of these sulfide-oxidizing populations are capable of partial denitrification, and transcriptionally active in a prior study. These results establish the importance of sulfide-oxidizing microorganisms in the microbial response to low oxygen in the Chesapeake Bay and suggest ties between the sulfur, nitrogen and oxygen cycles that could be important to capture when predicting the ecosystem response to remediation efforts or climate change
Data associated with the publication: Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry
No full textThis collection contains the raw native mass spectrometry (nMS) data for Energy-Resolved Mass Spectra (ERMS), collisional cross section (CCS) calculations, and surface-induced unfolding (SIU) plots. It also contains molecular dynamics (MD) trajectories of WT Hfq. From the abstract: RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfq’s integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry coupled with surface-induced dissociation and molecular dynamics simulations to disentangle the arrangement of the CTDs and their impact on the stability of Escherichia coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding
Data associated with the publication: Remote sensing-based vegetation and soil moisture constraints reduce irrigation estimation uncertainty
No full textThe datasets include processed monthly ALEXI evapotranspiration (ET) product, the Kullback-Leibler Divergence metrics for surface soil moisture, and monthly output of simulations performed with the Noah-Multiparameterization Land Surface Model v4.0.1 within NASA Land Information System. The simulations are conducted for the period of 2018 at 0.125° spatial resolution forced by the North America Land Data Assimilation System-Phase 2 (NLDAS-2) meteorological forcing fields. Data is provided in NETCDF format including monthly irrigation water amount, greenness vegetation fraction, and ET
Data associated with the publication: Evidence of pre-formed Lewis acid-base and Wheland-type complexes acting as dopants for p-type conjugated polymers
No full textFrom the publication abstract: Efficient doping of polymer semiconductors is essential for their development as conductors. Although Lewis acids such as B(C6F5)3have shown promise as dopants for polymers, their doping mechanism is not fully understood. We created 1:1 zwitterionic (including “Wheland-type”) complexes of B(C6F5)3 with conjugated molecules difluorobis(triethylsilylethynyl)anthradithiophene (diF-TES-ADT) and didodecylthienothiophene (DTT-12) and characterized them with 1H NMR, UV−vis spectroscopy, EPR spectroscopy, optical and scanning electron microscopy energy-dispersive X-ray spectroscopy (SEM-EDS), and X-ray diffraction. We employed these complexes as p-dopants for three conjugated polymers and established their doping abilities by conductivity measurements, Seebeck studies, field effect transistor (FET), and remote-gate sensing (RG-FET) measurements. Conductivity changes were dependent on the conjugated molecule adduct component, consistent with the adduct itself serving as the oxidant. The adduct complexes were capable of inducing changes in the surface potential of spun polymer films similar to the behavior shown by conventional dopants. Charge carrier density calculations by remote gate sensing revealed that these adducts can generate holes. We also studied the effect of adding the B(C6F5)3 first, followed by addition of the neat conjugated molecules; the observation of behavior that was different from that using preformed adducts was consistent with the adducts remaining intact during doping. When B(C6F5)3 was added to the polymers, followed by uncomplexed conjugated molecules, the generated hole carrier density is lower than that generated by the B(C6F5)3 dopant but often greater than that generated by the Wheland complexes, indicating a high probability of adduct formation in this case. Density functional theory calculations show that adduct formation between boranes and the conjugated molecules and segments of the polymers is energetically favorable and that some charge transfer between adducts and neutral polymers is plausible if Coulombic and entropic effects are taken into consideration. Thus, such adducts can be considered as possible doping sites for conjugated polymers
Data associated with the publication: A new polystyrene-polyvinyl pyridinium ionic copolymer dopant for n-type all-polymer thermoelectrics with high stable conductivity relative to Seebeck coefficient giving high power factor
No full textThe data consists of spectroscopic, morphological, electronic, and thermoelectric data for this manuscript, divided according to type of characterization
Data associated with publication: Evidence for the late arrival of hot Jupiters in systems with high host-star obliquities
No full textIn the associated publication, we homogeneously derive photospheric stellar parameters from photometry and then run stellar models in MESA to derive convective envelope masses. This data archive includes a machine-readable table containing the input and output data for the isochrone analysis as well as the surface convective envelope masses we derived using MESA models. The data archive also includes directories for each star containing the MESA configuration files for each star and the MESA output files for each star