Pitt Data Catalog A project by the Health Sciences Library System

• Horn, Charles C.
• Farr, Laura
• Sciullo, Michael

This data package contains 3D printing files (in multiple formats) and instructions for producing a testing chamber.

Peripheral nerves supply the inputs and outputs that determine how we sense and respond to both the internal and external environments; for example, the vagus detects the function of the interval organs and supplies motor output controlling the heart and gastrointestinal tract and other organs. This perfusion chamber model is designed to test evoked nerve responses using electrical stimulation of one nerve end and electrophysiological recording of the opposite nerve end (15 to 25 mm nerve length); responses can be recorded from teased fiber bundles or the whole nerve. The dissected nerve of laboratory animals, for example, musk shrew, mouse, and rat, can be placed in the middle perfusion compartment and kept alive with oxygenated Krebs solution flowing through the input port and exiting by way of the two outflow ports (2 are used to ensure that the compartment will not overflow). The lateral stimulation and recording compartments contain holes for placement of fine wire electrodes, which can be guided to the top of the model for connections to the stimulator and recording equipment (e.g., high impedance head stage and amplifier system). The lateral compartments are sealed from the middle perfusion compartment by running the nerve under thin plastic gates coated with vacuum grease; gates are lowered into grooves that are built into the model.

• Compound Action Potential
• Electrophysiology
• Equipment Design
• In Vitro Techniques
• Neurophysiology
• Peripheral Nervous System
• Printing, Three-Dimensional

• Rosenberg, David M.
• Horn, Charles C.

This Github repository contains raw data and code to explore open-source neurophysiology data analysis tools within an included Jupyter notebook. Software dependencies are listed within each data supplement folder, and can be downloaded with Docker via the associated Github repository described in the related data catalog record: Software: Docker image with JupyterLab, Python 3, Python 2, and R. The supplementary data were collected from electrophysiological recordings of the musk shrew vagus, a model system to investigate gut-brain communication.

• Electronic Lab Notebooks
• Electrophysiology
• Neurophysiology
• Software

• Horn, Charles C.

A Docker image with Jupyter Lab, Jupyter Notebook, Python 3, Python 2, R, and many R and Python packages for scientific computing. Docker is a container-based software system that allows easy download and installation of multiple software packages. The software included in this Docker image has wide relevance to various domains within scientific computing but are optimized for neurophysiological research, and can be used to explore the electrophysiological data included in Software: Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.

• Electronic Lab Notebooks
• Electrophysiology
• Neurophysiology
• Software

• Horn, Charles C.
• Sciullo, Michael
• Farr, Laura

This data package contains 3D printing files (in multiple formats) and instructions for producing a testing chamber.

The gastric vagus supplies critical information to the brain for the control of feeding and aversive signaling, such as nausea and vomiting. This perfusion chamber model (with a grid for testing mechanical stimuli) is designed to test mechanical or chemical stimuli applied to the stomach while recording electrophysiological responses from the vagus, from teased fiber bundles or the whole nerve. The dissected stomach, with attached vagus, of small laboratory animals, including musk shrew (a vomiting species) and mouse (a non-vomiting species), can be placed in the perfusion (stomach) compartment and kept alive with oxygenated Krebs solution flowing through the input port and exiting through the two outflow ports (2 are used to ensure that the compartment will not overflow). The included detachable grid allows the experimenter to record the placement of a mechanical probe in alphanumeric coordinates; Von Frey filaments (e.g., 10 mg force) can to used to apply mechanical stimulation. The recording compartment contains holes for placement of fine wire electrodes, which can be guided to the top of the model for connections to recording equipment (e.g., high impedance head stage and amplifier system). The two compartments are sealed by running the nerve connected to the stomach under a plastic gate, coated with vacuum grease; the gate is lowered into grooves that are part of the model. Based on this model, it is possible to produce a testing chamber for a larger species, such as the laboratory rat, by extending the size of the stomach compartment.

• Electrophysiology
• Equipment Design
• In Vitro Techniques
• Mechanoreceptors
• Neurophysiology
• Peripheral Nervous System
• Printing, Three-Dimensional

• Horn, Charles C.
• Rosenberg, David M.

This Github repository contains Python code to convert electrophysiology data files to Numpy arrays and save them to HDF5. The package contains example Spike2 data, a Jupyter notebook, and Python code to be executed within the notebook.

• Electrophysiology
• File conversion (Computer science)
• Software

• Spallek, Heiko
• Weinberg, Seth M.
• Manz, Michael C.
• Nanayakkara, Shanika
• 2 more author(s)...

Data were collected from 42 researchers in the International Association for Dental Research examining the respondents' attitudes towards data sharing, concerns related to data sharing, experiences sharing data through repositories and by request, data management practices, and use of new data analysis tools. The responses were unanimously positive towards the idea of data sharing, but included many expressions of concern about the appropriate use of data and the protection of research subjects. The results of this study may aid the development of improved data sharing processes for dental research, including the potential establishment of managed data clearinghouses.

• Data Curation
• Dental Research
• Dentistry
• Information Dissemination

• Iwema, Carrie L.
• Ratajeski, Melissa A.
• Bower, Margarete
• Mattern, Eleanor
• 1 more author(s)...

University of Pittsburgh librarians at the Health Sciences Library System and the University Library System conducted an 18-question Qualtrics survey in 2017 to learn what roles other academic and health sciences libraries are playing at their institutions in providing services and support to their users regarding electronic lab notebooks (ELNs). The PDF contains the survey questions, which are a mix of multiple choice and free text. The CSV file contains de-identifed survey responses (indicated as #####).

• Academic libraries
• Electronic Lab Notebooks
• Laboratory notebooks
• Medical libraries
• Research Data Management
• Research Notebooks
• Research Support Services

• Katnani, Husam
• Gandhi, Neeraj

We measured eye movements evoked by electrical stimulation delivered simultaneously to two sites in the superior colliculus of nonhuman primates. The effects of current frequency and intensity on movement trajectories are available. The data are potentially useful for understanding algorithms for decoding movement commands from population activity in the superior colliculus.

• Electric Stimulation
• Macaca mulatta
• Microstimulation
• Superior Colliculi
• Vector averaging
• Vector summation

• Modo, Michel
• Crum, William R.
• Gerwig, Madeline
• Vernon, Anthony C.
• 5 more author(s)...

Parkinson’s disease (PD) is the second most common neurodegenerative disorder producing a variety of motor and cognitive deficits with the causes remaining largely unknown. The gradual loss of the nigrostriatal pathway is currently considered the pivotal pathological event. To better understand the progression of PD and improve treatment management, defining the disease on a structural basis and expanding brain analysis to extra-nigral structures is indispensable. The anatomical complexity and the presence of neuromelanin, make the use of non-human primates an essential element in developing putative imaging biomarkers of PD. To this end, ex vivo T2-weighted magnetic resonance images were acquired from control and 1-methyl-4 phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated marmosets. Volume measurements of the caudate, putamen, and substantia nigra indicated significant atrophy and cortical thinning. Tensor-based morphometry provided a more extensive and hypothesis free assessment of widespread changes caused by the toxin insult to the brain, especially highlighting regional cortical atrophy. The results highlight the importance of developing imaging biomarkers of PD in non-human primate models considering their distinct neuroanatomy. It is essential to further develop these biomarkers in vivo to provide non-invasive tools to detect pre-symptomatic PD and to monitor potential disease altering therapeutics.

• 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine
• Callithrix
• Magnetic Resonance Imaging
• Parkinson Disease

• Cohen, Sheldon
• Janicki-Deverts, Denise
• Turner, Ronald B.
• Doyle, William J.

Perceived social support has been hypothesized to protect against the pathogenic effects of stress. How such protection might be conferred, however, is not well understood. Using a sample of 404 healthy adults, we examined the roles of perceived social support and received hugs in buffering against interpersonal stress-induced susceptibility to infectious disease. Perceived support was assessed by questionnaire, and daily interpersonal conflict and receipt of hugs were assessed by telephone interviews on 14 consecutive evenings. Subsequently, participants were exposed to a virus that causes a common cold and were monitored in quarantine to assess infection and illness signs. Perceived support protected against the rise in infection risk associated with increasing frequency of conflict. A similar stress-buffering effect emerged for hugging, which explained 32% of the attenuating effect of support. Among infected participants, greater perceived support and more-frequent hugs each predicted less-severe illness signs. These data suggest that hugging may effectively convey social support.

• Disease Susceptibility
• Interpersonal Relations
• Psychology
• Respiratory Tract Infections
• Social Support
• Stress, Psychological
• Touch
• Virology