Digital Publishing at Robert E. Kennedy Library: Project Blueprint

In August 2019, Kennedy Library launched our Digital Publishing Pilot— working with our donor funded Digital Publishing Research Fellow, jaime ding to raise the visibility and enhance access to Cal Poly scholarship by transposing the immersive onsite exhibits generated by faculty and students into a digital representation. As we embark on the second year of Kennedy Library’s Digital Publishing Pilot, we are already looking toward the future and are sharing our process through this project blueprint. The Digital Publishing program through “Poly Publishing” aims to enhance access to Cal Poly scholarship through a digitally immersive, interactive system that focuses on collaboration, accessible approaches, and recognition of individuals’ places within structural systems. This structural solution brings inclusive practices, equity, and justice to the forefront of scholarly publishing at Cal Poly — centering historically underrepresented identities, perspectives, and creativity

Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging.

Identifying genetic factors that modify an individual\u27s susceptibility to cognitive decline in aging is critical to understanding biological processes involved and mitigating risk associated with a number of age-related disorders. Recently, heterochromatin protein 1 binding protein 3 (Hp1bp3) was identified as a mediator of cognitive aging. Here, we provide a mechanistic explanation for these findings and show that targeted knockdown of Hp1bp3 in the hippocampus by 50%-75% is sufficient to induce cognitive deficits and transcriptional changes reminiscent of those observed in aging and Alzheimer\u27s disease brains. Specifically, neuroinflammatory-related pathways become activated following Hp1bp3 knockdown in combination with a robust decrease in genes involved in synaptic activity and neuronal function. To test the hypothesis that Hp1bp3 mediates susceptibility to cognitive deficits via a role in neuronal excitability, we performed slice electrophysiology demonstrate transcriptional changes after Hp1bp3 knockdown manifest functionally as a reduction in hippocampal neuronal intrinsic excitability and synaptic plasticity. In addition, as Hp1bp3 is a known mediator of miRNA biogenesis, here we profile the miRNA transcriptome and identify mir-223 as a putative regulator of a portion of observed mRNA changes, particularly those that are inflammatory-related. In summary, work here identifies Hp1bp3 as a critical mediator of aging-related changes at the phenotypic, cellular, and molecular level and will help inform the development of therapeutics designed to target either Hp1bp3 or its downstream effectors in order to promote cognitive longevity

The Caltech Tomography Database and Automatic Processing Pipeline

Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user’s “Inbox” and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups

Synergistic effect of phosphodiesterase 4 inhibitor and serum on migration of endotoxin-stimulated macrophages.

Macrophage migration is an essential step in host defense against infection and wound healing. Elevation of cAMP by inhibiting phosphodiesterase 4 (PDE4), enzymes that specifically degrade cAMP, is known to suppress various inflammatory responses in activated macrophages, but the role of PDE4 in macrophage migration is poorly understood. Here we show that the migration of Raw 264.7 macrophages stimulated with LPS was markedly and dose-dependently induced by the PDE4 inhibitor rolipram as assessed by scratch wound healing assay. Additionally, this response required the involvement of serum in the culture medium as serum starvation abrogated the effect. Further analysis revealed that rolipram and serum exhibited synergistic effect on the migration, and the influence of serum was independent of PDE4 mRNA expression in LPS-stimulated macrophages. Moreover, the enhanced migration by rolipram was mediated by activating cAMP/exchange proteins directly activated by cAMP (Epac) signaling, presumably via interaction with LPS/TLR4 signaling with the participation of unknown serum components. These results suggest that PDE4 inhibitors, together with serum components, may serve as positive regulators of macrophage recruitment for more efficient pathogen clearance and wound repair

The Implication of Substance P in the Development of Tendinopathy: A Case Control Study.

It was reported that substance P had beneficial effects in the healing of acute tendon injury. However, the relationship between substance P and degenerative tendinopathy development remains unclear. The purpose of this study was to determine the role of substance P in the pathogenesis of tendinopathy. Healthy and tendinopathy tendon were harvested from human and tenocytes were cultured individually. The expression levels of genes associated with tendinopathy were compared. Next, substance P was exogenously administered to the healthy tenocyte and the effect was evaluated. The results showed that tendinopathy tenocytes had higher levels of COL3A1, MMP1, COX2, SCX, ACTA2, and substance P gene expression compared to healthy tenocytes. Next, substance P treatment on the healthy tenocyte displayed similar changes to that of the tendinopathy tenocytes. These differences between the two groups were also determined by Western blot. Additionally, cells with substance P had the tendinopathy change morphologically although cellular proliferation was significantly higher compared to that of the control group. In conclusion, substance P enhanced cellular proliferation, but concomitantly increased immature collagen (type 3 collagen). Substance P plays a crucial role in tendinopathy development and could be a future therapeutic target for treatment

Preliminary Results of BTDF Calibration of Transmissive Solar Diffusers for Remote Sensing

Satellite instruments operating in the reflected solar wavelength region require accurate and precise determination of the optical properties of their diffusers used in pre-flight and post-flight calibrations. The majority of recent and current space instruments use reflective diffusers. As a result, numerous Bidirectional Reflectance Distribution Function (BRDF) calibration comparisons have been conducted between the National Institute of Standards and Technology (NIST) and other industry and university-based metrology laboratories. However, based on literature searches and communications with NIST and other laboratories, no Bidirectional Transmittance Distribution Function (BTDF) measurement comparisons have been conducted between National Measurement Laboratories (NMLs) and other metrology laboratories. On the other hand, there is a growing interest in the use of transmissive diffusers in the calibration of satellite, air-borne, and ground-based remote sensing instruments. Current remote sensing instruments employing transmissive diffusers include the Ozone Mapping and Profiler Suite instrument (OMPS) Limb instrument on the Suomi-National Polar-orbiting Partnership (S-NPP) platform,, the Geostationary Ocean Color Imager (GOCI) on the Korea Aerospace Research Institute's (KARI) Communication, Ocean, and Meteorological Satellite (COMS), the Ozone Monitoring Instrument (OMI) on NASA's Earth Observing System (EOS) Aura platform, the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument and the Geostationary Environmental Monitoring Spectrometer (GEMS).. This ensemble of instruments requires validated BTDF measurements of their on-board transmissive diffusers from the ultraviolet through the near infrared. This paper presents the preliminary results of a BTDF comparison between the NASA Diffuser Calibration Laboratory (DCL) and NIST on quartz and thin Spectralon samples

Spectralon BRDF and DHR Measurements in Support of Satellite Instruments Operating Through Shortwave Infrared

Satellite instruments operating in the reflective solar wavelength region require accurate and precise determination of the Bidirectional Reflectance Distribution Functions (BRDFs) of the laboratory and flight diffusers used in their pre-flight and on-orbit calibrations. This paper advances that initial work and presents a comparison of spectral Bidirectional Reflectance Distribution Function (BRDF) and Directional Hemispherical Reflectance (DHR) of Spectralon*, a common material for laboratory and onorbit flight diffusers. A new measurement setup for BRDF measurements from 900 nm to 2500 nm located at NASA Goddard Space Flight Center (GSFC) is described. The GSFC setup employs an extended indium gallium arsenide detector, bandpass filters, and a supercontinuum light source. Comparisons of the GSFC BRDF measurements in the ShortWave InfraRed (SWIR) with those made by the NIST Spectral Trifunction Automated Reference Reflectometer (STARR) are presented. The Spectralon sample used in this study was 2 inch diameter, 99% white pressed and sintered Polytetrafluoroethylene (PTFE) target. The NASA/NIST BRDF comparison measurements were made at an incident angle of 0 deg and viewing angle of 45 deg. Additional BRDF data not compared to NIST were measured at additional incident and viewing angle geometries and are not presented here The total combined uncertainty for the measurement of BRDF in the SWIR range made by the GSFC scatterometer is less than 1% (k=1). This study is in support of the calibration of the Joint Polar Satellite System (JPSS) Radiation Budget Instrument (RBI) and Visible Infrared Imaging Radiometer Suite (VIIRS) of and other current and future NASA remote sensing missions operating across the reflected solar wavelength region

ETDB-Caltech: a blockchain-based distributed public database for electron tomography

Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets

Calm Your Thoughts With Tater Tots: a tater tot casserole recipe coloring book

Calm Your Thoughts with Tater Tots: a tater tot casserole recipe coloring book was crafted by student assistants and staff from Robert E. Kennedy’s Creative Works department during spring quarter 2020. The coloring book was created as a grounding project for creativity, encouragement, and relaxation, following adrienne maree brown’s #pleasureactivism, and offers an example of how to use virtual resources offered by the library