Publications

Practices of openness have grown popular across diverse domains (e.g. open science, open source software, open education) as they can spur innovation and liberalize society. But to date, we know little about how groups and leaders achieve such goals through openness, largely because knowledge remains siloed within fields. Thus, needs exist for interdisciplinary terminology and guidance on “doing openness.” In this Perspective, we address these needs first by defining an interdisciplinary concept – open organizing – that describes how people collectively pursue goals along dimensions of transparency, inclusion, and distribution of decision rights. Next, we distill four lessons for managing open ecosystems: balanced organization design, transparent power allocation, flexible information tools, and intentional social norm development. We do this by integrating expertise from academia and industry across multiple domains (including open scholarship, open education, open strategy, open source software, open design, and open innovation). Finally, we call for more research on openness – both within and across domains – to support those who seek to address great challenges of our time through openness.

A project generated for the UKRN /COS Train-the-Trainer programme on Openness and Reproducibility Research Practices. Slides and instructor notes for each week are shared in each week’s component for participants to review and adapt.

Self-guided training through a series of presentations on the fundamentals of preregistration and registered reports

Data access point for the Global Flourishing Study, a longitudinal five-year annual study of 200,000 participants from 20+ geographically and culturally diverse countries and territories across a broad range of well-being outcomes

As research becomes more interdisciplinary, fast-paced, data-intensive, and collaborative, there is an increasing need to share data and other research products in accordance with Open Science principles. In response to this need, we created an Open Science & Data Collaborations (OSDC) program at the Carnegie Mellon University Libraries that provides Open Science tools, training, collaboration opportunities, and community-building events to support Open Research and Open Science adoption. This program presents a unique end-to-end model for Open Science programs because it extends open science support beyond open repositories and open access publishing to the entire research lifecycle. We developed a logic model and a preliminary assessment metrics framework to evaluate the impact of the program activities based on existing data collected through event and workshop registrations and platform usage. The combination of these evaluation instruments has provided initial insight into our service productivity and impact. It will further help to answer more in-depth questions regarding the program impact, launch targeted surveys, and identify priority service areas and interesting Open Science projects.

Dataset used to develop assessment metrics to evaluate the success of the Open Science & Data Collaborations Program at Carnegie Mellon University and to inform future decision making. User data were collected from a variety of open science tools, events and workshops offered by the program and were aggregated and de-identified before use.\textlessbr\textgreaterRelated paper:Related protocol: http://dx.doi.org/10.17504/protocols.io.b29gqh3w

Ithaka S+R’s Research Support Services program explores current trends and support needs in academic research. Our most recent project in this program, “Supporting Big Data Research,” focused specifically on the rapidly emerging use of big data in research across disciplines and fields. As part of our study, we partnered with librarians from more than 20 colleges and universities, who then conducted over 200 interviews with faculty. These interviews provided insights into the research methodologies and support needs of researchers working across a wide range of disciplines. This report provides a detailed account of how big data research is pursued in academic contexts, focusing on identifying typical methodologies, workflows, outputs, and challenges big data researchers face. Full details and actionable recommendations for stakeholders are offered in the body of the report, which offers guidance to universities, funders, and others interested in improving institutional capacities and fostering intellectual climates to better support big data research.

Lipid droplets (LDs) store lipids for energy and are central to cellular lipid homeostasis. The mechanisms coordinating lipid storage in LDs with cellular metabolism are unclear but relevant to obesity-related diseases. Here we utilized genome-wide screening to identify genes that modulate lipid storage in macrophages, a cell type involved in metabolic diseases. Among ∼550 identified screen hits is MLX, a basic helix-loop-helix leucine-zipper transcription factor that regulates metabolic processes. We show that MLX and glucose-sensing family members MLXIP/MondoA and MLXIPL/ChREBP bind LDs via C-terminal amphipathic helices. When LDs accumulate in cells, these transcription factors bind to LDs, reducing their availability for transcriptional activity and attenuating the response to glucose. Conversely, the absence of LDs results in hyperactivation of MLX target genes. Our findings uncover a paradigm for a lipid storage response in which binding of MLX transcription factors to LD surfaces adjusts the expression of metabolic genes to lipid storage levels.

A report summarizing main themes and takeaways from two joint Symposia: Artificial Intelligence for Data Discovery and Reuse (AIDR) and Open Science Symposium (OSS), hosted by the Open Science & Data Collaborations program at Carnegie Mellon University Libraries in 2020.

Chat reference service has been used in academic libraries to more efficiently serve patrons in the digital age. Identifying question topics on chat can help librarians understand patrons’ needs and improve reference services. Researchers have used qualitative methods to understand question types in chat records; however, these methods are inefficient to analyze large chat datasets. Here, we conducted a novel research using Latent Dirichlet Allocation (LDA) topic modeling to automatically extract topics from chat transcripts generated in 5 years from a large university library. With little human intervention, the model identified major topics based on statistical distributions of terms- document relationships in chat transcripts. We also applied VOSviewer to analyze the same dataset and found consistent results. From these results, we found that the most prominent chat topics were about accessing various library resources. This finding can help libraries allocate resources, design educational materials, and provide trainings for future librarians.

The ACRL Framework for Information Literacy presents opportunities for moving beyond ‘one- shot’ information literacy sessions and creating a more scaffolded and embedded approach for instruction. We collaborated with faculty at Carnegie Mellon University to create Framework- inspired information literacy learning objectives for first-year and third-year science undergraduates and are continuously refining the objectives as the curriculum evolves. This article describes our learning objective design and refinement process, challenges encountered, and ideas on how to create opportunities for embedding information literacy into a curriculum. We also share our full activity lesson plans and assessment tool.

There is great value embedded in reusing scientific data for secondary discoveries. However, it is challenging to find and reuse the large amount of existing scientific data distributed across the web and data repositories. Some of the challenges reside in the volume and complexity of scientific data, others pertain to the current practices and workflow of research data management. AIDR 2019 (Artificial Intelligence for Data Discovery and Reuse) is a new conference that brings together researchers across a broad range of disciplines, computer scientists, tool developers, data providers, and data curators, to share innovative solutions that apply artificial intelligence to scientific data discovery and reuse, and discuss how various stakeholders work together to create a health data ecosystem. This editorial summarizes the main themes and takeaways from the inaugural AIDR conference.

Deleterious mutations in the serine lipase DDHD2 are a causative basis of complex hereditary spastic paraplegia (HSP, subtype SPG54) in humans. We recently found that DDHD2 is a principal triglyceride hydrolase in the central nervous system (CNS) and that genetic deletion of this enzyme in mice leads to ectopic lipid droplet (LD) accumulation in neurons throughout the brain. Nonetheless, how HSP-related mutations in DDHD2 relate to triglyceride metabolism and LD formation remains poorly understood. Here, we have characterized a set of HSP-related mutations in DDHD2 and found that they disrupt triglyceride hydrolase activity in vitro and impair the capacity of DDHD2 to protect cells from LD accumulation following exposure to free fatty acid, an outcome that was also observed with a DDHD2-selective inhibitor. We furthermore isolated and characterized LDs from brain tissue of DDHD2–/– mice, revealing that they contain both established LD-associated proteins identified previously in other organs and CNS-enric...

How proteins control the biogenesis of cellular lipid droplets (LDs) is poorly understood. Using Drosophila and human cells, we show here that seipin, an ER protein implicated in LD biology, mediates a discrete step in LD formation-the conversion of small, nascent LDs to larger, mature LDs. Seipin forms discrete and dynamic foci in the ER that interact with nascent LDs to enable their growth. In the absence of seipin, numerous small, nascent LDs accumulate near the ER and most often fail to grow. Those that do grow prematurely acquire lipid synthesis enzymes and undergo expansion, eventually leading to the giant LDs characteristic of seipin deficiency. Our studies identify a discrete step of LD formation, namely the conversion of nascent LDs to mature LDs, and define a molecular role for seipin in this process, most likely by acting at ER-LD contact sites to enable lipid transfer to nascent LDs.

Lipid droplets (LDs) store metabolic energy and membrane lipid precursors. With excess metabolic energy, cells synthesize triacylglycerol (TG) and form LDs that grow dramatically. It is unclear how TG synthesis relates to LD formation and growth. Here, we identify two LD subpopulations: smaller LDs of relatively constant size, and LDs that grow larger. The latter population contains isoenzymes for each step of TG synthesis. Glycerol-3-phosphate acyltransferase 4 (GPAT4), which catalyzes the first and rate-limiting step, relocalizes from the endoplasmic reticulum (ER) to a subset of forming LDs, where it becomes stably associated. ER-to-LD targeting of GPAT4 and other LD-localized TG synthesis isozymes is required for LD growth. Key features of GPAT4 ER-to-LD targeting and function in LD growth are conserved between Drosophila and mammalian cells. Our results explain how TG synthesis is coupled with LD growth and identify two distinct LD subpopulations based on their capacity for localized TG synthesis. ?? 2013 Elsevier Inc.

The liver plays an important role in triacylglycerol (TG) metabolism. It can store large amounts of TG in cytosolic lipid droplets (CLDs), or it can package TG into very-low density lipoproteins (VLDL) that are secreted from the cell. TG packaged into VLDL is derived from TG stored within the endoplasmic reticulum in lumenal lipid droplets (LLDs). Therefore, the liver contains at least three kinds of LDs that differ in their protein composition, subcellular localization, and function. Hepatic LDs undergo tremendous changes in their size and protein composition depending on the energetic (fasting/feeding) and pathological (viral infection, nonalcoholic fatty liver disease, etc.) states. It is crucial to develop methodologies that allow the isolation and analyses of the various hepatic LDs in order to gain insight into the differential metabolism of these important lipid storage/transport particles in health and disease. Here, we present detailed protocols for the isolation and analysis of CLDs and LLDs and for monitoring CLD dynamics. ?? 2013 Elsevier Inc.

UNLABELLED Induction of endoplasmic reticulum (ER) stress was previously shown to impair hepatic apolipoprotein B100 (apoB) production by enhancing cotranslational and posttranslational degradation of newly synthesized apoB. Here, we report the involvement of autophagy in ER stress-induced degradation of apoB and provide evidence for a significant role of autophagy in regulating apoB biogenesis in primary hepatocyte systems. Induction of ER stress following short-term glucosamine treatment of McA-RH7777 cells resulted in significantly increased colocalization of apoB with green fluorescent protein-microtubule-associated protein 1 light chain 3 (GFP-LC3), referred to as apoB-GFP-LC3 puncta, in a dose-dependent manner. Colocalization with this autophagic marker correlated positively with the reduction in newly synthesized apoB100. Treatment of McA-RH7777 cells with 4-phenyl butyric acid, a chemical ER stress inhibitor, prevented glucosamine- and tunicamycin-induced increases in GRP78 and phosphorylated eIF2α, rescued newly synthesized [(35) S]-labeled apoB100, and substantially blocked the colocalization of apoB with GFP-LC3. Autophagic apoB degradation was also observed in primary rat and hamster hepatocytes at basal conditions as well as upon the induction of ER stress. In contrast, this pathway was inactive in HepG2 cells under ER stress conditions, unless proteasomal degradation was blocked with N-acetyl-leucinyl-leucinyl-norleucinal and the medium was supplemented with oleate. Transient transfection of McA-RH7777 cells with a wild-type protein kinase R-like ER kinase (PERK) complementary DNA resulted in dramatic induction of apoB autophagy. In contrast, transfection with a kinase inactive mutant PERK gave rise to reduced apoB autophagy, suggesting that apoB autophagy may occur via a PERK signaling-dependent mechanism. CONCLUSION Taken together, these data suggest that induction of ER stress leads to markedly enhanced apoB autophagy in a PERK-dependent pathway, which can be blocked with the chemical chaperone 4-phenyl butyric acid. ApoB autophagy rather than proteasomal degradation may be a more pertinent physiological mechanism regulating hepatic lipoprotein production in primary hepatocytes.

Lipin-1 proteins are phosphatidic acid phosphatases (PAPs) catalyzing the conversion from phosphatidic acid (PA) to diacylglycerol (DG). Two alternative splicing isoforms, lipin-1?? and -1??, are localized at different subcellular compartments. A third splicing isoform, lipin-1?? was recently cloned and its subcellular localization is unknown. Here, we demonstrate that lipin-1?? is localized to lipid droplets (LDs), an association mediated by a hydrophobic, lipin-1??-specific domain. Additional expression of lipin-1?? altered LD morphology without affecting the triacylglycerol (TG) level. In human tissues, lipin-1?? is the main lipin-1 isoform expressed in normal human brain, suggesting a specialized role in regulating brain lipid metabolism. ?? 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Lipid droplets (LDs) form from the endoplasmic reticulum (ER) and grow in size by obtaining triacylglycerols (TG). Triacylglycerol hydrolase (TGH), a lipase residing in the ER, is involved in the mobilization of TG stored in LDs for the secretion of very-low-density lipoproteins. In this study, we investigated TGH-mediated changes in cytosolic LD dynamics. We have found that TGH deficiency resulted in decreased size and increased number of LDs in hepatocytes. Using fluorescent fatty acid analogues to trace LD formation, we observed that TGH deficiency did not affect the formation of nascent LDs on the ER. However, the rate of lipid transfer into preformed LDs was significantly slower in the absence of TGH. Absence of TGH expression resulted in increased levels of membrane diacylglycerol and augmented phospholipid synthesis, which may be responsible for the delayed lipid transfer. Therefore, altered maturation (growth) rather than nascent formation (de novo synthesis) may be responsible for the observed morphological changes of LDs in TGH-deficient hepatocytes.

Excessive accumulation of triacylglycerol in peripheral tissues is tightly associated with obesity and has been identified as an independent risk factor for insulin resistance, type 2 diabetes, and cardiovascular complications. Here we show that ablation of carboxylesterase 3 (Ces3)/triacylglycerol hydrolase (TGH) expression in mice (Tgh-/-) results in decreased plasma triacylglycerol, apolipoprotein B, and fatty acid levels in both fasted and fed states. Despite the attenuation of very low-density lipoprotein secretion, TGH deficiency does not increase hepatic triacylglycerol levels. Tgh-/- mice exhibit increased food intake, respiratory quotient, and energy expenditure without change in body weight. These metabolic changes are accompanied by improved insulin sensitivity and glucose tolerance. Tgh-/- mice have smaller sized pancreatic islets but maintain normal glucose-stimulated insulin secretion. These studies demonstrate the potential of TGH as a therapeutic target for lowering blood lipid levels. ?? 2010 Elsevier Inc. All rights reserved.

The assembly of very low density lipoproteins involves the formation of a primordial, poorly lipidated apoB-containing particle in the endoplasmic reticulum, followed by the addition of neutral lipid from luminal lipid droplets (LLD). However, the lipid and protein compositions of LLD have not been determined. We have isolated LLD from mouse liver microsomes and analyzed their lipid and protein compositions. LLD are variably sized particles relatively poor in triacylglycerol (TG) content when compared with the lipid composition of cytosolic lipid droplets (CLD). They are devoid of apoB, adipophilin, and albumin but contain numerous proteins different from those found on CLD, including TG hydrolase (TGH), carboxylesterase 1 (Ces1), microsomal triglyceride transfer protein (MTP), and apoE. Ectopic expression of TGH in McArdle RH7777 hepatoma cells resulted in decreased cellular TG levels, demonstrating a role for TGH in the mobilization of hepatic neutral lipid stores. The isolation and characterization of LLD provide new supporting evidence for the two-step assembly of very low density lipoproteins.