cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7924/r4cj8j090
title: Oscillating pulse SABRE

description: SABRE (Signal Amplification by Reversible Exchange) methods provide a simple, fast, and cost-effective method to hyperpolarize a wide variety of molecules in solution, and have been demonstrated with protons and, more recently, with heteronuclei (X-SABRE). The conventional analysis of the SABRE effect is based on level anti-crossings (LACs), which requires very low magnetic fields (~ 0.6µT) to achieve resonance and transfer spin order from the para-hydrogen to target heteronuclei. We have demonstrated in our recent study that the validity of LACs used in SABRE is very limited, so the maximum SABRE polarization predicted with LACs is not correct. Here, we present several oscillating pulse sequences that use magnetic fields far away from the resonance condition and can commonly triple the polarization. An analysis with average Hamiltonian theory indicates that the oscillating pulse, in effect, adjusts the J-couplings between hydrides and target nuclei and that a much weaker coupling produces maximum polarization. This theoretical treatment, combined with simulations and experiment, show substantial magnetization improvements relative to traditional X-SABRE methods. It also shows that, in contrast to most pulse sequence applications, waveforms with reduced time symmetry in the toggling frame make magnetization generation more robust to experimental imperfections.
DOI: 10.7924/r4nv9kp8v
title: Data from: Gigapixel behavioral and neural activity imaging with a novel multi-camera array microscope

description: The dynamics of living organisms are organized across many spatial scales, yet existing, cost-effective imaging systems can measure only a subset of these scales at once. Here, we have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from cellular structures to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies near cellular resolution and 5 um sensitivity over hundreds of square centimeters. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. The MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Further, we demonstrate the ability to acquire dual color fluorescence video of multiple freely moving zebrafish, recording neural activity via ratiometric calcium imaging. Overall, the MCAM provides a powerful platform for investigating cellular and behavioral processes across a wide range of spatial scales, but without the bottlenecks imposed by single-camera image acquisition systems.
DOI: 10.7924/r44b36p48
title: Data from: Sex-specific dna methylation and associations with in utero tobacco smoke exposure at nuclear-encoded mitochondrial genes

description: Sex-linked differences in mitochondrial ATP production, enzyme activities, and reactive oxygen species generation have been reported in multiple tissue and cell types. While the effects of reproductive hormones underlie many of these differences, regulation of sexually dimorphic mitochondrial function has not been fully characterized. We hypothesized that sex-specific DNA methylation contributes to sex-specific expression of genes that influence mitochondrial function. Herein, we analysed DNA methylation data specifically focused on nuclear-encoded mitochondrial genes in 191 males and 190 females. We found 596 differentially methylated sites (DMSs) (FDR p < 0.05), corresponding to 324 genes, with at least a 1% difference in methylation between sexes. To investigate the potential functional significance, we utilized gene expression microarray data. Of the 324 genes containing DMSs, 17 showed differences in gene expression by sex. Particularly striking was that ATP5G2, encoding subunit C of ATP synthase, contains seven DMSs and exhibits a sex difference in expression (p = 0.04). Finally, we also found that alterations in DNA methylation associated with in utero tobacco smoke exposure were sex-specific in these nuclear-encoded mitochondrial genes. Interestingly, the level of sex differences in DNA methylation at nuclear-encoded mitochondrial genes and the level of methylation changes associated with 25 smoke exposure were less prominent than that of other genes. This suggests more conservative regulation on DNA methylation at these genes compared to others. Overall, our findings suggest
that sex-specific DNA methylation may help establish sex differences in expression and function and that sex-specific alterations in DNA methylation in response to exposures could contribute to sex-variable toxicological responses.
DOI: 10.7924/r4wm1df10
title: Data from: Students' knowledge, attitudes and awareness before and after a community-centered design STEM learning intervention

description: Background: Through the human-centered design process (HCD), students can contextualize engineering concepts with a personal lens and engage in problem-solving (Goldman and Kabayadondo 2016). The Ignite program, created by the Center for Global Women’s Health Technologies (GWHT) at Duke University, integrates the HCD process with STEM knowledge to engage secondary school students in advancing social justice by engineering for pressing global issues outlined by the United Nations as Sustainable Development Goals (SDGs).  

Purpose: This work evaluates the efficacy of the Ignite Water curriculum as an intervention for STEM opportunity gaps, SDG #4, and clean water, SDG #6, as a scalable and sustainable method for social change.   

Methods:  Knowledge Attitude and Practices (K.A.P.) methodology was used to capture changes in three indicators of behavior change: (1) learners’ relevant content knowledge, (2) their awareness of the local water contamination issue, and (3) their attitudes towards STEM as a tool for local civic action. The mixed methods research tabulated survey data, interviews and student artifacts to determine best practices for STEM outreach programs.  Of the 697 participants, 523 learners across 7 schools served as a sample population for this study. 

Results: The innovative Ignite program engaged a diverse population in engineering solutions for the water pollution in Lake Atitlán, Guatemala. The intervention increased learners’ knowledge and awareness related to the local water contamination; especially, the causes of contamination and the engineering treatment options. Female learners demonstrated an increase in self-efficacy in engineering careers. While, male learners’ self-efficacy for math and community problem solving increased. Overall, learners' knowledge and awareness of water pollution and their attitudes towards STEM improved. Trainers echoed this in semi-structured interviews.
DOI: 10.7924/r4833xs44
title: Data from: Drones reveal spatial patterning of sympatric Alaskan pinniped species and drivers of their local distributions

description: This dataset features raw drone imagery, photogrammetric surface models and orthomosaic products, derived terrain rasters, and pinniped locations from a survey of Otter Island, AK, conducted on September 3, 2018. The study that uses these data leverages emerging remote sensing techniques to reveal fine-scale drivers of distribution and terrestrial habitat use of two sympatric sentinel species of the central Bering Sea, the Pacific harbor seal (Phoca vitulina richardsi) and the northern fur seal (Callorhinus ursinus), at non-breeding haul-outs in the Pribilof Islands. We surveyed these species using unoccupied aircraft systems with thermal and visible-light photography, and we applied distributional modeling techniques to quantify the relative influence of habitat characteristics and social dynamics on the local distributions of these species.
DOI: 10.7924/r41v5n80b
title: Data from: Top-down and bottom-up control of Spartina alterniflora characteristics beyond standing biomass

description: While the effects of top-down and bottom-up forces on aboveground plant growth have been extensively examined, less is known about the relative impacts of these factors on other aspects of plant life history, including belowground characteristics, litter production, and reproduction. In a season-long, fully factorial field experiment in a salt marsh in Virginia, USA, we manipulated grazing intensity (a top-down force) and nutrient availability (a bottom-up force) and measured the response in a suite of traits of smooth cordgrass (Spartina alterniflora), the dominant foundation species in the ecosystem. Three categories of traits and characteristics were measured: belowground characteristics, litter production, and reproduction, encompassing ten total responses. Of the ten response variables measured, nine were affected by treatments. Six response variables showed independent effects of grazing and fertilization, while three showed interactive effects. In general, fertilization led to increased cordgrass reproduction and belowground biomass, the latter of which conflicts with previous findings. Higher grazing intensity had negative impacts on both reproduction and belowground biomass. Our results indicate a complicated, yet predictable set of interactions between grazing and nutrient availability that influence relatively understudied traits of wetland plant structure. As many of these traits have been linked to key ecosystem functions, such as carbon burial, nutrient cycling, and ecosystem expansion, synthesizing the ecological knowledge and theory of top-down and bottom-up forces with trait-based methodologies may provide a promising path forward in predicting variability in ecosystem function.
DOI: 10.7924/r4dn48h0w
title: Data from: Quantifying art historical narratives

description: My project surveys the development of Jansons History of Art across its eight editions as well as Gardners Art Through the Ages through its sixteen editions, looking particularly at the change in artist demographic through time. Additionally, this paper investigates which external variables such as artist gender, ethnicity, race, nationality, number of exhibitions at the Museum of Modern Art and The Whitney, and if any, predict the magnitude of an artists inclusion in art history survey texts. I conduct data analysis to assess the demographic representation of artists through editions of Jansons History of Art and Gardners Art Through the Ages, a proxy for the art history survey. I compare artist demographics through editions of Janson and Gardner. My findings indicate that coverage of minority artists (defined as non-white and/or Hispanic or Latinx and/or female) increases across editions of Jansons History of Art and Gardners Art Through the Ages, but remains negligible compared to white male non-Hispanic or Latinx artists.
DOI: 10.7924/r4sb46t2c
title: Data from: UAS-based monitoring of coastal wetlands: Considerations and tradeoffs

description: This study addresses variability introduced by common UAS study techniques and forms recommendations for optimal survey designs in vegetated coastal habitats. Applying these parameters, we assess alignment of computed estimations with manually collected measurements by comparing UAS-SfM mapping products to ground-based data. This study demonstrates that, with careful consideration in study design and analysis, there exists great potential for UAS to provide accurate, large-scale estimates of common vegetative characteristics in coastal salt marshes.
DOI: 10.7924/r4223221q
title: Data from: Estimation of intertidal oyster reef density using spectral and structural characteristics derived from unoccupied aircraft systems and structure from motion photogrammetry

description: Eastern oysters (Crassostrea virginica) are an important component of the ecology and economy in coastal zones. Through the long-term consolidation of densely clustered shells, oyster reefs generate three-dimensional and complex structures that yield a suite of ecosystem services such as nursery habitat, stabilizing shorelines, regulating nutrients, and increasing biological diversity. The decline of global oyster habitat has been well documented and can be attributed to factors such as overharvesting, pollution, and disease. Monitoring oyster reefs is necessary to evaluate persistence and track changes in habitat condition, but can be time and labor intensive. In this present study, spectral and structural metrics of intertidal oyster reefs derived from Unoccupied Aircraft Systems (UAS) and Structure from Motion (SfM) outputs demonstrate how intertidal oyster density can be accurately estimated. This workflow provides a remote, rapid, nondestructive, and potentially standardizable method to assess large-scale intertidal oyster reef density that will significantly improve management strategies to protect this important coastal resource from habitat degradation.
DOI: 10.7924/r4ns0wt0d
title: Data from: A Community of Interests: A Social History of the British in Buenos Aires, 1860-1914

description: Data on approximately 15,000 British residents of Buenos Aires were collected from the first (1869) and second (1895) national censuses of Argentina.  They include names, sex, marital status, nationality of individual, spouse and children, occupation, address, and type of living situation.
DOI: 10.7924/r4x92bd76
title: Data from: Human variation impacting MCOLN2 restricts Salmonella Typhi replication by magnesium deprivation

description: Human genetic diversity can reveal critical factors in host-pathogen interactions. This is especially useful for human-restricted pathogens like Salmonella enterica serovar Typhi (S. Typhi), the cause of Typhoid fever. One key dynamic during infection is competition for nutrients: host cells attempt to restrict intracellular replication by depriving bacteria of key nutrients or delivering toxic metabolites in a process called nutritional immunity. Here, a cellular genome-wide association study of intracellular replication by S. Typhi in nearly a thousand cell lines from around the world and extensive follow-up using intracellular S. Typhi transcriptomics and manipulation of magnesium concentrations demonstrates that the divalent cation channel mucolipin-2 (MCOLN2) restricts S. Typhi intracellular replication through magnesium deprivation. Our results reveal natural diversity in Mg2+ limitation as a key component of nutritional immunity against S. Typhi.
DOI: 10.7924/r4m61nk31
title: Data from: Ildr1 gene deletion protects against diet-induced obesity and hyperglycemia

description: Objective
Immunoglobulin-like Domain-Containing Receptor 1 (ILDR1) is expressed on nutrient sensing cholecystokinin-positive enteroendocrine cells of the gastrointestinal tract and it has the unique ability to induce fat-mediated CCK secretion. However, the role of ILDR1 in cholecystokinin-mediated regulation of satiety is unknown. In this study, we examined the effects of ILDR1 on food intake and metabolic activity using mice with genetically-deleted Ildr1.

Methods
The expression of ILDR1 in murine tissues and the measurement of adipocyte cell size were evaluated by light and fluorescence confocal microscopy. The effects of Ildr1 deletion on mouse metabolism were quantitated using CLAMS chambers and by targeted metabolomics assays of multiple tissues. Hormone levels were measured by ELISA. The effects of Ildr1 gene deletion on glucose and insulin levels were determined using in vivo oral glucose tolerance, meal tolerance, and insulin tolerance tests, as well as ex vivo islet perifusion.

Results
ILDR1 is expressed in a wide range of tissues. Analysis of metabolic data revealed that although Ildr1-/- mice consumed more food than wild-type littermates, they gained less weight on a high fat diet and exhibited increased metabolic activity. Adipocytes in Ildr1-/- mice were significantly smaller than in wild-type mice fed either low or high fat diets. ILDR1 was expressed in both alpha and beta cells of pancreatic islets. Based on oral glucose and mixed meal tolerance tests, Ildr1-/- mice were more effective at lowering post-prandial glucose levels, had improved insulin sensitivity, and glucose-regulated insulin secretion was enhanced in mice lacking ILDR1.

Conclusion
Ildr1 loss significantly modified metabolic activity in these mutant mice. While Ildr1 gene deletion increased high fat food intake, it reduced weight gain and improved glucose tolerance. These findings indicate that ILDR1 modulates metabolic responses to feeding in mice.
DOI: 10.7924/r4v125f95
title: Data from: An atlas of genetic variation linking pathogen-induced cellular traits to human disease

description: Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HOST Phenome Project (H2P2): a catalog of cellular genome-wide association studies (GWAS) comprising 79 infection-related phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance for infection-associated phenotypes ranging from pathogen replication to cytokine production. We combined H2P2 with clinical association data from patients to identify a SNP near CXCL10 as a risk factor for inflammatory bowel disease. A SNP in the transcriptional repressor ZBTB20 demonstrated pleiotropy, likely through suppression of multiple target genes, and was associated with viral hepatitis. These data are available on a web portal to facilitate interpreting human genome variation through the lens of cell biology and should serve as a rich resource for the research community.
DOI: 10.7924/r49g5s86k
title: Youth activist oral histories, 2010-2021

description: Youth activists are often left out of political history archives. This is true despite the fact that youth social movements repeatedly change the course of history. To contribute to rectifying this imbalance in archival sources, students in Duke professor Wesley Hogan's Fall 2021 FOCUS Program class, "US Youth Movements since 2010: Expanding Human Rights for All," created an archive of their oral history interviews with youth activists in the Black Lives Matter, environmental justice, LGBTQ+, gender equity, and Indigenous rights movements. 

Each interview contains an MP3 or MP4 file, an interview transcript approved by the narrator, a
brief introduction to the narrator, and an index of the interview.
DOI: 10.7924/r45q52g2t
title: Data from: Mutual information: Measuring nonlinear dependence in longitudinal epidemiological data

description: Given a large clinical database of longitudinal patient information including many covariates, it is computationally prohibitive to consider all types of interdependence between patient variables of interest. This challenge motivates the use of mutual information (MI), a statistical summary of data interdependence with appealing properties that make it a suitable alternative or addition to correlation for identifying relationships in data. MI: (i) captures all types of dependence, both linear and nonlinear, (ii) is zero only when random variables are independent, (iii) serves as a measure of relationship strength (similar to but more general than R2), and (iv) is interpreted the same way for numerical and categorical data. Unfortunately, MI typically receives little to no attention in introductory statistics courses and is more difficult than correlation to estimate from data. In this article, we motivate the use of MI in the analyses of epidemiologic data, while providing a general introduction to estimation and interpretation. We illustrate its utility through a retrospective study relating intraoperative heart rate (HR) and mean arterial pressure (MAP). We: (i) show postoperative mortality is associated with decreased MI between HR and MAP and (ii) improve existing postoperative mortality risk assessment by including MI and additional hemodynamic statistics.
DOI: 10.7924/r48k7ft9j
title: Data from: Statistical significance for maximally persistent topological features via the Gumbel distribution

description: Topological data analysis (TDA) is finding traction as a novel way to discover and quantify structure in data. While there has been great success in descriptive characterizations, a rigorous statistical framework for the field is still in development. Here we look at a commonly used metric -- the length of the maximally persistent feature in a point cloud -- and develop a framework for hypothesis testing. Because the distribution of persistence lengths in Poisson spatial point clouds is well-aligned with the probabilistic theory of extreme values, we argue that critical values of the Gumbel distribution should be used when assessing statistical significance. For one-dimensional topological features (holes) in two-dimensional point clouds, we use the theory to predict an asymptotic rescaling of maximally persistent features that results in convergence in distribution to an approximately standard Gumbel random variable. We then propose a model for critical values as a function of point density and demonstrate its effectiveness on some standard TDA challenges.
DOI: 10.7924/r4n87d05r
title: Data from: Responses of model cortical neurons to temporal interference stimulation and other transcranial alternating current stimulation modalities

description: Background: Temporal interference stimulation (TIS) has been proposed as a non-invasive, focal, and steerable deep brain stimulation method. However, the mechanisms underlying experimentally observed TIS effects are unknown, and prior simulation studies have limitations in the representations of the TIS electric field (E-field) and cerebral neurons. Objective: To examine the E-field and neural response characteristics for TIS and other transcranial alternating current stimulation modalities. Methods: We simulated a range of stimulation parameters in layer 5 pyramidal  neurons, including different orientations, frequencies, amplitude ratios, amplitude modulation, and phase difference of the E-fields, and obtained thresholds for both activation and block. Results: TIS has unique E-field characteristics. At the target region in the cortex, where the two E-fields have similar amplitudes, TIS generates an amplitude-modulated total E-field. The TIS E-field also exhibits rotation where the E-field orientations are not aligned, which generally co-localizes with the target. TIS activation thresholds are similar to high-frequency stimulation with or without modulation and/or rotation (75–230 V/m). Outside the target region, the TIS E-field is dominated by the high-frequency carrier, with minimal amplitude modulation and/or rotation, and it is less effective at activation and more effective at block. TIS creates block for some combinations of E-field orientations and amplitude ratios at very high amplitudes (>1700 V/m), whereas amplitude modulated single-carrier high-frequency stimulation cannot achieve similar effects, regardless of orientation. Conclusion: All observed effects occurred at E-field strengths that are too high to be delivered tolerably through scalp electrodes, suggesting limited significance of suprathreshold TIS.