cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7924/r4br8v905
title: Data and scripts from: Rubenstein Library card catalog

description: This data includes the dataset, code, and files used and created by the Duke University Data+ 2021 Rubenstein Library Card Catalog Team. Working with the digitized cards from the David M. Rubenstein Rare Book and Manuscript Library's physical card catalogs, our team explored the files as a way to further the library's initiative of finding and describing historically marginalized voices in their collections.

We created a structured dataset using natural language processing and some manual editing, sorted by collection of items within the catalog and containing important metadata such as author, location, and date written from the OCRed text of the scanned cards.  With the dataset we created, we analyzed what and who is present in these cards, and displayed these findings in Jupyter Notebook files. We explored the demographics of the authors and items cataloged, as well as analyzed how the information within the cards relates to the history of Duke University and delved into the common topics of the data. We completed spatial frequency mapping on the level of the United States and of North Carolina counties, in addition to visualizing the international countries present in the cards. There is copious rich information present in the files, and our Data+ project is just the tip of the iceberg. We hope that future research teams will continue to dissect the card files to gain insights into Duke's history and the contents of the library's collections.
DOI: 10.7924/r4jm2bv29
title: Data from: Benchmarking deep learning architectures for artificial electromagnetic material problems

description: Artificial electromagnetic materials (AEMs), including metamaterials, derive their electromagnetic properties from geometry rather than chemistry. With the appropriate geometric design, AEMs have achieved exotic properties not realizable with conventional materials (e.g., cloaking or negative refractive index). However, understanding the relationship between the AEM structure and its properties is often poorly understood. While computational electromagnetic simulation (CEMS) may help design new AEMs, its use is limited due to its long computational time. Recently, it has been shown that deep learning can be an alternative solution to infer the relationship between an AEM geometry and its properties using a (relatively) small pool of CEMS data. However, the limited publicly released datasets and models and no widely-used benchmark for comparison have made using deep learning approaches even more difficult. Furthermore, configuring CEMS for a specific problem requires substantial expertise and time, making reproducibility challenging. Here, we develop a collection of three classes of AEM problems: metamaterials, nanophotonics, and color filter designs. We also publicly release software, allowing other researchers to conduct additional simulations for each system easily. Finally, we conduct experiments on our benchmark datasets with three recent neural network architectures: the multilayer perceptron (MLP), MLP-mixer, and transformer. We identify the methods and models that generalize best over the three problems to establish the best practice and baseline results upon which future research can build.
DOI: 10.7924/r48w3hk9t
title: Research Vessel Cape Hatteras science logs, 1981-2013

description: Dataset contains the station log records from the cruises between 1981 and 2013 of the Research Vessel Cape Hatteras, which was operated out of the Duke University Marine Lab. The vessel did not make any cruises in the year 1996. Logs record station coordinates and/or loran measurements; start/finish times; depths; and gear used.
DOI: 10.7924/r4cc1366g
title: Data from: Neural dynamics underlying birdsong practice and performance

description: The dataset pertains to a study that examined brain activity during vocal practice and audience-directed performance.  Data include optical imaging data of neural activity, vocal data, anatomical data, and electrophysiological data.
DOI: 10.7924/r4td9ws23
title: Data from: A Causal Mediation Model for Studying Longitudinal Animal Behavior and Survival Outcomes

description: Causal mediation analysis studies how the treatment effect of an exposure on outcomes is mediated through intermediate variables. Although many applications involve longitudinal data, the existing methods are not directly applicable to settings where the mediators are measured on irregular time grids. In this paper, we propose a causal mediation method that accommodates longitudinal mediators on arbitrary time grids and survival outcomes simultaneously. We take a functional data analysis perspective and view longitudinal mediators as realizations of underlying smooth stochastic processes. We define causal estimands of direct and indirect effects accordingly and provide corresponding identification assumptions. We employ a functional principal component analysis approach to estimate the mediator process, and propose a Cox hazard model for the survival outcome that flexibly adjusts the mediator process. We then derive a g-computation formula to express the causal estimands using the model coefficients. The proposed method is applied to a longitudinal data set from the Amboseli Baboon Research Project to investigate the causal relationships between early adversity, adult physiological stress responses, and survival among wild female baboons. We find that adversity experienced in early life has a significant direct effect on females' life expectancy and survival probability, but find little evidence that these effects were mediated by markers of the stress response in adulthood. We further developed a sensitivity analysis method to assess the impact of potential violation to the key assumption of sequential ignorability.
DOI: 10.7924/r4pn9600q
title: Data from: Female reproductive aging in seven primate species: patterns and consequences

description: Age-related changes in fertility have increasingly been documented in wild animal populations: in many species the youngest and oldest reproducers are disadvantaged relative to prime adults. How do these effects evolve, and what explains their diversity across species? Tackling this question requires detailed data on patterns of age-related reproductive performance in multiple animal species. Here, we compare patterns and consequences of age-related changes in female reproductive performance in seven primate populations that have been subjects of long-term continuous study for 29 to 57 years. We document evidence of age effects on fertility and on offspring performance in most, but not all, of these primate species. Specifically, females of six species showed longer interbirth intervals in the oldest age classes, youngest age classes, or both, and the oldest females also showed relatively fewer completed IBIs. In addition, five species showed markedly lower survival among offspring born to the oldest mothers, and two species showed reduced survival for offspring born to both the youngest and the oldest mothers. In contrast, we found mixed evidence that maternal age affects the age at which daughters first reproduce: only in muriquis and to some extent in chimpanzees, the only two species with female-biased dispersal, did relatively young mothers produce daughters that tended to have earlier first reproduction. Our findings demonstrate shared patterns as well as contrasts in age-related changes in female fertility across species of nonhuman primates, and highlight species-specific behavior and life history patterns as possible explanations for species-level differences.
DOI: 10.7924/r47w6gq34
title: Data from: Maturational changes in song sparrow song

description: Age-related changes in the production of sexually selected assessment signals have been identified across a diverse range of taxa, and in some cases these changes have been shown to affect receiver response to those signals. One important type of change occurs even after a signaler reaches breeding age, a phenomenon known as delayed maturation. Delayed maturation has been observed in the songs of several bird species, with potential fitness consequences for males as a byproduct of female choosiness or male competition. Here, we analyzed songs recorded across the first three years of life in a cohort of hand-reared song sparrows (Melospiza melodia) to detect early-life age-related changes in song. We focused on three measures of song complexity, including within song type variation, the average number of notes and the number of unique note types for the most common variant of each song type, and five measures of song production patterns, including singing rate, time interval between songs within a bout of the same song type, time interval between bouts (i.e., when the song type changes), within-song stereotypy, and between-song consistency. All measures of song complexity and most measures of song production patterns (excluding within-song stereotypy) changed significantly within individuals as birds aged from 1 to 2 years of age as well as from 1 to 3 years of age (excluding within-bout time interval), whereas no significant changes occurred from 2 to 3 years of age. Based on these features, a linear discriminant model could distinguish between the song of young (age 1) and older (age 2 and 3) adult males, providing support that song could serve as an indicator of age in this species. We discuss potential implications of these results for mate choice and male-male competition in song sparrows.
DOI: 10.7924/r46977v2r
title: Dredge Locations
DOI: 10.7924/r44q80q5d
title: Data from: Behavior and Fs activation reveal that male and female rats differentially assess affective valence during CTA learning and expression

description: Females are more affected by psychiatric illnesses including eating disorders, depression, and post-traumatic stress disorder than males. However, the neural mechanisms mediating these sex differences are poorly understood. Animal models can be useful in exploring such neural mechanisms. Conditioned taste aversion (CTA) is a behavioral task that assesses how animals process the competition between associated reinforcing and aversive stimuli in subsequent task performance, a process critical to healthy behavior in many domains.  The purpose of the present study was to identify sex differences in this behavior and associated neural responses. We hypothesized that females would value the rewarding stimulus (Boost®) relative to the aversive stimulus (LiCl) more than males in performing CTA. We evaluated behavior (Boost® intake, LiCl-induced behaviors, ultrasonic vocalizations (USVs), CTA performance) and Fos activation in relevant brain regions after the acute stimuli [acute Boost® (AB), acute LiCl (AL)] and the context-only task control (COT), Boost® only task (BOT) and Boost®-LiCl task (BLT). Acutely, females drank more Boost® than males but showed similar aversive behaviors after LiCl. Females and males performed CTA similarly. Both sexes produced 55 kHz USVs anticipating BOT and inhibited these calls in the BLT. However, more females emitted both 22 kHz and 55 kHz USVs in the BLT than males: the latter correlated with less CTA. Estrous cycle stage also influenced 55 kHz USVs. Fos responses were similar in males and females after AB or AL. Females engaged the gustatory cortex and ventral tegmental area (VTA) more than males during the BOT and males engaged the amygdala more than females in both the BOT and BLT. Network analysis of correlated Fos responses across brain regions identified two unique networks characterizing the BOT and BLT, in both of which the VTA played a central role. In situ hybridization with RNAscope identified a population of D1-receptor expressing cells in the CeA that responded to Boost® and D2 receptor-expressing cells that responded to LiCl. The present study suggests that males and females differentially process the affective valence of a stimulus to produce the same goal-directed behavior.

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DOI: 10.7924/r43r0zt6t
title: Data from: RNA sequencing of rabbit placentas exposed to PFBS

description: <strong>*Data will be embargoed until publication of related article, or up to no more than 1 year from data upload.*</strong>

Per- and polyfluoralkyl substances (PFAS) are persistent environmental contaminants, and
human exposure is ubiquitous and associated with many adverse health outcomes. In recognition of these health risks, legacy PFAS compounds such as perfluorooctane sulfonate (PFOS) have been replaced with “safer” alternatives such as perfluorobutane sulfonate (PFBS), although their toxicity is largely unknown. Recent studies suggest that maternal PFAS exposure leads to adverse pregnancy outcomes including maternal hypertensive disorders, thyroid hormone disruption, and low birth weight, though the epidemiologic literature varies and biological mechanisms remain undetermined. Of concern, maternal PFBS exposure was recently associated with an increased risk of preeclampsia, a life-threatening pregnancy complication resulting from dysregulated placentation. Using our established rabbit model, dams were exposed to PFBS-contaminated drinking water throughout pregnancy. Pregnancy outcomes were evaluated, including placentation. Differential gene expression was evaluated in rabbit placentas by RNAseqencing.
DOI: 10.7924/r4w66k88z
title: Data from: RNA sequencing of rabbit placentas exposed to a PFAS-mixture

description: <strong>*Data will be embargoed until publication of related article, or up to no more than 1 year from data upload.*</strong>

A mixture of per and polyfluoroalkyl substances (PFAS) are found in drinking water, diet, and household dust. These environmental contaminants are detected in up to 99% of human serum samples; yet very little is known about how exposures to exposure to mixtures of these compounds affect maternal and fetal health during pregnancy. We investigated the maternal, fetal, and placental outcomes after maternal exposure to an environmentally relevant PFAS-mixture during pregnancy in a New Zealand White (NZW) rabbit model. Female NZW rabbits were supplied control (no detectable PFAS levels) or PFAS-contaminated drinking water, which was formulated with PFAS to resemble levels measured in tap water collected from Pittsboro, NC (10 PFAS compounds; total PFAS load = 758.6 ng/L). Maternal, fetal, and placental outcomes were evaluated at necropsy. Further, dysregulated gene expression in the placenta was determined by RNA sequencing. 14 genes (p<0.1) were identified as significantly different, 9 of which are associated with adverse placental function related to pregnancy complications.
DOI: 10.7924/r4kd20t7c
title: Data from: Mechanisms of inbreeding avoidance in a wild primate

description: Inbreeding often imposes net fitness costs, leading to the expectation that animals will engage in inbreeding avoidance when the costs of doing so are not prohibitive. However, one recent meta-analysis indicates that animals of many species do not avoid mating with kin in experimental settings, and another reports that behavioral inbreeding avoidance generally evolves only when kin regularly encounter each other and inbreeding costs are high. These results raise questions about the processes that separate kin, how these processes depend on kin class and context, and whether kin classes differ in how effectively they avoid inbreeding via mate choice—in turn demanding detailed demographic and behavioral data within individual populations. Here we address these questions in a wild mammal population, the baboons of the Amboseli ecosystem in Kenya. We find that death and dispersal are very effective at separating opposite-sex pairs of close adult kin. Nonetheless, adult kin pairs do sometimes co-reside, and we find strong evidence for inbreeding avoidance via mate choice in kin classes with relatedness 0.25. Notably, maternal kin avoid inbreeding more effectively than paternal kin despite having identical coefficients of relatedness, pointing to kin discrimination as a potential constraint on effective inbreeding avoidance. Overall, demographic and behavioral processes ensure that inbred offspring are rare in undisturbed social groups (1% of offspring). However, in an anthropogenically disturbed social group with reduced male dispersal, we find inbreeding rates 10x higher. Our study reinforces the importance of demographic and behavioral contexts for understanding the evolution of inbreeding avoidance.
DOI: 10.7924/r4ks6tf5q
title: Data from: GLP-1 receptor blockade reduces stimulated insulin secretion in fasted subjects with low circulating GLP-1

description: Context: Glucagon-like peptide 1 (GLP-1), an insulinotropic peptide released into the circulation from intestinal enteroendocrine cells, is considered a hormonal mediator of insulin secretion. However, the physiological actions of circulating GLP-1 have long been questioned because of the short half-life of the active peptide. Moreover, there is mounting evidence for localized, intra-islet mediation of GLP-1 receptor (GLP-1r) signaling including a role for islet dipeptidyl-peptidase 4 (DPP4).
Objective: To determine whether GLP-1r signaling contributes to insulin secretion in the absence of enteral stimulation and increased plasma levels, and whether this is affected by DPP4.
Setting: Single-site study conducted at an academic medical center.
Participants: 20 nondiabetic subjects and 13 subjects with type 2 diabetes.
Design & Interventions: Cross-over study in which subjects received either a DPP4 inhibitor (DPP4i; sitagliptin) or placebo on two separate days. On each day they received a bolus of intravenous (IV) arginine during sequential 60 minute infusions of the GLP-1r blocker exendin[9-39] (Ex-9) and saline. 
Main Outcome Measures: Arginine-stimulated secretion of C-Peptide (C-PArg) and insulin (InsArg).
Results: Plasma GLP-1 remained at fasting levels throughout the experiments and IV arginine stimulated both - and β-cell secretion in all subjects. Ex-9 infusion reduced C-PArg in both the diabetic and nondiabetic groups by ~14% (p < 0.03 for both groups). Sitagliptin lowered baseline glycemia but did not affect the primary measures of insulin secretion. However, a significant interaction between sitagliptin and Ex-9 suggested a greater effect of GLP-1r activation with DPP4i treatment in diabetic subjects.
Conclusions: GLP-1r activation contributes to β-cell secretion in diabetic and nondiabetic humans during -cell activation, but in the absence of increased circulating GLP-1. These results are compatible with regulation of β-cells by paracrine signals from -cells. This process may be affected by DPP4 inhibition.
DOI: 10.7924/r4br8ws2t
title: Data from: COVID-19 Emotion regulation survey study

description: The COVID-19 pandemic has affected the lives of people around the world due to changes including job loss, illness, loss of loved ones, financial insecurity, and social distancing. Emerging research suggests this pandemic has also been deleterious on the mental health of many individuals. There is a critical need to continue evaluating the mental health impact of these events. Additionally, while research is beginning to show an increase in mental health conditions such as depression and anxiety, little work has been conducted exploring the impact of COVID-19 on emotion regulation itself. This information will guide treatment efforts as the world continues to cope with this pandemic.
DOI: 10.7924/r4g163n0s
title: Data from: Single-cell genome-wide association reveals a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus

description: Diversity in the human genome is one factor that confers resistance and susceptibility to infectious diseases. This is observed most dramatically during pandemics, where individuals exhibit large differences in risk and clinical outcomes against a pathogen infecting large portions of the world’s populations. Here, we developed scHi-HOST (single cell High-throughput Human in vitrO Susceptibility Testing), a method for rapidly identifying genetic variants that confer resistance and susceptibility to pathogens. scHi-HOST leverages scRNA-seq (single-cell RNA-sequencing) to simultaneously assign genetic identity to individual cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral entry and replication, and identify expression quantitative trait loci (eQTL). Applying scHi-HOST to influenza A virus (IAV), we identified eQTL at baseline and in genes that are induced by IAV infection. Integration of scHi-HOST with a human IAV challenge study (Prometheus) revealed that a missense variant in ERAP1 (Endoplasmic reticulum aminopeptidase 1; rs27895) was associated with flu burden in cells and in human volunteers. Functional studies using RNA interference and overexpression of alternative alleles revealed that ERAP1 is exploited by IAV to promote infection. Specifically, the nonsynonymous substitution, which results in a glycine to aspartate substitution at ERAP1 residue 348, would disrupt the substrate binding pocket of ERAP1 likely resulting in a significant altered preference for substrates, poorer catalytic efficiency, or both. Finally, rs27895 exhibits substantial population differentiation, with the higher frequency of the minor T allele in two African populations likely contributing to the greater permissivity of cells from these populations to IAV infection. The synthesis of scHi-HOST with human challenge studies is a broadly applicable method that facilitates identification of common human genetic differences that confer resistance and susceptibility to pathogens.
DOI: 10.7924/r47s7t64c
title: Data from: The cortical evoked potential corresponds with deep brain stimulation efficacy in rats

description: Objective. Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an effective treatment for the motor symptoms of Parkinson's disease, although its mechanism of action is uncertain. Previous work has demonstrated that a critical component to its mechanism may be the activation of the primary motor cortex (M1) via the antidromic firing of neurons within the hyperdirect pathway from STN to M1. This antidromic firing exhibits high rates of spike failure when stimulated at high frequencies, and the spike failure rate appears to correlate with DBS efficacy. This synchronous antidromic spiking takes the form of a short-latency evoked potential in electrocorticography (ECoG) recordings of M1, with the magnitude of the cortical evoked potential (cEP) similarly declining at high stimulation frequencies. In this study, we aimed to characterize the cEP in response to various stimulation conditions and to determine whether changes in the cEP correlate with symptom reduction from DBS. Approach. We used the unilateral 6-hydroxydopamine lesioned rat model in female, Sprague Dawley rats, with stimulating electrodes implanted in the STN and the ECoG recorded above M1. We then recorded the cEP during various stimulation conditions and while performing behavioral assessments of hypokinetic symptoms. Main results. We found that the cEP is strongly affected by stimulation conditions, with the cEP magnitude declining and cEP latency increasing with higher stimulation frequencies. These effects occur over multiple minutes, and likely with multiple time-scales. Additionally, the cEP magnitude and latency each correlate strongly with symptom reduction from DBS, with superior correlations to conventional spectral-based biomarkers from ECoG. Significance. This study demonstrates the potential clinical utility of the cEP as a biomarker for symptom reduction from DBS, which may be used in determining proper lead location, stimulation parameter selection, or closed-loop control. Additionally, it provides further insight into the cortical mechanism by which DBS relieves symptoms, suggesting that it may be related to a potential desynchronizing effect caused by high rates of sporadic antidromic spike failure during high frequency DBS.