Big bibliographic datasets hold promise for revolutionizing the scientific enterprise when combined with state-of-the-science computational capabilities. Yet, hosting proprietary and open big ...bibliographic datasets poses significant difficulties for libraries, both large and small. Libraries face significant barriers to hosting such assets, including cost and expertise, which has limited their ability to provide stewardship for big datasets, and thus has hampered researchers' access to them. What is needed is a solution to address the libraries' and researchers' joint needs. This article outlines the theoretical framework that underpins the Collaborative Archive and Data Research Environment project. We recommend a shared cloud-based infrastructure to address this need built on five pillars: 1)
ommunity-a community of libraries and industry partners who support and maintain the platform and a community of researchers who use it; 2)
ccess-the sharing platform should be accessible and affordable to both proprietary data customers and the general public; 3)
ata-Centric-the platform is optimized for efficient and high-quality bibliographic data services, satisfying diverse data needs; 4)
eproducibility-the platform should be designed to foster and encourage reproducible research; 5)
mpowerment-the platform should empower researchers to perform big data analytics on the hosted datasets. In this article, we describe the many facets of the problem faced by American academic libraries and researchers wanting to work with big datasets. We propose a practical solution based on the five pillars: The Collaborative Archive and Data Research Environment. Finally, we address potential barriers to implementing this solution and strategies for overcoming them.
ABSTRACT
Silver nanoparticles (AgNPs) are employed in a variety of consumer products; however, in vivo rodent studies indicate that AgNPs can cause lung inflammation and toxicity in a strain‐ and ...particle type–dependent manner, but mechanisms of susceptibility remain unclear. The aim of this study was to assess the variation in AgNP‐induced lung inflammation and toxicity across multiple inbred mouse strains and to use genome‐wide association (GWA) mapping to identify potential candidate susceptibility genes. Mice received doses of 0.25 mg/kg of either 20‐nm citrate‐coated AgNPs or citrate buffer using oropharyngeal aspiration. Neutrophils in bronchoalveolar lavage fluid (BALF) served as markers of inflammation. We found significant strain‐ and treatment‐dependent variation in neutrophils in BALF. GWA mapping identified 10 significant single‐nucleotide polymorphisms (false discovery rate, 15%) in 4 quantitative trait loci on mouse chromosomes 1, 4, 15, and 18, and Nedd4l (neural precursor cell expressed developmentally downregulated gene 4‐like; chromosome 18), Ano6 (anocatmin 6; chromosome 15), and Rnf220 (Ring finger protein 220; chromosome 4) were considered candidate genes. Quantitative RT‐PCR revealed significant inverse associations between mRNA levels of these genes and neutrophil influx. Nedd4l, Ano6, and Rnf220 are candidate susceptibility genes for AgNP‐induced lung inflammation that warrant additional exploration in future studies.—Scoville, D. K., Botta, D., Galdanes, K., Schmuck, S. C., White, C. C., Stapleton, P. L., Bammler, T. K., MacDonald, J. W., Altemeier, W. A., Hernandez, M., Kleeberger, S. R., Chen, L.‐C., Gordon, T., Kavanagh, T. J. Genetic determinants of susceptibility to silver nanoparticle‐induced acute lung inflammation in mice. FASEB J. 31, 4600–4611 (2017). www.fasebj.org
Amphibian skin secretions are enriched with complex cocktails of bioactive molecules such as proteins, peptides, biogenic amines, alkaloids guanidine derivatives, steroids and other minor components ...spanning a wide spectrum of pharmacological actions exploited for centuries in folk medicine. This study presents evidence on the protein profile of the skin secretions of the canyon tree frog,
. At the same time, it presents the reverse-phase liquid chromatography isolation, mass spectrometry characterization and identification at mRNA level of a novel 58 amino acids Kunitz-like polypeptide from the skin secretions of
, arenin. Cell viability assays performed on HDFa, CaCo2 and MCF7 cells cultured with different concentrations of arenin showed a discrete effect at low concentrations (2, 4, 8 and 16 µg/mL) suggesting a multi-target interaction in a hormetic-like dose-response. Further work is required to investigate the mechanisms underlying the variable effect on cell viability produced by different concentrations of arenin.
Although the zebrafish has become a popular model organism for biomedical studies, we propose that the wealth of morphological novelties that characterize this cypriniform fish makes it well suited ...for investigating the development of evolutionary innovations. Morphological novelties associated with feeding in cypriniform fishes include: a unique structure of the pharyngeal jaws in which the lower pharyngeal jaws are enlarged and opposed to a pad on the basioccipital process; a palatal organ found on the roof of the buccal chamber that is thought to help process detrital food within the buccal chamber; and, the kinethmoid, a novel ossification that effects a unique means of premaxillary protrusion. We present new morphological and developmental data and review functional data regarding the role of the kinethmoid in premaxillary protrusion in the zebrafish. Premaxillary protrusion plays an important role in effective prey acquisition in teleosts and the evolution of a unique means of premaxillary protrusion within Cypriniformes may have led to a number of trophic radiations within this clade. Ontogenetic data from zebrafish show that substantial premaxillary protrusion is not seen until these fish have undergone metamorphosis at which point the adductor mandibulae musculature becomes divided and all ligamentous attachments become established. A comparative study of families within Cypriniformes shows diverse morphologies of the kinethmoid. The morphological diversification that characterizes the kinethmoid suggests that this feeding structure has played a role in trophic radiations within Cypriniformes, since the morphology of this feature is correlated with feeding habits.
In previous studies, we reported that key antioxidant and DNA repair genes are regulated differently in normal bronchial epithelial cells of lung cancer cases compared with non-lung cancer controls. ...In an effort to develop a biomarker for lung cancer risk, we evaluated the transcript expressions of 14 antioxidant, DNA repair, and transcription factor genes in normal bronchial epithelial cells (HUGO names CAT, CEBPG, E2F1, ERCC4, ERCC5, GPX1, GPX3, GSTM3, GSTP1, GSTT1, GSTZ1, MGST1, SOD1, and XRCC1). A test comprising these 14 genes accurately identified the lung cancer cases in two case-control studies. The receiver operating characteristic-area under the curve was 0.82 (95% confidence intervals, 0.68-0.91) for the first case-control set (25 lung cancer cases and 24 controls), and 0.87 (95% confidence intervals, 0.73-0.96) for the second set (18 cases and 22 controls). For each gene included in the test, the key difference between cases and controls was altered distribution of transcript expression among cancer cases compared with controls, with more lung cancer cases expressing at both extremes among all genes (Kolmorogov-Smirnov test, D = 0.0795; P = 0.041). A novel statistical approach was used to identify the lower and upper boundaries of transcript expression that optimally classifies cases and controls for each gene. Based on the data presented here, there is an increased prevalence of lung cancer diagnosis among individuals that express a threshold number of key antioxidant, DNA repair, and transcription factor genes at either very high or very low levels in the normal airway epithelium.
Abstract only
Cypriniform fishes are characterized by a number of evolutionary trophic novelties. These feeding novelties have allowed cypriniforms to take full advantage of a number of unique ...trophic niches. One such feeding innovation, the palatal organ, is a complex muscular structure located on the pharyngeal roof of cypriniform fishes. The palatal organ is a dorsal mass of complexly arranged muscle fibers within the buccopharyngeal cavity innervated by the vagal lobe and covered by a taste bud coated epithelium. Here we use developmental data from zebrafish, functional data from carp and goldfish, and histological data and modeling approaches from assorted cypriniform species to address how the palatal organ developed and explain some of its functional evolution. Using zebrafish we first describe the origin and ontogenetic development of the palatal organ. Comparative data on histological structure and myosin composition of the palatal organ across a wide phylogenetic sampling of cypriniforms is then used to determine the variation in structure and potential function of the palatal organ across Cypriniformes. The general assumption has been that the function of the palatal organ is conserved across cypriniforms, and requires the careful sensory control made possible by a hypertrophied vagal lobe to function properly. Few have considered the possibility that the palatal organ may have become adapted for different functions during the course of cypriniform evolution. Its possible role in other feeding modes has been largely overlooked as it has been presumed that the palatal organ's only function is in sorting during benthic feeding events. Using electromyography and high‐speed video to examine palatal organ activity in the common carp and goldfish, muscle activation patterns demonstrate that the palatal organ is likely employed just prior to suction generation, during suction feeding behaviors, during prey processing events, and may even play a role in respiration during stressful conditions. Furthermore, the palatal organ shows behavioral modulation when different food types and positions are used. These data suggest that the palatal organ is a multi‐functional structure with a much wider range of functional repertoires than previously shown. While sorting during benthic feeding may have been the primitive function of the palatal organ, it has likely been secondarily adapted for increasing dietary breadth during the course of cypriniform evolution. This muscular pad has become secondarily modified for different forms of feeding but may even play a more generalized role in suction feeding and prey processing within cypriniforms.
We conducted a cross-sectional study among 1,717 children and adolescents of Mexican origin ages 5–19 years living in Mexico and Texas to explore the influence of country of birth and country of ...longest residence on their overweight and obesity status. Descriptive statistics were used to compare demographic and anthropometric characteristics of participants born and raised in Mexico (Mexicans), born in Mexico and raised in the United States (Mexican immigrants), and born and raised in the United States (Mexican–Americans). Univariate and multivariate nominal logistic regression was used to determine the demographic predictors of obesity adjusted by country of birth, country of residence, age, and gender. Almost half (48.8%) of the Mexican–Americans and 43.2% of the Mexican immigrants had body mass index at the 85th percentile or above, compared to only 29.3% of the Mexicans (
P
< .001). Thus, Mexican–Americans and Mexican immigrants were more likely to be obese than their Mexican peers Mexican–Americans: odds ratio (OR) = 2.5 (95% confidence interval CI 1.8–3.4); Mexican immigrants: OR = 2.2 (95% CI 1.6–3.0). In addition, males were more likely than females to be obese OR = 1.6 (95% CI 1.2–2.1), and adolescents 15–19 years of age were less likely than their younger counterparts OR = 0.5 (95% CI 0.4–0.7) to be obese. The high prevalence of obesity among children of Mexican origin in the United States is of great concern and underscores the urgent need to develop and implement obesity preventive interventions targeting younger children of Mexican origin, especially newly arrived immigrant children. In addition, future obesity research should take into consideration the country of origin of the study population to develop more culturally specific obesity interventions.
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