cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Comparison of phenolic content and antioxidant activity of Actaea racemosa L. and Actaea cordifolia DC
Creators: name: Grażyna Szymczak
name: Wójciak–Kosior, Magdalena
name: Sowa, Ireneusz
name: Zapała, Karolina
name: Bogucka-Kocka, Anna
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Plant Biology
subject: FOS: Biological sciences
subject: Biological Sciences
subject: Ecology
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Biotechnology
subject: Biochemistry

description: Actaea racemosa L. is used as a component of drugs or dietary supplements to alleviate the menopause symptoms. Its biological activity is associated with the presence of phenolic compounds. In our work, the analysis of isoflavones and phenolic acids – caffeic acid (CA), ferulic acid and isoferulic acid (iFA) – both free and bonded in two species of Actaea, was conducted using HPLC-PAD technique. Moreover, the antioxidant effect of extracts from different parts of the investigated plants was determined on the basis of DPPH assay. Significant variation of CA and iFA content was observed. The highest content of CA was found in A. racemosa, while Actaea cordifolia contained the highest amount of iFA. Isoflavones were not found in the investigated plants. The antioxidant activity assay showed the high free radical-scavenging ability of the extracts obtained from different parts of the plant.
Physical activity and diet associations with the gut microbiota in the Coronary Artery Risk Development in Young Adults (CARDIA) study
Creators: name: Meyer, K.A.
name: Jones, C.
name: Shikany, J.M.
name: North, K.E.
name: Launer, L.J.
name: Lulla, A.
name: Jacobs, D.R., Jr
name: Memili, A.
name: Liu, H.
name: Langsetmo, L.
Publisher: name: Elsevier B.V.
Year: 2023

description: Background: Gut microbiota may influence metabolic pathways related to chronic health conditions. Evidence for physical activity and diet influences on gut microbial composition exists, but data from diverse population-based cohort studies are limited. Objectives: We hypothesized that gut microbial diversity and genera are associated with physical activity and diet quality. Methods: Data were from 537 participants in the Coronary Artery Risk Development in Young Adults (CARDIA) Study, a prospective cohort, who attended the year 30 follow-up examination (2015–2016; aged 47–61 y; 45% Black race/55% White race; 45% men/55% women). The 16S ribosomal RNA marker gene was sequenced from stool DNA, and genus-level taxonomy was assigned. Within-person microbial diversity (α-diversity) was assessed with Shannon diversity index and richness scores; between-person diversity (β-diversity) measures were generated with principal coordinates analysis (PCoA). Current and long-term physical activity and diet quality measures were derived from data collected over 30 y of follow-up. Multivariable-adjusted regression analysis controlled for: sociodemographic variables (age, race, sex, education, and field center), other health behaviors (smoking, alcohol consumption, and medication use), and adjusted for multiple comparisons with the false discovery rate (<0.20). Results: Based on PCoA β-diversity, participants’ microbial community compositions differed significantly (P < 0.001), with respect to both current and long-term physical activity and diet quality. α-Diversity was associated only with current physical activity (positively) in multivariable-adjusted analysis. Multiple genera (n = 45) were associated with physical activity and fewer with diet (n = 5), including positive associations with Lachnospiraceae UCG-001 and Ruminococcaceae Incertae Sedis with both behaviors. Conclusions: Physical activity and diet quality were associated with gut microbial composition among 537 participants in the CARDIA study. Multiple genera were associated with physical activity. Physical activity and diet quality were associated with genera consistent with pathways related to inflammation and short-chain fatty acid production.
amshehata@uqu.edu_.sa_.pdf
Creators: name: Shehata, Ahmed
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 410502
subject: Noise and wave pollution processes and measurement

description: This study presents an analytical approach to evaluating the hazard risk in public spaces. Throughout the study, users' activities were recorded in terms of location and periods. Noise levels were recorded within these space areas. A comparison between users' activities and noise levels in the main and sub-zones of the study space was conducted. Excellent and effective solutions became possible depending on the results of this comparison. The research concluded with general recommendations for urban designers and decision-makers of such public places, and specific recommendations for the case study were given to reduce the impact of exposure to noise by the most vulnerable groups of users in the long and short term.
A new sponge-dwelling goby (Gobiidae: Bathygobius) from Indonesia, Philippines, and Australia
Creators: name: Allen, Gerald R.
name: Erdmann, Mark
name: Ishida, Nesha
Publisher: name: Zenodo
Year: 2024
Subjects: taxonomy
ichthyology
systematics
coral reef fishes
gobies
tropical western pacific
Indo-Pacific
commensal

description: A new species of goby, Bathygobius mero, is described from eastern Bali, Indonesia on the basis of 8 adult specimens, 26.3–36.0 mm SL. There are also photographic records from Sumba, Indonesia, Cebu, Philippines, and Queensland, Australia. Diagnostic features include 19–21 (usually 20) pectoral-fin rays with the upper three rays free from the membranous portion of the fin and each with two filamentous tips, a mostly scaleless predorsal midline except for two or three scales in front of first dorsal-fin origin, and 33 or 34 lateral scales. The live coloration is overall pale greyish with a dense covering of reddish-brown freckles, a brown spot (about one third of pupil size) at the uppermost part of the gill opening, and reddish-brown spotting on the fins. The new species has a commensal association with the large barrel sponge (Xestospongia testudinaria), unlike other members of the genus, which are typically free-living bottom dwellers. It also inhabits deeper water (9–30 m, but usually below about 15 m) than most Bathygobius, which are mainly confined to shallow water less than 10 m deep.
Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants
Creators: name: Lim, E.
name: Boorgula, M.P.
name: Fohner, A.E.
name: Rich, S.S.
name: Aslibekyan, S.
name: McDonald, M.-L.
name: Prokić, I.
name: Wiggins, K.L.
name: Kooperberg, C.
name: Xu, H.
name: Graff, M.
name: Heard-Costa, N.L.
name: Young, K.L.
name: Liu, C.-T.
name: Fisher, V.
name: Smith, J.A.
name: Zhang, D.
name: McKnight, B.
name: Redline, S.
name: Kardia, S.L.R.
name: Jain, D.
name: Haessler, J.
name: Regan, E.A.
name: Rivadeneira, F.
name: De Andrade, M.
name: Medina-Gomez, C.
name: Broome, J.G.
name: Hidalgo, B.
name: Mitchell, B.D.
name: Province, M.
name: North, K.E.
name: Kim, W.
name: An, P.
name: Yanek, L.R.
name: Leal, S.
name: Lin, B.M.
name: Tao, R.
name: Irvin, M.R.
name: Chavan, S.
name: Brody, J.A.
name: Barnes, K.
name: Reiner, A.P.
name: Sitlani, C.
name: Smith, A.V.
name: Mathias, R.A.
name: Amin, N.
name: Kraaij, R.
name: Buth, E.J.
name: Weiss, S.
name: Guo, X.
name: Arnett, D.
name: Deng, X.
name: Cupples, L.A.
name: Rotter, J.I.
name: Lin, D.
name: Kalyani, R.R.
name: Heavner, B.D.
name: van Rooij, J.
name: Peyser, P.A.
name: van Duijn, C.M.
name: Darbar, D.
name: Lenzini, P.
Publisher: name: Cell Press
Year: 2023

description: Anthropometric traits, measuring body size and shape, are highly heritable and significant clinical risk factors for cardiometabolic disorders. These traits have been extensively studied in genome-wide association studies (GWASs), with hundreds of genome-wide significant loci identified. We performed a whole-exome sequence analysis of the genetics of height, body mass index (BMI) and waist/hip ratio (WHR). We meta-analyzed single-variant and gene-based associations of whole-exome sequence variation with height, BMI, and WHR in up to 22,004 individuals, and we assessed replication of our findings in up to 16,418 individuals from 10 independent cohorts from Trans-Omics for Precision Medicine (TOPMed). We identified four trait associations with single-nucleotide variants (SNVs; two for height and two for BMI) and replicated the LECT2 gene association with height. Our expression quantitative trait locus (eQTL) analysis within previously reported GWAS loci implicated CEP63 and RFT1 as potential functional genes for known height loci. We further assessed enrichment of SNVs, which were monogenic or syndromic variants within loci associated with our three traits. This led to the significant enrichment results for height, whereas we observed no Bonferroni-corrected significance for all SNVs. With a sample size of ∼20,000 whole-exome sequences in our discovery dataset, our findings demonstrate the importance of genomic sequencing in genetic association studies, yet they also illustrate the challenges in identifying effects of rare genetic variants.
Lipoxygenase inhibitory activity of Cuspidaria pulchra and isolated compounds
Creators: name: Tavane A. Alvarenga
name: Bertanha, Camila S.
name: Pollyanna F. De Oliveira
name: Tavares, Denise C.
name: Gimenez, Valéria M.M.
name: Silva, Márcio L.A.
name: Cunha, Wilson R.
name: Januário, Ana H.
name: Pauletti, Patrícia M.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Pharmacology
subject: Microbiology
subject: Biochemistry

description: This work evaluated the in vitro inhibitory activity of the crude ethanolic extract from the aerial parts of Cuspidaria pulchra (Cham.) L.G. Lohmann against 15-lipoxygenase (15-LOX). The bioassay-guided fractionation of the n-butanol fraction, which displayed the highest activity, led to the isolation of three compounds: caffeoylcalleryanin (1), verbascoside (2) and 6-hydroxyluteolin-7-O-β-glucoside (3). Assessment of the ability of the isolated compounds to inhibit 15-LOX revealed that compounds 1, 2 and 3 exerted strong 15-LOX inhibitory activity; IC50 values were 1.59, 1.76 and 2.35 μM respectively. The XTT assay showed that none of the isolated compounds seemed to be significantly toxic.
Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals
Creators: name: Kooperberg, C.
name: Mester, R.
name: Conti, D.V.
name: Fornage, M.
name: Buyske, S.
name: Kenny, E.E.
name: Kim, M.
name: Lange, L.
name: Haiman, C.
name: Xu, Z.
name: Bhattacharya, A.
name: North, K.E.
name: Rotter, J.I.
name: Wheeler, H.E.
name: Zhou, Y.
name: Gignoux, C.
name: Pasaniuc, B.
name: Rich, S.S.
name: Wu, Y.
name: Wojcik, G.L.
name: Peters, U.
name: Rasmussen-Torvik, L.J.
name: Guo, X.
name: Sankararaman, S.
name: Hou, K.
name: Ding, Y.
name: Belbin, G.M.
name: Manichaikul, A.
name: Darst, B.F.
Publisher: name: Nature Research
Year: 2023

description: Individuals of admixed ancestries (for example, African Americans) inherit a mosaic of ancestry segments (local ancestry) originating from multiple continental ancestral populations. This offers the unique opportunity of investigating the similarity of genetic effects on traits across ancestries within the same population. Here we introduce an approach to estimate correlation of causal genetic effects (radmix) across local ancestries and analyze 38 complex traits in African-European admixed individuals (N = 53,001) to observe very high correlations (meta-analysis radmix = 0.95, 95% credible interval 0.93–0.97), much higher than correlation of causal effects across continental ancestries. We replicate our results using regression-based methods from marginal genome-wide association study summary statistics. We also report realistic scenarios where regression-based methods yield inflated heterogeneity-by-ancestry due to ancestry-specific tagging of causal effects, and/or polygenicity. Our results motivate genetic analyses that assume minimal heterogeneity in causal effects by ancestry, with implications for the inclusion of ancestry-diverse individuals in studies.
Patrizicampa Conde 1962
Creators: name: Sendra, Alberto
name: Antić, Dragan
name: Barranco, Pablo
name: Borko, Špela
name: Christian, Erhard
name: Delić, Teo
name: Fadrique, Floren
name: Faille, Arnaud
name: Galli, Loris
name: Gasparo, Fulvio
name: Georgiev, Dilian
name: Giachino, Pier Mauro
name: Kovac, L'ubomír
name: Lukić, Marko
name: Marcia, Paolo
name: Miculinić, Kazimir
name: Nicolosi, Giuseppe
name: Palero, Ferran
name: Paragamian, Kaloust
name: Pérez, Toni
name: Polak, Slavko
name: Prieto, Carlos E.
name: Turbanov, Ilya
name: Vailati, Dante
name: Reboleira, Ana Sofia P. S.
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplura
Campodeidae
Patrizicampa

description: Patrizicampa Condé, 1962
Patrizicampa Condé, 1962: 199.
Diagnosis (Condé 1962)
Without dorsal femoral macrosetae or ventral tibial macrosetae; abundant macrosetae on all urosternites, including 3+3 macrosetae on urosternite VIII. Its apomorphic feature, the shape of the laminar pretarsal lateral process, is unique among diplurans. It starts with a large laminar lateral process, well barbed on the ventral side and ending in a thin, smooth, pointed process.
description: Published as part of Sendra, Alberto, Antić, Dragan, Barranco, Pablo, Borko, Špela, Christian, Erhard, Delić, Teo, Fadrique, Floren, Faille, Arnaud, Galli, Loris, Gasparo, Fulvio, Georgiev, Dilian, Giachino, Pier Mauro, Kovac, L'ubomír, Lukić, Marko, Marcia, Paolo, Miculinić, Kazimir, Nicolosi, Giuseppe, Palero, Ferran, Paragamian, Kaloust, Pérez, Toni, Polak, Slavko, Prieto, Carlos E., Turbanov, Ilya, Vailati, Dante & Reboleira, Ana Sofia P. S., 2020, Flourishing in subterranean ecosystems: Euro-Mediterranean Plusiocampinae and tachycampoids (Diplura, Campodeidae), pp. 1-138 in European Journal of Taxonomy 591 on page 12, DOI: 10.5852/ejt.2020.591, http://zenodo.org/record/3659823
Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations
Creators: name: Arevalo, J.
name: Buetow, K.
name: Rodriguez, D.E.
name: Ayroles, J.F.
name: Cole, S.W.
name: Hooper, P.L.
name: Kaplan, H.
name: Kraft, T.
name: Gurven, M.D.
name: Gutierrez, M.
name: Stieglitz, J.
name: Lea, A.J.
name: Garcia, A.
name: Highland, H.M.
name: Trumble, B.C.
name: Justice, A.
name: North, K.E.
Publisher: name: National Academy of Sciences
Year: 2023

description: A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype-phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as well as minimal cardiometabolic disease or dementia. We therefore generated genome-wide genotype data for Tsimane individuals to study natural selection, and paired this with blood mRNA-seq as well as cardiometabolic and immune biomarker data generated from a larger sample that included both populations. In the Tsimane, we identified 21 regions that are candidates for selective sweeps, as well as 5 immune traits that show evidence for polygenic selection (e.g., C-reactive protein levels and the response to coronaviruses). Genes overlapping candidate regions were strongly enriched for known involvement in immune-related traits, such as abundance of lymphocytes and eosinophils. Importantly, we were also able to draw on extensive phenotype information for the Tsimane and Moseten and link five regions (containing PSD4, MUC21 and MUC22, TOX2, ANXA6, and ABCA1) with biomarkers of immune and metabolic function. Together, our work highlights the utility of pairing evolutionary analyses with anthropological and biomedical data to gain insight into the genetic basis of health-related traits.
title: Rencontre Université Prison : La place du numérique - 2016
Publisher: name: Université Paul-Valéry Montpellier 3 - IDEFI / Initiative d'Excellence en Formations Innovantes
Year: 2016

description: La première Rencontre Université – Prison (RUP) organisée par l’Université Paul-Valéry Montpellier 3 propose à ses participants d’échanger sur les problématiques relatives à l’accès, la transmission, la médiatisation et l’apprentissage des savoirs et savoir-faire destinés à un public spécifque, en particulier les personnes placées sous main de justice.
Cumulative socioeconomic status and incident type 2 diabetes among African American adults from the Jackson heart study
Creators: name: Green-Howard, A.
name: Adatorwovor, R.
name: Glover, L.M.
name: Loehr, L.
name: Staley-Salil, B.
name: Sims, M.
name: North, K.E.
name: Martin, C.L.
Publisher: name: Elsevier Ltd
Year: 2023

description: Background: The cumulative socioeconomic status (SES) model posits that childhood and adult experiences accumulate to influence disease risk. While individual SES indicators such as education and income are independently associated with incident type 2 diabetes (T2D), the association of cumulative SES and incident T2D is unclear, especially in African American adults. Methods: We utilized cohort data of African American participants (n = 3681, mean age 52.6 years) enrolled in the Jackson Heart Study from 2000 to 2013 free of T2D or cardiovascular disease at baseline (2000–2004). Cumulative SES scores at baseline were derived using six SES indicators (education, wealth, income, occupation, employment status, and mother's education) categorized as low, middle, and high. Incident T2D was defined at exam 2 (2005–2008) or exam 3 (2009–2013) based on fasting glucose ≥126 mg/dL, HbA1c ≥ 6.5, reported diabetic medication use, or self-reported physician diagnosis. Proportional hazards regression, allowing for interval censoring, was used to estimate the association between cumulative SES and incident T2D (hazard ratio(HR), 95% confidence interval (CI)) after adjustment for covariates. Sex and age differences were tested using interaction terms. Results: There were 544 incident T2D cases. The association between low (versus high) cumulative SES and incident T2D was not significant (HR 1.04 [95% CI 0.85, 1.28]) and did not differ by sex (p value for interaction>0.05). However, there were differences by (age p value for interaction = 0.0052 for middle-aged adults and 0.0186 for older adults). Low (versus high) cumulative SES was associated a greater hazard of incident T2D among those 20–46 years (HR 1.12 [95% CI 1.03, 1.21]), 47–59 years (HR 1.25 [95% CI 1.06, 1.47]) and those 60–93 years (HR 1.39 [95% CI 1.09, 1.78]) after adjustment for sex and family history of diabetes. Associations attenuated after adding behavioral and lifestyle risk factors. Conclusion: The association of low cumulative SES and incident T2D differed by age, which may suggest interventionist should consider impacts of SES on T2D by age.
Antimicrobial activity of plant extracts against sexually transmitted pathogens
Creators: name: Jadhav, Nutan
name: Kulkarni, Sangeeta
name: Arati Mane
name: Kulkarni, Roshan
name: Palshetker, Aparna
name: Kamalinder Singh
name: Joshi, Swati
name: Risbud, Arun
name: Kulkarni, Smita
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: Plant Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Cancer
subject: Biological Sciences
subject: Ecology
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Biotechnology
subject: Pharmacology
subject: Molecular Biology
subject: Cell Biology
subject: Biochemistry

description: Comprehensive management of sexually transmitted infections (STIs) using vaginal or rectal microbicide-based intervention is one of the strategies for prevention of HIV infection. Herbal products have been used for treating STIs traditionally. Herein, we present in vitro activity of 10 plant extracts and their 34 fractions against three sexually transmitted/reproductive tract pathogens – Neisseria gonorrhoeae, Haemophilus ducreyi and Candida albicans. The plant parts were selected; the extracts/fractions were prepared and screened by disc diffusion method. The minimum inhibitory and minimum cidal concentrations were determined. The qualitative phytochemical analysis of selected extracts/fractions showing activity was performed. Of the extracts/fractions tested, three inhibited C. albicans, ten inhibited N. gonorrhoeae and five inhibited H. ducreyi growth. Our study demonstrated that Terminalia paniculata Roth. extracts/fractions inhibited growth of all three organisms. The ethyl acetate fraction of Syzygium cumini Linn. and Bridelia retusa (L.) Spreng. extracts was found to inhibit N. gonorrhoeae at lowest concentrations.
متطلبات تنمية استراتيجيات مواجهة التنمر السيبراني لتعزيز الامن الفكري الاخلاقي والديني  في ظل الجائحة لدى عينة من الشباب؛ دراسة ميدانية
Creators: name: علة نذير, عيشة
Publisher: name: Humanities Commons
Year: 2022

description: الهدف من هذه الدراسة هو تحديد متطلبات تنمية استراتيجيات مواجهة التنمر السيبراني لتعزيز الأمن الفكري الاخلاقي والديني في ظل الجائحة لدى عينة من الشباب، وأيضا طبيعة الفروق حسب المتغيرات الديموغرافية التالية: (النوع)، وتكونت العينة من 300 فرد بواقع الإناث=150 والذكور=150؛ وقد اشتملت أدوات الدراسة على مقياس استراتيجيات مواجهة التنمر السيبراني من إعداد الباحثة ومقياس الفكر الامني اعداد رباب (2021)، تمّ اعتماد المنهج الوصفي، وقد أسفرت الدراسة على النتائج التالية: -	يمكن التنبؤ بمتطلبات تنمية استراتيجيات مواجهة التنمر السيبراني لتعزيز الأمن الفكري الاخلاقي والديني في ظل الجائحة لدى عينة من الشباب من خلال محاور الأمن الفكري. -	ليس هناك فروق دالة إحصائياً عند (α ≥ 0.01) في متوسط درجات متطلبات تنمية استراتيجيات مواجهة التنمر السيبراني لتعزيز الأمن الفكري الاخلاقي والديني في ظل الجائحة لدى عينة من الشباب تعزى لمتغير الجنس.
Social and scientific motivations to move beyond groups in allele frequencies: The TOPMed experience
Creators: name: Rich, S.S.
name: Mitchell, B.D.
name: Nelson, S.C.
name: Isasi, C.R.
name: North, K.E.
name: Taylor, M.R.G.
name: Sofer, T.
name: Gogarten, S.M.
name: Fullerton, S.M.
name: Zöllner, S.
Publisher: name: Cell Press
Year: 2022

description: For the genomics community, allele frequencies within defined groups (or “strata”) are useful across multiple research and clinical contexts. Benefits include allowing researchers to identify populations for replication or “look up” studies, enabling researchers to compare population-specific frequencies to validate findings, and facilitating assessment of variant pathogenicity in clinical contexts. However, there are potential concerns with stratified allele frequencies. These include potential re-identification (determining whether or not an individual participated in a given research study based on allele frequencies and individual-level genetic data), harm from associating stigmatizing variants with specific groups, potential reification of race as a biological rather than a socio-political category, and whether presenting stratified frequencies—and the downstream applications that this presentation enables—is consistent with participants’ informed consents. The NHLBI Trans-Omics for Precision Medicine (TOPMed) program considered the scientific and social implications of different approaches for adding stratified frequencies to the TOPMed BRAVO (Browse All Variants Online) variant server. We recommend a novel approach of presenting ancestry-specific allele frequencies using a statistical method based upon local genetic ancestry inference. Notably, this approach does not require grouping individuals by either predominant global ancestry or race/ethnicity and, therefore, mitigates re-identification and other concerns as the mixture distribution of ancestral allele frequencies varies across the genome. Here we describe our considerations and approach, which can assist other genomics research programs facing similar issues of how to define and present stratified frequencies in publicly available variant databases.
Huperzine A production by Paecilomyces tenuis YS-13, an endophytic fungus isolated from Huperzia serrata
Creators: name: Jingqian Su
name: Minhe Yang
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Biotechnology
subject: Pharmacology
subject: Microbiology
subject: Biochemistry

description: Huperzine A (HupA), a naturally occurring alkaloid in the plant family Huperziaceae, has drawn great interest for its potential application in Alzheimer disease therapy. Our primary objective was to identify alkaloid- and HupA-producing fungi from the Chinese folk herb, Huperzia serrata. We established a rapid and efficient model for screening HupA-producing endophytic fungal strains. The presence of HupA in Paecilomyces tenuis YS-13 was analysed by thin-layer chromatography, high-performance liquid chromatography and mass spectrometry. The fermentation yield of HupA was 21.0 μg/L, and the IC50 of the crude extract of YS-13 fermentation broth was 1.27 ± 0.04 mg/mL. This is the first report of P. tenuis as a HupA-producing endophyte isolated from Huperziaceae.
Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing
Creators: name: Bielak, L.F.
name: Psaty, B.M.
name: Peralta, J.M.
name: Barr, R.G.
name: Hobbs, B.D.
name: Levy, D.
name: McGarvey, S.T.
name: Bis, J.C.
name: Hawley, N.L.
name: Lutz, S.M.
name: Minster, R.L.
name: Blangero, J.
name: He, J.
name: Becker, D.M.
name: Kaufman, J.D.
name: Weissenkampen, J.D.
name: Sheu, W.H.-H.
name: Sun, X.
name: Sims, M.
name: Weir, D.R.
name: Yanek, L.R.
name: Liu, D.J.
name: Jaffe, A.E.
name: Jiang, B.
name: Deka, R.
name: Fuentes, L.
name: Khunsriraksakul, C.
name: Wang, X.
name: Rotter, J.I.
name: Quach, B.C.
name: Reupena, M.S.
name: Rafaels, N.
name: Young, K.A.
name: Yang, L.
name: Weeks, D.E.
name: Lee, I.-T.
name: Moussa, K.A.
name: Smith, J.A.
name: Martin, L.W.
name: Duggirala, R.
name: Marx, O.
name: Chen, Y.-D.I.
name: Chasman, D.I.
name: Hyde, T.M.
name: Chavan, S.
name: Kooperberg, C.
name: Peyser, P.A.
name: Ashley-Koch, A.E.
name: Hall, M.E.
name: Hsiung, C.A.
name: Hwang, S.-J.
name: Chen, F.
name: Arnett, D.K.
name: Jang, S.-K.
name: Barnes, K.C.
name: Kardia, S.L.R.
name: Shadyab, A.H.
name: Schwartz, D.A.
name: Gharib, S.A.
name: Guo, X.
name: Hokanson, J.E.
name: Hancock, D.B.
name: Johnson, E.O.
name: Vrieze, S.
name: Curran, J.E.
name: Kaplan, R.
name: David, S.P.
name: Sauteraud, R.
name: Correa, A.
name: North, K.E.
name: Allred, N.D.D.
name: Oelsner, E.C.
name: Raffield, L.M.
name: Telen, M.J.
name: Rich, S.S.
name: Watson, H.
name: Young, K.L.
name: Albert, C.M.
name: Taylor, K.D.
name: Zhao, W.
name: Naseri, T.
name: Moll, M.
name: Manichaikul, A.W.
name: Faul, J.D.
name: Garrett, M.E.
name: Boorgula, M.P.
name: Chuang, L.-M.
name: Kelly, T.N.
name: Kleinman, J.E.
name: Irvin, M.R.
Publisher: name: Nature Research
Year: 2023

description: Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.
title: Crisis of the soul
title: a studio based enquiry in painting
titleType: Subtitle
Creators: name: Tripp, Freya
Publisher: name: Charles Darwin University
Year: 2015

description: For this research project I sought to investigate ways in which to engage with the painted space, in order to explore relational aspects of my own human experience. I sought to attain visual evocations - thinking through painting - as a way of attending to anxieties that are symptomatic of ongoing processes of realignment. This body of visual research is aimed at contributing to the field of oil painting through an exploration of the painting process as it pertains to visual practice. Furthermore, the experience of that process for a range of artists who use oil painting as a means to express ideas related to both socio-political and personal experience. I ask “can painting, and in particular oil painting - as evidenced by historical and contemporary painters - be an effective method for exploring existential anxiety and relational aspects of ones own human experience? How might the work of other painters inform my approach to formulating my own visual language and theoretical concepts? The methodology I employed used oil painting techniques such as Alla Prima painting, glazing, Tenebrism and Chiaroscuro effects as the catalyst for producing a volume of paintings, before arriving at a select series for exhibition. The development of this body of work is supported through research and critical engagement with the historical and contemporary practices of Francisco de Goya, Albert Tucker, Odd Nerdrum, Ben Quilty and Billy Benn Perurrle. It has drawn on the writings of Mikhail Bakhtin and Alain de Botton as well as Kitsch painting, Grotesque aesthetics and the tradition of Vanitas and Still Life painting. A small number of paintings for exhibition, formed from a rigorous research process, comprise fully resolved artworks and demonstrate considerable conceptual and painterly skill. Painted in Arrernte country (Mbantua/Alice Springs) and exhibited an Nan Geise Gallery Darwin, the exhibition was thoughtfully curated and installed in a way that integrated seemingly disparate subject matter into a cohesive whole.
Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries
Creators: name: Kenny, E.
name: Haiman, C.
name: Ramachandran, S.
name: Wojcik, G.
name: Zhang, S.
name: Peters, U.
name: Shahamatdar, S.
name: Crawford, L.
name: Gignoux, C.
name: Graff, M.
name: Smith, S.P.
name: North, K.E.
name: Matise, T.C.
name: Paik, J.
name: Cheng, W.
Publisher: name: Cell Press
Year: 2022

description: Since 2005, genome-wide association (GWA) datasets have been largely biased toward sampling European ancestry individuals, and recent studies have shown that GWA results estimated from self-identified European individuals are not transferable to non-European individuals because of various confounding challenges. Here, we demonstrate that enrichment analyses that aggregate SNP-level association statistics at multiple genomic scales—from genes to genomic regions and pathways—have been underutilized in the GWA era and can generate biologically interpretable hypotheses regarding the genetic basis of complex trait architecture. We illustrate examples of the robust associations generated by enrichment analyses while studying 25 continuous traits assayed in 566,786 individuals from seven diverse self-identified human ancestries in the UK Biobank and the Biobank Japan as well as 44,348 admixed individuals from the PAGE consortium including cohorts of African American, Hispanic and Latin American, Native Hawaiian, and American Indian/Alaska Native individuals. We identify 1,000 gene-level associations that are genome-wide significant in at least two ancestry cohorts across these 25 traits as well as highly conserved pathway associations with triglyceride levels in European, East Asian, and Native Hawaiian cohorts.
Quantitative discursive institutionalism: a comparison of labour market policy discourse across Western Europe
Creators: name: Wueest, Bruno
name: Fossati, Flavia
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Science Policy
subject: Cancer
subject: Immunology
subject: FOS: Clinical medicine
subject: Sociology
subject: FOS: Sociology
subject: Cell Biology
subject: Medicine

description: ABSTRACTCalls for more generalizable empirical examinations rank among the top priorities of discursive institutionalists. However, there are hardly any approaches that address the specific challenges of such examinations with regard to the systematic comparison of public discourses across countries. This contribution first develops a methodological framework for a comprehensive study of public discourse and subsequently applies it to study labour market policy discourse in six Western European countries from 2004 until 2006. Subsequently, the frame analysis shows that ideas brought forward in these public discourses relate to the three major concepts identified by the comparative political economy literature: corporatism; neoliberalism; and compensation. Furthermore, the findings corroborate the expectations derived from the discursive institutionalist literature, since the salience of the frames does systematically vary according to the institutional legacies of the countries, as well as to the interests of the actors involved.
Design, synthesis and structure of uranyl coordination polymers from 2-D layer to 3-D network structure
Creators: name: Wei, Si Yue
name: Bai, Feng Ying
name: Hou, Ya Nan
name: Zhang, Xiao Xi
name: Xu, Xue Ting
name: Wang, Ji Xiao
name: Zhang, Huan Zhi
name: Xing, Yong Heng
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Biological Sciences
Chemistry
Physics
Biochemistry
Biophysics

description: Solvothermal reaction of uranyl acetate and succinic acid in DMF resulted in formation of three uranyl coordination polymers, [(UO2)4(μ2-OH)7(OH)6]·2(H2O)·(H3O)·4NH2(CH3)2 (1), [(UO2)(μ2-OH)(OH)3]·2NH2(CH3)2] (2), and [(DMF)2(UO2)(μ2-OH)4(UO2))] (3). The products were characterized by elemental analysis, IR spectroscopy, X-ray single crystal, and powder diffraction. Structural analysis shows that 1 is a layer, 2 and 3 are 3-D network structures.
Participatory development of decision support systems: which features of the process lead to improved uptake and better outcomes?
Creators: name: Valls-Donderis, Pablo
name: Ray, Duncan
name: Peace, Andrew
name: Stewart, Amy
name: Lawrence, Anna
name: Galiana, Francisco
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Science Policy
Developmental Biology
Biological Sciences
Earth and Environmental Sciences
Engineering

description: Decision support systems (DSSs) are important in decision-making environments with conflicting interests. Many DSSs developed have not been used in practice. Experts argue that these tools do not respond to real user needs and that the inclusion of stakeholders in the development process is the solution. However, it is not clear which features of participatory development of DSSs result in improved uptake and better outcomes. A review of papers, reporting on case studies where DSSs and other decision tools (information systems, software and scenario tools) were developed with elements of participation, was carried out. The cases were analysed according to a framework created as part of this research; it includes criteria to evaluate the development process and the outcomes. Relevant aspects to consider in the participatory development processes include establishing clear objectives, timing and location of the process; keeping discussions on track; favouring participation and interaction of individuals and groups; and challenging creative thinking of the tool and future scenarios. The case studies that address these issues show better outcomes; however, there is a large degree of uncertainty concerning them because developers have typically neither asked participants about their perceptions of the processes and resultant tools nor have they monitored the use and legacy of the tools over the long term.
Ensuring the validity of private forest owner typologies by controlling for response style bias and the robustness of statistical methods
Creators: name: Ficko, Andrej
name: Bončina, Andrej
Publisher: name: Taylor & Francis
Year: 2014
Subjects: subject: Science Policy
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Engineering

description: In survey-based segmentation of forest owners, two threats to the validity of results have largely been ignored: (1) response style bias and (2) the robustness of the statistical methods. This study demonstrates response style bias detection, presents an approach for correcting for acquiescence – the systematic tendency to agree with survey items, and explores the sensitivity of a probabilistic clustering algorithm to requirements for the validity of the typology. Structural equation modeling and Monte Carlo data generation techniques were employed to detect acquiescence and estimate its effect on construct validity. A survey of the relevance of management information for private forest owners (N = 364) was used as an example. Although acquiescence was confirmed, it had minor effect on the results and no effect on the substantive construct. Uncertainty about the number of forest owner types and membership can be reduced by using probabilistic clustering and observing the number of clusters while changing the requirements for the validity of clusters. The expectation maximization algorithm proved to be robust even to stringent requirements for the validity of clusters. By controlling for response style and the robustness of statistical methods, the validity of private forest owner typologies can be better ensured.
Participatory development of decision support systems: which features of the process lead to improved uptake and better outcomes?
Creators: name: Valls-Donderis, Pablo
name: Ray, Duncan
name: Peace, Andrew
name: Stewart, Amy
name: Lawrence, Anna
name: Galiana, Francisco
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Science Policy
Developmental Biology
Biological Sciences
Earth and Environmental Sciences
Engineering

description: Decision support systems (DSSs) are important in decision-making environments with conflicting interests. Many DSSs developed have not been used in practice. Experts argue that these tools do not respond to real user needs and that the inclusion of stakeholders in the development process is the solution. However, it is not clear which features of participatory development of DSSs result in improved uptake and better outcomes. A review of papers, reporting on case studies where DSSs and other decision tools (information systems, software and scenario tools) were developed with elements of participation, was carried out. The cases were analysed according to a framework created as part of this research; it includes criteria to evaluate the development process and the outcomes. Relevant aspects to consider in the participatory development processes include establishing clear objectives, timing and location of the process; keeping discussions on track; favouring participation and interaction of individuals and groups; and challenging creative thinking of the tool and future scenarios. The case studies that address these issues show better outcomes; however, there is a large degree of uncertainty concerning them because developers have typically neither asked participants about their perceptions of the processes and resultant tools nor have they monitored the use and legacy of the tools over the long term.
Novel diabetes gene discovery through comprehensive characterization and integrative analysis of longitudinal gene expression changes
Creators: name: North, K.E.
name: Petty, L.E.
name: Below, J.E.
name: Gamazon, E.R.
name: Chen, H.-H.
name: Fisher-Hoch, S.P.
name: McCormick, J.B.
Publisher: name: Oxford University Press
Year: 2022

description: Type 2 diabetes is a complex, systemic disease affected by both genetic and environmental factors. Previous research has identified genetic variants associated with type 2 diabetes risk; however, gene regulatory changes underlying progression to metabolic dysfunction are still largely unknown. We investigated RNA expression changes that occur during diabetes progression using a two-stage approach. In our discovery stage, we compared changes in gene expression using two longitudinally collected blood samples from subjects whose fasting blood glucose transitioned to a level consistent with type 2 diabetes diagnosis between the time points against those who did not with a novel analytical network approach. Our network methodology identified 17 networks, one of which was significantly associated with transition status. This 822-gene network harbors many genes novel to the type 2 diabetes literature but is also significantly enriched for genes previously associated with type 2 diabetes. In the validation stage, we queried associations of genetically determined expression with diabetes-related traits in a large biobank with linked electronic health records. We observed a significant enrichment of genes in our identified network whose genetically determined expression is associated with type 2 diabetes and other metabolic traits and validated 31 genes that are not near previously reported type 2 diabetes loci. Finally, we provide additional functional support, which suggests that the genes in this network are regulated by enhancers that operate in human pancreatic islet cells. We present an innovative and systematic approach that identified and validated key gene expression changes associated with type 2 diabetes transition status and demonstrated their translational relevance in a large clinical resource.
Design, synthesis and structure of uranyl coordination polymers from 2D layer to 3D network structure
Creators: name: Wei, Si Yue
name: Bai, Feng Ying
name: Hou, Ya Nan
name: Zhang, Xiao Xi
name: Xu, Xue Ting
name: Wang, Ji Xiao
name: Zhang, Huan Zhi
name: Xing, Yong Heng
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Biological Sciences
Chemistry
Physics
Biochemistry
Biophysics

description: Solvothermal reaction of uranyl acetate and succinic acid in DMF resulted in formation of three uranyl coordination polymers, [(UO2)4(μ2-OH)7(OH)6]·2(H2O)·(H3O)·4NH2(CH3)2 (1), [(UO2)(μ2-OH)(OH)3]·2NH2(CH3)2] (2) and [(DMF)2(UO2)(μ2-OH)4(UO2))] (3). The products were characterized by elemental analysis, IR spectroscopy, X-ray single-crystal and powder diffraction. Structural analysis shows that 1 is a layer, 2 and 3 are 3D network structures.
Ensuring the validity of private forest owner typologies by controlling for response style bias and the robustness of statistical methods
Creators: name: Ficko, Andrej
name: Bončina, Andrej
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Science Policy
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Engineering

description: In survey-based segmentation of forest owners, two threats to the validity of results have largely been ignored: (1) response style bias and (2) the robustness of the statistical methods. This study demonstrates response style bias detection, presents an approach for correcting for acquiescence – the systematic tendency to agree with survey items, and explores the sensitivity of a probabilistic clustering algorithm to requirements for the validity of the typology. Structural equation modeling and Monte Carlo data generation techniques were employed to detect acquiescence and estimate its effect on construct validity. A survey of the relevance of management information for private forest owners (N = 364) was used as an example. Although acquiescence was confirmed, it had minor effect on the results and no effect on the substantive construct. Uncertainty about the number of forest owner types and membership can be reduced by using probabilistic clustering and observing the number of clusters while changing the requirements for the validity of clusters. The expectation maximization algorithm proved to be robust even to stringent requirements for the validity of clusters. By controlling for response style and the robustness of statistical methods, the validity of private forest owner typologies can be better ensured.
Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative
Creators: name: Thibord, F.
name: Wheeler, M.
name: Broome, J.
name: Manichaikul, A.
name: Blangero, J.
name: Heard-Costa, N.
name: Li, Y.
name: Hou, L.
name: Thornton, T.
name: Surendran, P.
name: Ryan, K.
name: Brody, J.A.
name: Mchugh, C.
name: Fornage, M.
name: Chami, N.
name: Almasy, L.
name: Reiner, A.P.
name: O'connell, J.R.
name: Nickerson, D.A.
name: Blackwell, T.W.
name: Lewis, J.P.
name: Smith, N.L.
name: Tang, H.
name: Yanek, L.R.
name: Jorgenson, E.
name: Jain, D.
name: Lloyd-Jones, D.M.
name: Ekunwe, L.
name: Wang, Z.
name: Glahn, D.C.
name: De Vries, P.S.
name: Conomos, M.P.
name: Auer, P.L.
name: Laurie, C.A.
name: Correa, A.
name: Butterworth, A.S.
name: Mitchell, B.D.
name: Choquet, H.
name: Pankratz, N.
name: Rich, S.S.
name: Bhan, A.
name: Curran, J.E.
name: Faraday, N.
name: Abecasis, G.R.
name: Moon, J.-Y.
name: North, K.E.
name: Hobbs, B.D.
name: Kooperberg, C.
name: Smith, A.V.
name: Loos, R.J.F.
name: Hu, Y.
name: Beaty, T.H.
name: Preuss, M.H.
name: Tracy, R.P.
name: Morrison, A.C.
name: Mathias, R.A.
name: Boerwinkle, E.
name: Becker, L.C.
name: Psaty, B.M.
name: Little, A.
name: Min, Y.-I.
name: Sun, Q.
name: Johnson, A.D.
name: Rotter, J.I.
name: Raffield, L.M.
name: Vasan, R.S.
name: Chen, M.-H.
Publisher: name: Oxford University Press
Year: 2022

description: Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.