bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers
Authors: Wang Hui , Khera Pawan , Huang Bingyan , Yuan Mei , Katam Ramesh , Zhuang Weijian , Harris‐Shultz Karen , Moore Kim M. , Culbreath Albert K. , Zhang Xinyou , Varshney Rajeev K. , Xie Lianhui , Guo Baozhu 
Published: July 2015

AbstractCultivated peanut is grown worldwide as rich‐source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country‐wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.
The “Difficult Game” of Selling Brazilian Ethanol: Untangling Science–Business Relationships in the Global Biofuel Policy Nexus
Authors: Newberry Derek 
Published: July 2015

ResumenO etanol brasileiro tem sido criticado por seus potenciais contribuições à mudança climática, criando uma controvérsia científica com grandes implicações econômicas, sendo que o resultado vai afeitar políticas globais que regulam exportações dessa energia. Os cientistas brasileiros envolvidos neste conflito político são vistos como motivados por interesses econômicos e nacionais, devido à sua colaboração com representantes da indústria de cana de açúcar em influenciar a política internacional de biocombustíveis. Proponho que esse alinhamento é um fenômeno emergente que é formado pelo envolvimento desses cientistas num processo político que é percebido como dominado pelas preocupações e normas dos participantes americanos e europeios. Definindo redes de políticas internacionais assim, como ambientes institucionais que influenciam e restringem ativamente os interesses dos atores envolvidos, teremos uma análise mais útil de como "interesses brasileiros" em relação a questões como a produção de energia e mudança climática são formados e traduzidos em políticas públicas.
Fibroblast growth factor 2 mRNA expression evoked by amitriptyline involves extracellular signal‐regulated kinase‐dependent early growth response 1 production in rat primary cultured astrocytes
Authors: Kajitani Naoto , Hisaoka‐Nakashima Kazue , Okada‐Tsuchioka Mami , Hosoi Mayu , Yokoe Toshiki , Morioka Norimitsu , Nakata Yoshihiro , Takebayashi Minoru 
Published: July 2015

AbstractRecently, we demonstrated that several antidepressants including amitriptyline increased fibroblast growth factor 2 (FGF2) mRNA expression slowly over 24 h through de novo protein synthesis in rat primary cultured astrocytes. This study defined the signaling cascade that mediates amitriptyline‐induced FGF2 production in rat primary cultured astrocytes. Amitriptyline treatment significantly increased early growth response 1 (EGR1), a transcription factor known to regulate FGF2 expression. Knockdown of EGR1 using siRNA blocked amitriptyline‐evoked FGF2 mRNA expression. Treatment with several different classes of antidepressants leads to expression of EGR1 mRNA as well as FGF2 mRNA. These results confirm that EGR1 production is likely to be indispensable for the amitriptyline‐evoked FGF2 mRNA expression. Signal transduction inhibitors were used to elaborate the cellular signaling cascade that leads to EGR1‐mediated FGF2 expression following amitriptyline treatment. Amitriptyline‐evoked EGR1‐mediated FGF2 mRNA expression was blocked by mitogen‐activated protein kinase/extracellular signal‐regulated kinase kinase (MEK)1/2 inhibitor. Furthermore, extracellular signal‐regulated kinase/EGR1‐mediated FGF2 mRNA expression evoked by amitriptyline was blocked by inhibitors of the FGF receptor, epidermal growth factor receptor (EGFR), and matrix metalloproteinase. Taken together, these results demonstrate that amitriptyline increases FGF2 mRNA expression through a matrix metalloproteinase/receptor tyrosine kinases (RTK) (FGF receptor and EGFR)/extracellular signal‐regulated kinase/EGR1 signaling pathway in rat primary cultured astrocytes.
imageRecent studies suggest that fibroblast growth factor 2 (FGF2) is involved in the antidepressant effect in the model of depression. The production of ERK‐dependent early growth response 1 (EGR1) is a crucial part of the amitriptyline‐induced FGF2 expression signaling cascade in rat primary cultured astrocytes. The findings elaborate an astrocytic mechanism that could be used to develop antidepressants.
Early intervention with glucagon‐like peptide 1 analog liraglutide prevents tau hyperphosphorylation in diabetic db/db mice
Authors: Ma De‐Lin , Chen Fu‐Qiong , Xu Wei‐Jie , Yue Wen‐Zhu , Yuan Gang , Yang Yan 
Published: July 2015

AbstractIncreasing evidence has shown that type 2 diabetes (T2D) is a risk factor for Alzheimer's disease. Neurofibrillary tangles, which consist of hyperphosphorylated tau and misfolded microtubules, is one of the neuropathological hallmarks of Alzheimer's disease. Db/db mice, a rodent model of T2D, also exhibited age‐dependent tau hyperphosphorylation. Glucagon‐like peptide‐1 (GLP‐1) mimetics, a type of drug used in T2D, has been found to have neuroprotective effects. The aim of this study was to explore the potential effects of liraglutide (a GLP‐1 analog), or insulin, on tau phosphorylation in T2D animals. Male db/db mice (3–3.5 weeks) were daily injected subcutaneously with liraglutide (n = 27), insulin (n = 27), or saline (n = 26), and five to seven mice were killed every 2 weeks for analysis of plasma and cerebrospinal (CSF) insulin levels by ELISA, and protein levels in the hippocampal formation by western blot. We found that db/db mice treated with saline exhibited an age‐dependent decrease in CSF insulin and an increase in hippocampal tau phosphorylation. Liraglutide injection reversed the CSF insulin to ~1 mIU/L by the end of 8 weeks treatment, and prevented the hyperphosphorylation of tau protein in the hippocampal formation. By contrast, insulin injection had no effects on CSF insulin or phosphorylation of tau protein. In summary, this study indicates that early GLP‐1 analog intervention prevented the age‐dependent tau hyperphosphorylation in T2D mice brain, probably by facilitating sequential activation in an insulin signaling pathway reflected in increased basal activation of Akt and basal suppression of glycogen synthase kinase‐3 beta.
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We found that liraglutide, a GLP‐1 (glucagon‐like peptide‐1) analog, prevented the age‐dependent Alzheimer‐like tau hyperphosphorylation in diabetic db/db mice. We proposed that liraglutide crosses the blood–brain barrier, and binds GLP‐1 receptors from which G beta gamma dissociates intracellularly to activate PI3K, resulting in activation of Akt, which suppress GSK‐3β (glycogen synthase kinase‐3β), and thereby prevents it from phosphorylating tau. IRS‐1: insulin receptor substrate 1; IRS‐2: insulin receptor substrate 2; PI3K: phosphatidylinositol 3‐kinase.
Experience of self‐management of medications among older people with multimorbidity
Authors: Summer Meranius Martina , Engstrom Gabriella 
Published: July 2015

Aims and objectivesTo explore the experience of self‐managing medication among older people with multimorbidity.BackgroundOlder people with multimorbidity are now more likely to live at home and to self‐medicate. Reduced assistance from professional caregivers is associated with medical errors.DesignFace‐to‐face interviews were conducted with older people with multimorbidity.MethodsParticipants aged ≥75 years with ≥2 medical diagnoses and living at home or in special accommodation were interviewed. Twenty‐eight men and women (mean age 84 years) participated. Interviews lasted from 45 minutes–2 hours and were transcribed verbatim. A lifeworld‐based phenomenological method was used for analysis.ResultsUncertainty among the participants increased with their experience of side effects and concern that the medication might be harmful. These uncertainties were reinforced by a fear of malpractice when several physicians were involved. This meant living with ambivalence when taking the medication, which required a trade‐off between symptom relief and reducing side effects. A lack of continuity with physicians and nurses led to uncertainty in maintaining an overview of the medications. By contrast, when the relationships were supportive and caring, the uncertainties diminished. Four concepts were used to describe the various meanings of this experience: adapting to a new lifestyle; ambivalence towards medicine; experience of side effects and concerns about medical errors; and relationships as sources of feeling secure.ConclusionsMedications can cause side effects, and unclear benefits increase the uncertainty for older people with multimorbidity. Health care professionals need to develop an understanding of each patient's experience of such uncertainty.Relevance to clinical practiceHealth care professionals can give support and show understanding for older people's existential uncertainty by creating good relationships and continuity in care, and offering appropriate information. Regular visits should be scheduled to manage any problems patients might have when self‐medicating.
Nursing staffs' emotional well‐being and caring behaviours
Authors: Chana Navtej , Kennedy Paul , Chessell Zoë J 
Published: July 2015

Aims and objectivesTo examine the relationships between structural factors (work stressors), individual factors (demographics and the personal resources of resilience and social support) and transactional factors (appraisals and coping), and nursing staffs' levels of burnout, psychological distress and caring behaviours. A further aim was to examine the relationships between nursing staffs' levels of burnout and psychological distress and their caring behaviours.BackgroundBurnout and psychological distress levels have been found to be high in National Health Service nursing staff and furthermore this emotional distress has been found to affect patient care. In a National Health Service striving to provide high‐quality patient‐centred care, it is essential that factors affecting nursing staffs' well‐being and their caring behaviours are examined.DesignA cross‐sectional correlation‐based survey design.MethodsA sample of 102 nursing staff from an Acute National Health Service Trust were recruited in 2010. Participants completed the questionnaires: Nursing Stress Scale, Social Support Questionnaire‐Short Form, Connor and Davidson Resilience Scale‐2, Occupational Coping Self‐Efficacy Scale for Nurses, PsychNurse Scale, Maslach Burnout Inventory, The Hospital Anxiety and Depression Scale and Caring Behaviours Inventory‐revised. Due to the nonparametric nature of part of the data, Spearman's Rho correlations were used for analysis.ResultsDemographics were not found to be regularly correlated with nursing staffs' burnout, psychological distress or caring behaviours. Work stressors, coping strategies and self‐efficacy were found to be significantly correlated with nursing staffs' burnout and psychological distress. Caring behaviours were also correlated with coping strategies and self‐efficacy. Importantly, correlations were found between caring behaviours and nursing staffs' burnout and psychological distress.ConclusionIt is extremely important that the emotional well‐being of nursing staff is supported, both for them, and for the effect this has on patient care. Action points are suggested for National Health Service employers to enable this to happen.Relevance to clinical practiceTo address the poor emotional well‐being found, it is suggested that changes are needed within current clinical practice, for example through provision of enhanced training, use of model‐based clinical supervision and reviews conducted on staffing levels and workload issues.
A phase 1, randomized, dose‐ranging study of GS‐5816, a once‐daily NS5A inhibitor, in patients with genotype 1–4 hepatitis C virus
Authors: Lawitz E. , Freilich B. , Link J. , German P. , Mo H. , Han L. , Brainard D. M. , McNally J. , Marbury T. , Rodriguez‐Torres M. 
Published: July 2015

SummaryGS‐5816 is an inhibitor of the hepatitis C virus (HCV) NS5A protein that has demonstrated pan‐genotypic activity and a high barrier to resistance in HCV replicon assays. The aim of this study was to evaluate the safety, antiviral activity and pharmacokinetics of once‐daily doses of GS‐5816 in patients with genotype 1–4 HCV infection. Patients with genotype 1–4 HCV infection were randomized to 3 days of GS‐5816 at doses ranging from 5 to 150 mg or placebo. Adverse events were recorded, and plasma samples obtained for analysis of pharmacokinetics, HCV RNA and NS5A sequencing studies. GS‐5816 5–150 mg for 3 days was well tolerated and resulted in rapid declines in HCV RNA that were sustained over the dosing period. In patients treated with the 150 mg dose of GS‐5816, the mean maximal HCV RNA declines were 4.0, 4.0, 4.4, 3.3 and 3.5 log10 IU/mL in patients with genotype 1a, 1b, 2, 3 and 4 HCV infection, respectively. Pretreatment NS5A resistance‐associated polymorphisms were detected in 31% (22/70) of patients. Genotype 1 and 3 HCV‐infected patients without pretreatment NS5A resistance‐associated polymorphisms had greater declines in HCV RNA than patients with resistance‐associated polymorphisms. Plasma pharmacokinetics were supportive of once‐daily dosing. GS‐5816 demonstrated pangenotypic antiviral activity in patients with genotype 1‐4 HCV infection. It will be further evaluated in combination with other pangenotypic direct‐acting antivirals to achieve the goal of developing a well‐tolerated, highly effective treatment for all HCV genotypes.
Thromboelastographic Evaluation of Dogs with Acute Liver Disease
Authors: Kelley D. , Lester C. , Shaw S. , de Laforcade A. , Webster C.R.L. 
Published: July 2015

BackgroundGiven the liver's pivotal role in hemostasis and fibrinolysis, the coagulopathy accompanying hepatic disease is complex.Hypothesis/ObjectivesTo prospectively evaluate kaolin‐activated thromboelastography (TEG) in dogs with acute liver disease (ALD) and compare with plasma‐based coagulation tests.AnimalsTwenty‐one dogs with a diagnosis of ALD based on recent onset of clinical signs accompanied by increases in serum bilirubin concentration and alanine aminotransferase activity.MethodsClinical presentation, CBC, serum biochemistry, platelet count, prothrombin time (PT), activated partial thromboplastin time (aPTT), and TEG analysis were evaluated in 21 dogs with a subset also having fibrinogen, antithrombin (AT) activity, protein C (PC) activity, d‐dimers, and von Willebrand's factor (vWF) activity analyzed. A PT >1.5 times the upper limit of normal defined acute liver failure (ALF).ResultsDogs with ALD had mean increases in R, K, LY30, PT, aPTT, and vWF activity, and decreases in angle, maximal amplitude (MA), G, AT activity, and PC activity. The TEG results defined dogs as hypocoagulable (11/21), normocoagulable (8/21), or hypercoagulable (2/21). Increases in LY30 defined 8/21 dogs as hyperfibrinolytic. Hypocoagulable and hyperfibrinolytic dogs had lower fibrinogen and PC activity than dogs without these abnormalities. Overall, ALF dogs had greater increases in K and LY30, and decreases in MA, G, and PC activity than dogs with less severe hepatic impairment. Results for MA and LY30 were positively correlated with serum bilirubin concentration and white blood cell count, and negatively correlated with serum cholesterol concentration.Conclusions and Clinical ImportanceALD dogs have a range of coagulation abnormalities that trend toward hypocoagulability and hyperfibrinolysis as functional impairment occurs.
Supermarket Speak: Increasing Talk Among Low‐Socioeconomic Status Families
Authors: Ridge Katherine E. , Weisberg Deena Skolnick , Ilgaz Hande , Hirsh‐Pasek Kathryn A. , Golinkoff Roberta Michnick 
Published: July 2015

ABSTRACTChildren from low‐socioeconomic status (SES) families often fall behind their middle‐class peers in early language development. But interventions designed to support their language skills are often costly and labor‐intensive. This study implements an inexpensive and subtle language intervention aimed at sparking parent–child interaction in a place that families naturally visit: the supermarket. We placed signs encouraging adult–child dialogue in supermarkets serving low‐ and mid‐SES neighborhoods. Using an unobtrusive observational methodology, we tested how these signs affected adult–child interactions. When signs were present in supermarkets serving low‐SES neighborhoods, both the amount and the quality of talk between adults and children increased significantly, compared to when the signs were not present; signs had little effect in middle‐SES supermarkets. This study demonstrates that implementing simple, cost‐effective interventions in everyday environments may bolster children's language development and school readiness skills.
Diurnal and nocturnal transcriptomic variation in the Caribbean staghorn coral, Acropora cervicornis
Authors: Hemond Elizabeth M. , Vollmer Steven V. 
Published: July 2015

AbstractReef‐building corals experience large diel shifts in their environment, both externally due to changes in light intensity, predator activity and prey availability, and internally as a result of diel fluctuations in photosynthesis by their endosymbiotic algae, Symbiodinium. Diel patterns of tentacle behaviour, skeletal growth and gene expression indicate reactions of the coral animal in response to light and through circadian regulation. Some corals, such as the Caribbean Acroporas, have strong within‐colony division of labour, including specialized fast‐growing apical polyps, accompanied by large gene expression differences. Here we use RNA‐seq to evaluate how diel changes in gene expression vary within the branching Caribbean staghorn coral, Acropora cervicornis, between branch tips and branch bases. Multifactor generalized linear model analysis indicated that 6% (3005) of transcripts were differentially expressed between branch tips and bases, while 1% (441) of transcripts were differentially expressed between day and night. The gene expression patterns of 220 transcripts were affected by both time of day and location within the colony. In particular, photoreceptors, putative circadian genes, stress response genes and metabolic genes were differentially expressed between day and night, and some of these, including Amcry1, tef and hebp2, exhibited location‐specific regulation within the coral colony as well. These findings indicate that the genetic response of the coral to day and night conditions varies within the colony. Both time of day and location within the colony are factors that should be considered in future coral gene expression experiments.
A practical guide to environmental association analysis in landscape genomics
Authors: Rellstab Christian , Gugerli Felix , Eckert Andrew J. , Hancock Angela M. , Holderegger Rolf 
Published: July 2015

AbstractLandscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next‐generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced‐representation sequencing, candidate‐gene approaches, linearity of allele–environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies.
Bayesian inference of selection in a heterogeneous environment from genetic time‐series data
Authors: Gompert Zachariah 
Published: July 2015

AbstractEvolutionary geneticists have sought to characterize the causes and molecular targets of selection in natural populations for many years. Although this research programme has been somewhat successful, most statistical methods employed were designed to detect consistent, weak to moderate selection. In contrast, phenotypic studies in nature show that selection varies in time and that individual bouts of selection can be strong. Measurements of the genomic consequences of such fluctuating selection could help test and refine hypotheses concerning the causes of ecological specialization and the maintenance of genetic variation in populations. Herein, I proposed a Bayesian nonhomogeneous hidden Markov model to estimate effective population sizes and quantify variable selection in heterogeneous environments from genetic time‐series data. The model is described and then evaluated using a series of simulated data, including cases where selection occurs on a trait with a simple or polygenic molecular basis. The proposed method accurately distinguished neutral loci from non‐neutral loci under strong selection, but not from those under weak selection. Selection coefficients were accurately estimated when selection was constant or when the fitness values of genotypes varied linearly with the environment, but these estimates were less accurate when fitness was polygenic or the relationship between the environment and the fitness of genotypes was nonlinear. Past studies of temporal evolutionary dynamics in laboratory populations have been remarkably successful. The proposed method makes similar analyses of genetic time‐series data from natural populations more feasible and thereby could help answer fundamental questions about the causes and consequences of evolution in the wild.