Miracle-dz/UniFAR-FTUs huggingface dataset:
The Only African Wild Tobacco, Nicotiana africana: Alkaloid Content and the Effect of Herbivory

Herbivory in some Nicotiana species is known to induce alkaloid production. This study examined herbivore-induced defenses in the nornicotine-rich African tobacco N. africana, the only Nicotiana species indigenous to Africa. We tested the predictions that: 1) N. africana will have high constitutive levels of leaf, flower and nectar alkaloids; 2) leaf herbivory by the African bollworm Helicoverpa armigera will induce increased alkaloid levels in leaves, flowers and nectar; and 3) increased alkaloid concentrations in herbivore-damaged plants will negatively affect larval growth. We grew N. africana in large pots in a greenhouse and exposed flowering plants to densities of one, three and six fourth-instar larvae of H. armigera, for four days. Leaves, flowers and nectar were analyzed for nicotine, nornicotine and anabasine. The principal leaf alkaloid was nornicotine (mean: 28 µg/g dry mass) followed by anabasine (4.9 µg/g) and nicotine (0.6 µg/g). Nornicotine was found in low quantities in the flowers, but no nicotine or anabasine were recorded. The nectar contained none of the alkaloids measured. Larval growth was reduced when leaves of flowering plants were exposed to six larvae. As predicted by the optimal defense theory, herbivory had a localized effect and caused an increase in nornicotine concentrations in both undamaged top leaves of herbivore damaged plants and herbivore damaged leaves exposed to one and three larvae. The nicotine concentration increased in damaged compared to undamaged middle leaves. The nornicotine concentration was lower in damaged leaves of plants exposed to six compared to three larvae, suggesting that N. africana rather invests in new growth as opposed to protecting older leaves under severe attack. The results indicate that the nornicotine-rich N. africana will be unattractive to herbivores and more so when damaged, but that potential pollinators will be unaffected because the nectar remains alkaloid-free even after herbivory.
Peer characteristics associated with improved glycemic control in a randomized controlled trial of a reciprocal peer support program for diabetes

Objective In a secondary analysis of a randomized controlled trial of diabetes reciprocal peer support, we examined characteristics of peers associated with improvements in their partner’s glycemic control. Methods A total of 102 adults with diabetes were randomized to the reciprocal peer support arm (vs. a nurse care management arm). The primary outcome was change in A1c over six months. Intermediate outcomes were insulin initiation and peer engagement. A number of baseline characteristics of peers were hypothesized to influence outcomes for their peer, and concordant characteristics of peer dyads were hypothesized that would influence outcomes for both peer partners. Results Improvement in A1c was associated with having a peer older than oneself (P < .05) or with higher diabetes-related distress (P < .01). Participants with peers who reported poorer health at baseline had worse glycemic control at follow-up (P < .01). Hypothesized concordant characteristics were not associated with A1c improvements. Participants whose peers had a more controlled self-regulation style were more likely to initiate insulin (P < .05). Discussion The improved outcomes of peers whose partners were older and reported more diabetes distress at baseline supports the need for further research into the peer characteristics that lead to improved outcomes. This could allow for better matching and more effective partnerships.
Crowdsourcing for Cognitive Science – The Utility of Smartphones

By 2015, there will be an estimated two billion smartphone users worldwide. This technology presents exciting opportunities for cognitive science as a medium for rapid, large-scale experimentation and data collection. At present, cost and logistics limit most study populations to small samples, restricting the experimental questions that can be addressed. In this study we investigated whether the mass collection of experimental data using smartphone technology is valid, given the variability of data collection outside of a laboratory setting. We presented four classic experimental paradigms as short games, available as a free app and over the first month 20,800 users submitted data. We found that the large sample size vastly outweighed the noise inherent in collecting data outside a controlled laboratory setting, and show that for all four games canonical results were reproduced. For the first time, we provide experimental validation for the use of smartphones for data collection in cognitive science, which can lead to the collection of richer data sets and a significant cost reduction as well as provide an opportunity for efficient phenotypic screening of large populations.
Smoking Is So Ew!: College Smokers’ Reactions to Health- Versus Social-Focused Antismoking Threat Messages

ABSTRACT This study utilizes Terror Management Theory (TMT) to examine differences between eliciting social death and physical death anxiety related to smoking, smoking attitudes, and quitting intent among college students. Moreover, an important TMT variable—self-esteem—was used as a moderator. A 2 × 3 between-subjects factorial design crossed smoking-based self-esteem (low, high) with mortality salience manipulation (health-focused, social-focused, control). Results suggest while both making health-focused salient and making social-focused mortality salient were effective at getting smokers to quit, there was less effect for health-focused mortality salience on those whose self-esteem is strongly tied to smoking. Effect of social-focused mortality salience was more pronounced among participants who highly linked self-esteem with smoking. For smokers with low smoking-based self-esteem, both health-focused and social-focused mortality salience were effective at motivating attitude change toward smoking and quitting intentions. Implications for smoking cessation ad design and TMT are discussed.
Shifts in the Spring Herring (Clupea harengus membras) Larvae and Related Environment in the Eastern Baltic Sea over the Past 50 Years

Because of the high management relevance, commercial fish related aspects have often been central in marine ecosystem investigations. The iterative shiftogram method was applied to detect occurrence, type and timing of shifts in the single and multivariate time series linked to the spring spawning herring larvae in the Gulf of Riga (Baltic Sea). Altogether nineteen larval herring and related environmental variables were utilized during the period of 1957–2010. All the time series investigated, either single or multivariate, exhibited one or more shifts with variable type and timing. Multivariate shiftogram based on all time series identified two distinct states (1957–1983 and 1992–2010) in studied variables, separated by a smooth transition period lasting almost ten years. The observed shift was mainly related to hydroclimate and not to phenology or biota. Significantly increased variability was found in larval herring and recruitment abundances after the shift. While the shift in hydroclimate (1985–1991) was followed by the shift in phenology (1991–1997), the shift in biota occurred remarkably later (2003). It is likely that the dynamics in biota were affected by other drivers than those investigated in the current paper.
A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila, and Humans

Letting Pyruvate In Transport of pyruvate is an important event in metabolism whereby the pyruvate formed in glycolysis is transported into mitochondria to feed into the tricarboxylic acid cycle (see the Perspective by Murphy and Divakaruni). Two groups have now identified proteins that are components of the mitochondrial pyruvate transporter. Bricker et al. (p. 96, published online 24 May) found that the proteins mitochondrial pyruvate carrier 1 and 2 (MPC1 and MPC2) are required for full pyruvate transport in yeast and Drosophila cells and that humans with mutations in MPC1 have metabolic defects consistent with loss of the transporter. Herzig et al. (p. 93, published online 24 May) identified the same proteins as components of the carrier in yeast. Furthermore, expression of the mouse proteins in bacteria conferred increased transport of pyruvate into bacterial cells. The genes encoding two components of the pyruvate transporter in mitochondria have been identified. Pyruvate constitutes a critical branch point in cellular carbon metabolism. We have identified two proteins, Mpc1 and Mpc2, as essential for mitochondrial pyruvate transport in yeast, Drosophila, and humans. Mpc1 and Mpc2 associate to form an ~150-kilodalton complex in the inner mitochondrial membrane. Yeast and Drosophila mutants lacking MPC1 display impaired pyruvate metabolism, with an accumulation of upstream metabolites and a depletion of tricarboxylic acid cycle intermediates. Loss of yeast Mpc1 results in defective mitochondrial pyruvate uptake, and silencing of MPC1 or MPC2 in mammalian cells impairs pyruvate oxidation. A point mutation in MPC1 provides resistance to a known inhibitor of the mitochondrial pyruvate carrier. Human genetic studies of three families with children suffering from lactic acidosis and hyperpyruvatemia revealed a causal locus that mapped to MPC1, changing single amino acids that are conserved throughout eukaryotes. These data demonstrate that Mpc1 and Mpc2 form an essential part of the mitochondrial pyruvate carrier.
Deep Gaussian Embedding of Graphs: Unsupervised Inductive Learning via Ranking

Methods that learn representations of nodes in a graph play a critical role in network analysis since they enable many downstream learning tasks. We propose Graph2Gauss - an approach that can efficiently learn versatile node embeddings on large scale (attributed) graphs that show strong performance on tasks such as link prediction and node classification. Unlike most approaches that represent nodes as point vectors in a low-dimensional continuous space, we embed each node as a Gaussian distribution, allowing us to capture uncertainty about the representation. Furthermore, we propose an unsupervised method that handles inductive learning scenarios and is applicable to different types of graphs: plain/attributed, directed/undirected. By leveraging both the network structure and the associated node attributes, we are able to generalize to unseen nodes without additional training. To learn the embeddings we adopt a personalized ranking formulation w.r. t. the node distances that exploits the natural ordering of the nodes imposed by the network structure. Experiments on real world networks demonstrate the high performance of our approach, outperforming state-of-the-art network embedding methods on several different tasks. Additionally, we demonstrate the benefits of modeling uncertainty - by analyzing it we can estimate neighborhood diversity and detect the intrinsic latent dimensionality of a graph.
Ligand binding to a G protein–coupled receptor captured in a mass spectrometer

Drug binding to the P2Y1 receptor prevents phosphorylation and competes with an endogenous ligand. G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptors belong to the largest family of membrane-embedded cell surface proteins and are involved in a diverse array of physiological processes. Despite progress in the mass spectrometry of membrane protein complexes, G protein–coupled receptors have remained intractable because of their low yield and instability after extraction from cell membranes. We established conditions in the mass spectrometer that preserve noncovalent ligand binding to the human purinergic receptor P2Y1. Results established differing affinities for nucleotides and the drug MRS2500 and link antagonist binding with the absence of receptor phosphorylation. Overall, therefore, our results are consistent with drug binding, preventing the conformational changes that facilitate downstream signaling. More generally, we highlight opportunities for mass spectrometry to probe effects of ligand binding on G protein–coupled receptors.
Sequential parallel comparison design with binary and time‐to‐event outcomes

Sequential parallel comparison design (SPCD) has been proposed to increase the likelihood of success of clinical trials especially trials with possibly high placebo effect. Sequential parallel comparison design is conducted with 2 stages. Participants are randomized between active therapy and placebo in stage 1. Then, stage 1 placebo nonresponders are rerandomized between active therapy and placebo. Data from the 2 stages are pooled to yield a single P value. We consider SPCD with binary and with time‐to‐event outcomes. For time‐to‐event outcomes, response is defined as a favorable event prior to the end of follow‐up for a given stage of SPCD. We show that for these cases, the usual test statistics from stages 1 and 2 are asymptotically normal and uncorrelated under the null hypothesis, leading to a straightforward combined testing procedure. In addition, we show that the estimators of the treatment effects from the 2 stages are asymptotically normal and uncorrelated under the null and alternative hypothesis, yielding confidence interval procedures with correct coverage. Simulations and real data analysis demonstrate the utility of the binary and time‐to‐event SPCD.
HIV-associated executive dysfunction in the era of modern antiretroviral therapy: A systematic review and meta-analysis

ABSTRACT Objective: While some reports suggest that HIV+ individuals continue to display executive function (EF) impairment in the era of cART, findings have been contradictory and appear to differ based on the aspect of EF being measured. To improve the understanding of how discrete executive abilities may be differentially affected or spared in the context of HIV infection, we conducted a systematic review and meta-analysis to (a) determine whether and to what extent HIV+ adults experience deficits in EFs, and (b) understand how demographic and clinical characteristics may modify the associations between HIV infection and executive abilities. Method: Studies comparing HIV+ and HIV-uninfected groups on measures of working memory, set-shifting, inhibition, decision-making, and apathy between 2000 and 2017 were identified from three databases. Effect sizes (Cohen’s d) were calculated using inverse variance weighted random effects models. Meta-regression was used to examine the moderating effect of demographic and clinical variables. Results: Thirty-seven studies (n = 3935 HIV+; n = 2483 HIV-uninfected) were included in the meta-analysis. Pooled effect sizes for deficits associated with HIV infection were small for domains of set-shifting (d = −0.34, 95% CI [−0.47, −0.20]) and inhibition (d = −0.31, 95% CI [−0.40, −0.21]), somewhat larger for measures of decision-making (d = −0.41, 95% CI [−0.53, −0.28]) and working memory (d = −0.42, 95% CI [−0.59, −0.29]), and largest for apathy (d = −0.87, 95% CI [−1.09, −0.66]). Meta-regression demonstrated that age, sex, education, current CD4 count, and substance dependence differentially moderated the effects of HIV infection on specific EFs. However, lower nadir CD4 count was the only variable associated with greater deficits in nearly all EF domains. Conclusions: Our results suggest that discrete domains of EF may be differentially affected by HIV infection and moderating demographic and clinical variables. These findings have implications for the development of targeted cognitive remediation strategies.
Ecology and Caudal Skeletal Morphology in Birds: The Convergent Evolution of Pygostyle Shape in Underwater Foraging Taxa

Birds exhibit a specialized tail that serves as an integral part of the flight apparatus, supplementing the role of the wings in facilitating high performance aerial locomotion. The evolution of this function for the tail contributed to the diversification of birds by allowing them to utilize a wider range of flight behaviors and thus exploit a greater range of ecological niches. The shape of the wings and the tail feathers influence the aerodynamic properties of a bird. Accordingly, taxa that habitually utilize different flight behaviors are characterized by different flight apparatus morphologies. This study explores whether differences in flight behavior are also associated with variation in caudal vertebra and pygostyle morphology. Details of the tail skeleton were characterized in 51 Aequornithes and Charadriiformes species. Free caudal vertebral morphology was measured using linear metrics. Variation in pygostyle morphology was characterized using Elliptical Fourier Analysis, a geometric morphometric method for the analysis of outline shapes. Each taxon was categorized based on flight style (flap, flap-glide, dynamic soar, etc.) and foraging style (aerial, terrestrial, plunge dive, etc.). Phylogenetic MANOVAs and Flexible Discriminant Analyses were used to test whether caudal skeletal morphology can be used to predict flight behavior. Foraging style groups differ significantly in pygostyle shape, and pygostyle shape predicts foraging style with less than 4% misclassification error. Four distinct lineages of underwater foraging birds exhibit an elongate, straight pygostyle, whereas aerial and terrestrial birds are characterized by a short, dorsally deflected pygostyle. Convergent evolution of a common pygostyle phenotype in diving birds suggests that this morphology is related to the mechanical demands of using the tail as a rudder during underwater foraging. Thus, distinct locomotor behaviors influence not only feather attributes but also the underlying caudal skeleton, reinforcing the importance of the entire caudal locomotor module in avian ecological diversification.
RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

Genetic selection for enhanced growth rate in meat-type chickens (Gallus domesticus) is usually accompanied by excessive adiposity, which has negative impacts on both feed efficiency and carcass quality. Enhanced visceral fatness and several unique features of avian metabolism (i.e., fasting hyperglycemia and insulin insensitivity) mimic overt symptoms of obesity and related metabolic disorders in humans. Elucidation of the genetic and endocrine factors that contribute to excessive visceral fatness in chickens could also advance our understanding of human metabolic diseases. Here, RNA sequencing was used to examine differential gene expression in abdominal fat of genetically fat and lean chickens, which exhibit a 2.8-fold divergence in visceral fatness at 7 wk. Ingenuity Pathway Analysis revealed that many of 1687 differentially expressed genes are associated with hemostasis, endocrine function and metabolic syndrome in mammals. Among the highest expressed genes in abdominal fat, across both genotypes, were 25 differentially expressed genes associated with de novo synthesis and metabolism of lipids. Over-expression of numerous adipogenic and lipogenic genes in the FL chickens suggests that in situ lipogenesis in chickens could make a more substantial contribution to expansion of visceral fat mass than previously recognized. Distinguishing features of the abdominal fat transcriptome in lean chickens were high abundance of multiple hemostatic and vasoactive factors, transporters, and ectopic expression of several hormones/receptors, which could control local vasomotor tone and proteolytic processing of adipokines, hemostatic factors and novel endocrine factors. Over-expression of several thrombogenic genes in abdominal fat of lean chickens is quite opposite to the pro-thrombotic state found in obese humans. Clearly, divergent genetic selection for an extreme (2.5–2.8-fold) difference in visceral fatness provokes a number of novel regulatory responses that govern growth and metabolism of visceral fat in this unique avian model of juvenile-onset obesity and glucose-insulin imbalance.
Negative Density Dependence Regulates Two Tree Species at Later Life Stage in a Temperate Forest

Numerous studies have demonstrated that tree survival is influenced by negative density dependence (NDD) and differences among species in shade tolerance could enhance coexistence via resource partitioning, but it is still unclear how NDD affects tree species with different shade-tolerance guilds at later life stages. In this study, we analyzed the spatial patterns for trees with dbh (diameter at breast height) ≥2 cm using the pair-correlation g(r) function to test for NDD in a temperate forest in South Korea after removing the effects of habitat heterogeneity. The analyses were implemented for the most abundant shade-tolerant (Chamaecyparis obtusa) and shade-intolerant (Quercus serrata) species. We found NDD existed for both species at later life stages. We also found Quercus serrata experienced greater NDD compared with Chamaecyparis obtusa. This study indicates that NDD regulates the two abundant tree species at later life stages and it is important to consider variation in species' shade tolerance in NDD study.
Mycobacterium tuberculosis Requires the ECF Sigma Factor SigE to Arrest Phagosome Maturation

SigE represents one of the best characterized alternative sigma factors of Mycobacterium tuberculosis, playing a major role in the response to several environmental stresses and essential for growth in macrophages and virulence. In previous work we demonstrated that a mutant of M. tuberculosis in which the sigE gene was disrupted by a cassette conferring hygromycin resistance is a promising vaccine candidate conferring better protection than Mycobacterium bovis BCG in a mouse model of infection. In this work we describe the construction of a new unmarked mutant in which the entire sigE gene was disrupted in order to fulfill the requirements of the Geneva consensus to enter clinical trials. After showing that the phenotype of this mutant is superimposable to that of the previous one, we further characterized the role of SigE in the M tuberculosis intracellular behavior showing that it is dispensable for replication in human pneumocytes, while it is essential for the arrest of phagosome maturation in THP-1-derived macrophages.