Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatio‐temporal history of the endemic genera of Madagascar

Madagascar is renowned for its unparalleled species richness and levels of endemism, which have led, in combination with species extinction caused by an unprecedented rate of anthropogenic deforestation, to its designation as one of the most important biodiversity hotspots. It is home to 10 650 species (84% endemic) of angiosperms in 1621 genera (19% endemic). During the last two centuries, botanists have focused their efforts on the provision of a taxonomic framework for the flora of the island, but much remains to be investigated regarding the evolutionary processes that have shaped Madagascan botanical diversity. In this article, we review the current state of phylogenetic and biogeographical knowledge of the endemic angiosperm genera. We also propose a new stratified biogeographical model, based on palaeogeographical evidence, allowing the inference of the spatio-temporal history of Madagascan taxa. The implications of past climate change and extinction events on the evolutionary history of the endemic genera are also discussed in depth. Phylogenetic information was available for 184 of the 310 endemic genera (59.3%) and divergence time estimates were available for 67 (21.6%). Based on this evidence, we show the importance of phylogenetic clustering in the assemblage of the current Madagascan diversity (26% of the genera have a sister lineage from Madagascar) and confirm the strong floristic affinities with Africa, South-East Asia and India (22%, 9.1% and 6.2% of the genera, respectively). The close links with the Comoros, Mascarenes and Seychelles are also discussed. These results also support an Eocene/Oligocene onset for the origin of the Madagascan generic endemic flora, with the majority arising in the Miocene or more recently. These results therefore de-emphasize the importance of the Gondwanan break-up on the evolution of the flora. There is, however, some fossil evidence suggesting that recent extinctions (e.g. Sarcolaenaceae, a current Madagascan endemic, in southern Africa) might blur vicariance patterns and favour dispersal explanations for current biodiversity patterns. © 2013 The Linnean Society of London
CONDITIONS AFFECTING AUTOINDUCER-2-BASED QUORUM-SENSING OF ESCHERICHIA COLI O157:H7 ON FRESH BEEF

ABSTRACT This study evaluated whether inoculated (none, 1, 5 log colony-forming units [cfu]/cm2) Escherichia coli O157:H7 would result in detection of autoinducer (AI)-2-like activity on beef. Inoculated fresh beef, containing low (LNB) or high (HNB) initial levels of natural flora, was analyzed for bacterial populations and AI-2-like activity during aerobic or vacuum-packaged storage (4, 10, 25C). As expected, no growth of E. coli O157:H7 was detected at 4C, while at 10C, growth was detected only on LNB samples stored aerobically; AI-2-like activity was minimal (P ≥ 0.05) at both temperatures. E. coli O157:H7 showed more growth in LNB than HNB, and in aerobically than vacuum-packaged samples inoculated with 1 log cfu/cm2 of the pathogen during storage at 25C. AI-2-like activity was generally higher in LNB than HNB samples stored aerobically at 25C, while no significant AI-2-like activity was detected in samples stored in vacuum packages. The results indicated that E. coli O157:H7 may exhibit AI-2-like activity on aerobically stored beef in the presence of lower initial levels of natural flora, and at temperatures allowing prolific growth of the pathogen. Thus, AI-2-based quorum-sensing of E. coli O157:H7 may not be of importance in beef stored at low temperatures. PRACTICAL APPLICATIONS This study presents evidence that Escherichia coli O157:H7 showed autoinducer (AI)-2 activity and involved in quorum-sensing on fresh beefcontaining low initial levels of natural flora during aerobic storage at abusive storage temperatures. Thus, AI-2-based quorum-sensing of E. coli O157:H7 may not be important in beef stored at recommended low temperatures.
Rafting with Ebola

Lipid rafts are microdomains in the cell plasma membrane that are enriched in cholesterol, saturated fatty acids, and certain proteins. In a Perspective, [Freed][1] discusses new work published elsewhere showing that filoviruses, including the deadly human pathogens Ebola and Marburg, use these lipid rafts to infect host cells and to assemble new virus particles. [1]: http://www.sciencemag. org/cgi/content/full/296/5566/279
Dancing with Trojan horses: an interplay between the extracellular vesicles and viruses

Abstract Extracellular vesicles (EVs) are membrane-encapsulated particles released by eukaryotic and prokaryotic cells into the extracellular environment. Depending on their origin, size, and composition, EVs are grouped in several classes, with one of them being exosomes, which are small EVs (SEVs) generated within the endosomal compartment of eukaryotic cells via the unique multivesicular body pathway. Being able to deliver their content (proteins, lipids, small molecules, and nucleic acids) to other cells, exosomes/SEVs are considered as bioactive vesicles with multiple biological functions. Importantly, the composition of exosomes/SEVs depends on the cell and tissue of origin including a set of specific proteins. However, the pathological conditions may lead to the appearance of diseases-specific exosomes/SEVs containing pathology-specific cargoes utilized in the malicious cell-cell communication and spread of malady. Viruses demonstrate complex ‘dancing’ around the exosome biogenesis system, being able to hijack the host systems responsible for the exosome biogenesis. They use the exosome biogenesis system to promote packaging of their capsids, regulate virion production, and virus secretion. They also utilize a Trojan horse stratagem to place virions inside the SEVs and thereby to spread beyond their normal range of cell hosts using the normal EV uptake process. Another illustration of the virus-based utilization of Trojan horse strategy is given by the ability of human viruses to use exosomes/SEVs as carriers of their exogenous miRNA or viral proteins to the non-infected cells. Taken together, these strategies of dancing with Trojan horses can help viruses to fight with the host defense and to spread the infection. Communicated by Ramaswamy H. Sarma
A Qualitative Evaluation of Adverse Drug Reaction Reporting System in Pakistan: Findings from the Nurses’ Perspective

The contribution of all key healthcare professionals is vital to promote an efficient adverse drug reaction (ADR) reporting system. In this context, nurses are important as they are in a better position to observe a patient’s response regarding the drug therapy and to report an ADR. The aim of the study was to explore the perspectives of nurses about ADR reporting system in Lahore, Pakistan. A total of 21 nurses were interviewed. The thematic content analysis of the qualitative interviews yielded six major themes and eight subthemes. Major themes included: (1) Knowledge about the concept of the medication safety & the ADR; (2) Knowledge regarding pharmacovigilance activities; (3) Willingness to report; (4) Practices related to the ADR reporting; (5) Barriers to the ADR reporting; (6) Facilitators to the ADR reporting. The majority of the nurses were aware of medicine safety and ADRs, but in many cases, they were unable to report these ADRs. The study pointed out considerable concerns regarding the knowledge and practices of nurses about pharmacovigilance activities in their workplace, mainly due to increased workload, due to the absence of a reporting system and legal liability. The main challenges turned out to be the lack of knowledge and training, as well as the implementation of guidelines. Based on the findings, it is suggested that outcome of this study can serve as a guide to design policies that support ADR reporting by nurses in Pakistan.
Dietary behaviours and weight management: A thematic analysis of pregnant women's perceptions

Abstract Maternal obesity is associated with increased risk of gestational diabetes and other complications. Although antenatal interventions to help prevent these complications are ongoing, an understanding of overweight and obese pregnant women's opinions and attitudes is lacking. Therefore, this study aims to explore these women's experiences and perceptions of dietary behaviours and weight management during pregnancy. Secondary analysis of qualitative data originally collected to examine lifestyle behaviours in pregnant women was conducted. The data were from a purposive sample of overweight and obese pregnant women attending a public antenatal clinic in Cork, Ireland. The data were explored using thematic analysis. Interviews with 30 overweight and obese pregnant women were analysed. Three themes were developed relating to overweight and obese women's dietary behaviours and weight management perceptions including ‘pregnancy's influence on dietary behaviours’, ‘external influences on dietary behaviours’ and ‘perception of and preferences for weight related advice and resources’. Together these themes reveal women's experiences of diet and how pregnancy factors (physiological changes) and external factors (family and friends) can influence dietary behaviours. Furthermore, perceptions of weight management advice and lack thereof were highlighted with women drawing attention to potential resources for future use during pregnancy. This study provides important insights into overweight and obese pregnant women's dietary behaviours and perceptions of weight management. According to these findings, there is a need for clear and unambiguous information about weight management, acceptable weight gain, food safety and how to achieve a balanced diet.
DNA damage induced by an extract of Mangifera indica stem bark using in vitro Comet assay

The aqueous standard extract of Mangifera indica L stem bark (MSBE) is used as a food supplement in Cuba. In this study, the genotoxic effect of MSBE was measured using different variants of the in vitro Comet assay in human lymphocytes and rat hepatocytes incubated with MSBE at 37 C for 1 hour. Lymphocytes were incubated with MSBE for the subcellular (at two different pH conditions) and the standard Comet assays, in presence of catalase or S9 microsomal fraction. Hydrogen peroxide, benzo(a)pirene and UV radiation were used as positive controls. Results from standard and subcellular Comet assays clearly showed that MSBE (50 µg/mL) induced primary DNA damage to lymphocytes. This genotoxic effect was slightly reduced when lymphocytes were incubated with MSBE plus catalase, which suggests that hydrogen peroxide is involved in this DNA injury. S9 fraction also decreased MSBE-induced damage to DNA in human lymphocytes. Not genotoxic effect was observed when rat hepatocytes were exposed at MSBE, suggesting that the metabolic activity can be involved in the elimination of the DNA damage generated by the MSBE. In conclusion, MSBE causes primary DNA injury of human lymphocytes in vitro Comet assay, but not in rat hepatocytes in similar conditions.
A review of the Hawaiian Coccinellidae

TheCoccinellidae comprise a large family in the Coleoptera with about490 genera and 4200 species (Sasaji, 1971). The majority of these speciesare predacious oninsects and mites. Species of the subfamily Epilachninaeare phytophagous and are pests themselves. To date, none of these occurin Hawaii.The Coccinellidae are all thought to have been introduced into the
MICROPROPAGATION AND ELICITATION STUDIES IN ALOE VERA

ABSTRACT Objective: Micropropagation and elicitation studies of Aloe vera Methods: Standardisation of the regeneration protocol was done by using Murashige and Skoog (MS) media in combination with various plant growth regulators and elicitation studies were carried out by means of abiotic elicitors (salicylic acid, fructose and sodium chloride). Results: Direct regeneration through shoot tip gave the best response (0.2 mg/l Indole Butyric Acid (IBA) + 0.2mg/l 6-Benzylaminopurine (BAP)). Salicylic acid proved to be an effective abiotic elicitor, for suspension cultures of in vitro grown callus and also in vivo. It increased the content of polysaccharides, up to 7 times and phenolic compounds to almost 10 folds compared to untreated control kept under similar conditions. Conclusion: This study will make a path for the genetic transformation and metabolite enhancement along with their regulation, which can prove to be an asset towards pharmaceutical industry. Keywords: Aloe vera, Succulent plant, Micropropagation, Elicitation, Callus, Explant.
Target selection by gaze pointing and manual confirmation: performance improved by locking the gaze cursor

Abstract Eye movement-based human-computer interactions are emerging in diverse scenarios. When selecting targets on a user interface, the method of combining fast gaze pointing with reliable manual action is becoming increasingly popular. However, this method suffers from noise in gaze pointing caused by eye jitters and users’ habitual early move-away of gaze before manual actions. Here we propose a novel solution to mitigate these problems by locking the gaze cursor at the target for imminent manual selection. We compared this gaze-lock cursor with a conventional gaze cursor in a typing task with varying key sizes and key gaps. Results show that typing performance was significantly better with larger key size and gap. More importantly, the gaze-lock cursor significantly increased speed and decreased errors when compared to a conventional gaze cursor. Our findings demonstrate that the gaze-lock cursor is a promising tool for gaze interactions involving frequent target selections. Practitioner summary: Target selection by gaze pointing and manual confirmation suffers from eye jitters and users’ habitual early move-away of gaze before manual actions. The performance of this method can be improved by applying the gaze-lock cursor we proposed, increasing target size or increasing the target gap. Abbreviations: WTC: warping to target center; ALCM: automatic lock of cursor movement; LCD: liquid crystal display; EWMA: exponential weighted moving average; ER: error rate; ET: execution time; ED: edit distance; CV: coefficients of variation; ANOVA: analysis of variance; GUIs: general user interfaces
UDP‐Apiose/UDP‐Xylose Synthase

The UDP-apiose/UDP-xylose synthase from cell suspension cultures of parsley has been purified 1400-fold by an improved method. The ratio of apiose to xylose formed from UDP-D-glucuronic acid (UDP-GlcUA) remained constant throughout the purification procedure. Dodecylsulfate-gel electrophoresis and sedimentation equilibrium measurements showed that this enzyme preparation is composed of two proteins with molecular weights of 65000 and 86000. The two proteins which are present in a molar ratio of about 1:0.7 to 1:0.9 could not be separated by ammonium sulfate fractionation, chromatography on DEAE-cellulose at different pH-values, and on ω-aminoalkyl-Sepharose, and by gel filtration on Acrylex P-100. Each protein is composed of two apparently identical subunits. The presence of only two different subunits was confirmed by end group analysis in which glycine was found as N-terminal amino acid for the larger and lysine for the smaller protein. Crosslinking with dimethylsuberimidate gave dimers of the identical subunits but no hybrids. Separation of the two proteins was achieved on DEAE-cellulose in the presence of urea. After dialysis only the 86000-Mr protein showed enzyme activity with no significant change in the apiose/xylose ratio. However, in the absence of the 65000-Mr protein enzyme stability was decreased drastically. By equilibrium dialysis it was found that 0.5 mol UDP-GlcUA are bound per mole of 86000-Mr protein. NAD+ alone was not bound, but in the presence of UDP it was also bound in a ratio of 0.5 mol/mol catalytic protein. Experiments in which sodium borohydride was added to the enzyme incubation gave no indication that the 4-keto intermediate is bound as a Schiff base to the enzyme. Also no evidence for epimerization at C-3 of the 4-ulose intermediate prior to ring contraction to apiose was found.
Accounting for Unobserved Heterogeneity in The Relationship between External Trade Benefits and Standard of Living in Eswacs; 1980 -2013

Cross boundary trade activities are characterized with feedback effect which is referred to as common factors in terms of global shocks, International spill-over effects, dynamic feedback effects, recession, business cycle shocks, global financial crisis and imported inflation. These effects are often transmitted from one country to another within a particular trade region, and are most time unobserved hence unaccounted for. It is in the light of this worrythat this research is aimed at accounting for unobserved heterogeneity in the relationship between external trade benefits and standard of living in the five English Speaking West African Countries (ESWACs) from 1980 to 2013. These countries include The Gambia, Ghana, Liberia, Nigeria and Sierra Leone). The study expressed external trade benefits as increase in export earnings (EXE), trade openness (TOP), total government expenditure (TGE) and reduction in foreign exchange rate (FER), and standard of living (SLR). Theoretically, the study relied on two trade theories, in practice the study constructs a balanced panel data structure (BPDS) and methodologically, it adopted 2nd generation panel data econometric methods in its analyses. The results of the study reveal that external trade benefits have not been able to improve the status of standard of livingand the unobserved heterogeneity in the relationship between external trade benefits and standard of living in ESWACs is accounted for about 0.8746 (approximately 87%) with the period of study, indicating high level of unobserved heterogeneity in the relationship between external trade benefits and standard of living. Based on this result, the study therefore concluded that the inherent unobserved heterogeneity in the relationship between external trade benefits and standard of living has made the impact of external trade benefits on thestandard of living to be a trivial matter. Based on the findings and conclusion, the study recommended, among others, that the governments of ESWACs should encourage and support the real sector through subsidies and investment in social and physical infrastructure and agricultural and manufacturing sectors, and pay attention to investment in human capital as this will help to improve the standard of education and health status.
Growth, Cell Division, and Gene Expression of Escherichia coli at Elevated Concentrations of Magnesium Sulfate: Implications for Habitability of Europa and Mars

We perform quantitative studies of the growth, death, and gene expression of Escherichia coli in a wide range of magnesium sulfate (MgSO4) concentrations (0–2.5 M). Elevated concentration of MgSO4 causes the inhibition of cell growth, leading to an increase in the population doubling time. We find that cells exhibit three distinct morphological phenotypes—(i) normal, (ii) filamentous, and (iii) small cells at 1.25 M MgSO4. Filamentous cells arise due to the lack of cell division, while the small cells arise due to the partial plasmolysis of the cells. We further find that cell death starts for salt concentrations >1.25 M and increases with an increasing concentration of MgSO4. For salt concentrations ≥1.66 M, the growth of cells stops and all the cells become smaller than the control cells, suggesting the plasmolysis of the population. Cells grown at salt concentration up to 2.07 M are reversible in both the growth rate and morphology upon the removal of the salt stress. The time scale of reversibility increases with increasing salt concentration. Finally, we investigate the expression of an osmotically inducible gene (osmC), genes involved in magnesium transport (corA), sulfate transport (cysP), and osmotically driven transport of water (aqpZ). We find that a high concentration of magnesium sulfate leads to the upregulation of cysP and osmC.
Effect of Environmental Hyperoxia on Respiration of Yellowtail Exposed to Chattonella marina

We examined effect of aquatic hyperoxia on respiration of yellowtails exposed to Chattonella mari na and measured relevant physiological parameters of the fish during the exposure. Water 02 saturation level was elevated from 100% to 300% when arterial Pot (Pao2) was found to have declined below 30 mmHg during the exposure. In the first experiment (experiment 1, N=7), Chattonella exposure lasted 210 min, followed by a recovery period of 210 min in normoxic water free of Chattonella cells. In the second experiment (experiment 2, N=7), Chattonella exposure lasted 420 min in hyperoxia. Survival rates of yellowtail of the two experiments were 100% and ca. 60% (four fish survived, three fish died) in experiment I and 2, respectively. In both experiments, hyperoxia failed to elicit expected large increases in Pao2, which suggests that resistance to diffusion of oxygen through the respiratory epithelium was increased by the presence of Chattonella cells. Ventilatory pressure (VP) was consistently enhanced when Pao2 was initially depressed in normoxia, but such stimulation of VP did not always occur during hyperoxia even though Pao2 was often depressed under this condition. The gill showed variable degrees of lesions.
Somatosensory Neuron Subtypes and Sensory Transduction in Larval Zebrafish

Author(s): Palanca, Ana Marie Silo | Advisor(s): Sagasti, Alvaro | Abstract: Larval zebrafish are emerging as a model for describing the development and function of simple neural circuits. To analyze somatosensory neuron diversity in larval zebrafish, we identified several enhancers from the zebrafish and pufferfish genomes and used them to create five new reporter transgenes. Sequential deletions of three of these enhancers identified small sequence elements sufficient to drive expression in zebrafish trigeminal and Rohon-Beard (RB) neurons. One of these reporters highlighted a somatosensory neuron subtype that expressed both the p2rx3a and pkca; genes, as well as a previously described trpA1b reporter. To determine whether neurons of this subtype possess characteristic peripheral branching morphologies or central axon projection patterns, we analyzed the morphology of single neurons. Surprisingly, although these analyses revealed diversity in peripheral axon branching and central axon projection, PKCa/p2rx3a/trpA1b-expressing RB cells did not possess characteristic morphological features, suggesting that even within this molecularly defined subtype, individual neurons may possess distinct properties. Due to their external fertilization, rapid development, and optical clarity, zebrafish larvae are particularly well suited for optogenetic approaches to investigate neural circuit function. Here we demonstrate a procedure for expressing a light-sensitive ion channel in larval zebrafish somatosensory neurons, photo-activating single cells, and recording the resulting behaviors. Specifically, we created a transgene using a somatosensory neuron enhancer to drive the expression of the tagged channelrhodopsin variant, ChEF-tdTomato. Illuminating identified cells in these animals with light from a 473 nm DPSS laser, guided through a fiber optic cable, elicited behaviors that can be recorded with a high-speed video camera and analyzed quantitatively. By introducing a few modifications to previously established methods, this approach was used to elicit behavioral responses from single neurons activated up to at least 4 days post-fertilization (dpf). The new transgenes created in this study will be powerful tools for further characterizing the molecular, morphological, and development diversity of larval somatosensory neurons and in combination with genetic or pharmacological perturbations will be a powerful way to investigate circuit formation and function.