Miracle-dz/UniFAR-FTUs huggingface dataset:
Single Versus Multiple Arterial Revascularization in Patients With Reduced Renal Function

Supplemental Digital Content is available in the text Objective: To compare the long-term outcomes of MAR versus SAR in patients with renal insufficiency. Summary of Background Data: Previous studies have been insufficiently powered to address whether MAR confers long-term benefit over SAR in patients with renal dysfunction who require CABG. Methods: We conducted retrospective cohort study in Ontario, Canada of patients who underwent isolated CABG (n = 23,406). The primary outcome was MACE, defined as the composite of stroke, myocardial infarction, and repeat revascularization. We compared patients by matching them on the propensity to have received SAR versus MAR, within groups with preoperative glomerular filtration rate (GFR) ≥60 mL/min/1.73 m2; GFR between 30 and 60; and GFR <30. Results: In patients with GFR ≥60, the use of MAR versus SAR was associated with a lower rate of MACE [hazard ratio (HR) 0.87 (0.80–0.94)], and a lower rate of long-term mortality [HR 0.87 (0.79–0.97)]. In those with GFR between 30 and 60, MAR was not associated with a difference in MACE [HR 1.04 (0.87–1.26)], and a lower rate of long-term mortality [HR 0.75 (0.65–0.87)] was observed. In those with GFR <30, MAR was not associated with a difference in outcomes. Conclusions: MAR versus SAR does not correlate with a difference in MACE amongst patients with GFR between 30 and 60 and better survival raises the possibility of indication bias. Furthermore, MAR did not confer a benefit in those with severely reduced renal function. These data suggest that the potential long-term benefits of using MAR in CABG patients with renal insufficiency may be offset by competing health risks.
Sensory analysis of dehydrated plums and pears.

Smoked plums and pears are highly appreciated in Romanian food culture as traditional healthy dessert. Safety concerns about smoked fruits led to the application of slow dehydration at low temperatures (SDLT) as gentle method to prologue the product shelf life. The aim of this study was to evaluate the consumersâ€™ expectations and perception both prior and after tasting of dried plums and pears obtained by SDLT. A questionnaire of 15 questions with 5 point Hedonic scale was addressed to regular consumers of dried fruits (N=79). Alongside with willingness to buy and perception of product quality, the respondentâ€™s expectations were evaluated before tasting the product (for product general appearance, colour and expected taste) and after tasting (for taste and consistency). Promising results were obtained for both pears and plums, thus concluding that the respondents are open to accept new processing methods for traditional products as long as there is a beneficial sensorial advantage in the perceived quality of the product.
The spontaneous appeal by naïve subjects to nonaccidental properties when distinguishing among highly similar members of subspecies of birds closely resembles descriptions produced by experts

We have developed a program (illustrated below) that can parse subjects’ natural language descriptions of the birds into a list of parts/features, their descriptors (generally adjectives), and (if provided) their location/relation to the rest of the bird. Using a statistical part of speech tagger (Stanford POS Tagger, v. 3.0; Toutanova et al., 2003), some learning, and a small set of rules, the program currently extracts 70-90% of the part-descriptor-location triplets correctly (conditioned on description’s grammaticality and complexity).
Aesthetic preference is related to organized complexity

There is extensive evidence today linking exposure to natural environments to favorable changes in mental and even physical health. There is also a growing body of work indicating that there are specific geometric properties of natural scenes that mediate these effects, and that these properties can also be found in artificial structures like buildings, especially those designed before the emergence of modernism. These geometries are also associated with aesthetic preference–we seem to like what is good for us. Here, using a questionnaire-based survey, we have tried to elucidate some of the parameters that play a role in formulating a preference for one form over the other. The images used were nature scenes from the Alpine landscape with various manipulations to alter their complexity, or with additions of computer graphics or various buildings. In all cases, the presence of a natural scaling hierarchy and of either fractal graphics or of ornate, non-local pre-modern buildings was always preferable to the alternative. We discuss these findings under the light of recent evidence in the field and conclude that they support the idea of the existence of a preference of our perceptive system for certain types of visual organization.
Molecular genetic characteristics of the envelope glycoprotein (E2) gene of classical swine fever viruses isolated in Thailand

Thirteen classical swine fever virus (CSFV) isolates collected from field outbreaks in various locations of Thailand during 2001�2009 which had been identified by RTPCR were genetically analyzed by partial nucleotide sequencing of the envelope glycoprotein (E2) gene. These sequence data were then phylogenetically analyzed along with the sequences previously submitted to GenBank, as well as those from representatives of the different CSFV subgroups. The sequence and phylogenetic analyses of the E2 gene demonstrated that the thirteen isolates of this study were separated into three different groups. The first group consisted of 4 isolates sharing 98.9�100% and 96.8�100% homology among them in nucleotide and amin o acid sequences, respectively, and belonged to subgroup 1.1. The second group consisted of 5 isolates sharing 97.3�100% and 93.6� 100% homology in nucleotide and amino acid sequences, respectively, and belonged to subgroup 2.1. The last group consisted of 4 isolates sharing 91.5�100% and 92.0�96.8% homology in nucleotide and amino acid sequences, respectively, and belonged to subgroup 2.2. In addition, the isolates in the first group had 97.3�98.4% nucleotid e sequence and 93.6�96.8% amino acid sequence similarities with the CSFV Cstrain, whereas those in the second group had 88.3�89.9% nucleotide sequence and 95.2�96.8% amino acid sequence similariti es with the Italy strain, and those in the last group had 92.0�92.5% nucleotide sequence and 92.0�96. 8% amino acid sequence similarities with the GSJCstrain. These data help to understand the dynamics of Thai CSF virus subgroup evolution and support epidemiological observations.
Expression patterns of Arabidopsis ERF VIII-b subgroup genes during in vitro shoot regeneration and effects of their overexpression on shoot regeneration efficiency

The Arabidopsis ESR1, which encodes a member of the ERF family, is thought to be a key gene for commitment to shoot differentiation in tissue culture. The Arabidopsis genome has more than a hundred genes encoding the ERF family and ESR1 belongs to the ERF VIII-b subgroup. We examined ESR1 and 5 genes structurally similar to ESR1 (ESR2, ESL1, ESL2, ESL3 and LEP) on their expression patterns during in vitro shoot regeneration. All these genes' transcript levels increased 1–2 days after shoot induction by incubation on shoot-inducing medium and then decayed by day 7. These genes' overexpression demonstrated that ESR1 and ESR2 clearly enhanced shoot regeneration when overexpressed, but other genes did not. These results suggest that all 6 examined genes may be involved in early events of shoot regeneration, although only ESR1 and ESR2 enhanced shoot regeneration by their overexpression.
Density dependence in flower visitation rates of cockroach-pollinated Clusia blattophila on the Nouragues inselberg, French Guiana

Abstract: The effective floral neighbourhood is the radius around a plant where the density of flowering plants and other factors affect visitation rates and pollination success of plants. This study aims to determine this radius and focuses on the effects of conspecific plant density, plant sex and the amount of shrub vegetation on visitation rates of Clusia blattophila, a dioecious bush pollinated by Amazonina platystylata cockroaches. The number of visits did not differ between flower sexes but cockroaches spent less time on the rewardless female flowers. The density effect was scale dependent. The distribution of flowering individuals within the 15-m radius had a significant positive effect on flower visitation rates. At a larger scale (35–45-m radius), an increase in density of male plants led to a decrease in visitation rates, indicating competition for pollinators. Within the smaller radius, the facilitative effect was probably induced by elevated floral advertisement and high mobility of cockroaches at this scale. Within the larger radii, the results indicated that cockroach mobility was restricted and population density was stable at this scale. Density of male plants affected visitation rates because only male plants reward pollinators. Hence, male plants were the true competitors.
A preliminary study of population structure of kawakawa, Euthynnus affinis (Cantor 1849) in the straits of Malacca

Kawakawa, Euthynnus affinis, small epipelagic, migratory, neritic tuna is one of the major commercial tuna species being caught in Malaysia. Therefore, its sustainability needs to be ensured by effective management. In this study, genetic variation was assessed using sequence analyses of mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene. A 331 bp segment of cyt b gene was sequenced in 113 samples collected from 4 different sources (Kuala Perlis (KP), Bayan Baru (BB), Batu Lanchang (BL), and Jalan Tenggiri (JT)). Seventy four haplotype sequences were homologous (99%) to each other while thirty nine were divergent (3%) indicating a single population along the straits of Malacca. The results obtained need to be supported by more individuals and gene studied, examination of historical aspects of population distribution and further analysis.
MOLECULAR CHARACTERIZATION OF PHYTOPLASMAS ASSOCIATED WITH PEACH DISEASES IN IRAN

Recently, peach trees showing leaf rolling, little leaf, rosetting, yellowing, bronzing of foliage and tattered and shot-holed leaves symptoms were observed in peach growing areas in the central and north-western regions of Iran. Polymerase chain reaction (PCR) and nested PCR using phytoplasma universal primer pairs PI/Tint, R16F2/R2, PA2F/R and NPA2F/R were employed to detect phytoplasmas. The nested PCR assays detected phytoplasma infections in 51% of symptomatic peach trees in the major peach production areas in East Azerbaijan, Isfahan, ChaharMahal-O-Bakhtiari and Tehran provinces. Restriction fragment length polymorphism (RFLP) analyses of 485 bp fragments amplified using primer pair NPA2F/ R in nested PCR revealed that the phytoplasmas associated with infected peaches were genetically different and they were distinct from phytoplasmas that have been associated with peach and almond witches'-broom diseases in the south of Iran. Sequence analyses of partial 16S rDNA and 16S-23S rDNA intergenic spacer regions demonstrated that 'Candidatus Phytoplasma aurantifolia', 'Ca. Phytoplasma solani' and 'Ca. Phytoplasma trifolii' are prevalent in peach growing areas in the central and north-western regions of Iran.
Interannual Variability in Mantle Length Structure, Recruitment, and Sex Ratio of Jumbo Squid, Dosidicus gigas, in the Central Gulf of California, Mexico

ABSTRACT Changes in the number and abundance of the cohorts of jumbo squid are a demographic response associated with high variability in recruitment, and have implications for availability and accessibility to the fishing fleets. In this study, we analyzed the interannual changes in the size structure, recruitment, and sex ratio of jumbo squid Dosidicus gigas in the central Gulf of California, Mexico. Data were analyzed for the 2000 to 2009 fishing seasons (from March to November). The biological data were collected biweekly at the port of Santa Rosalía, Baja California Sur, during each fishing season. We recorded mantle length and mantle weight, and sex (male or female) was identified from morphochromatic properties of fresh gonads. We concluded that the mantle length structure of jumbo squid changed between 1 cohort and 3 cohorts from 2000 to 2009. In the study zone, the presence of 2 cohorts is common. The species shows positive allometric growth, and the females are more abundant than the males in the region. The comparison between the most important fishing grounds in the central Gulf of California (Santa Rosalia and Guaymas) showed similar patterns, such as the number of cohorts, sex ratios, growth pattern, and migration pattern identified between both coasts. We believe that this could be evidence of one population that is widely distributed in the central Gulf of California.
Origination, extinction, invasion, and extirpation components of the brachiopod latitudinal biodiversity gradient through the Phanerozoic Eon

Abstract. The geographic distribution of brachiopod genus occurrences over the Phanerozoic shows that secular declines in origination and extinction rates were paralleled by increases in invasion and extirpation rates. Origination and extinction rates declined in two phases, the first from the Cambrian to latest Permian Periods and the second from the latest Permian Period to the present, which were accompanied by concomitant increases in invasion and extirpation rates. In addition to the temporal correlation, an inverse correlation was also weakly evident among time-averaged latitudinal gradients of rates. Compared with faunas at higher latitudes, low-latitude faunas experienced higher origination and extinction rates, and lower invasion and extirpation rates. We suggest that progressive increases in migration ability lowered origination and extinction rates because species that were better equipped to track a preferred habitat, for example, by the ability to disperse larvae over large distances, were less likely to evolve or become extinct in response to local environmental changes. The two phases were separated by the end-Permian mass extinction, which reset to high levels the origination and extinction rates of a taxonomically and ecologically altered global brachiopod fauna. Our data also allow us to quantify the relative contributions of origination, extinction, invasion, and extirpation to regional diversity (quantified as 10° latitudinal zones) more generally. Overall, invasion and extirpation explained slightly more variation in diversity than in situ origination and extinction. The four variables usually occurred in combinations that maintained rather than altered the shape of the latitudinal diversity gradient. For most of the Phanerozoic Eon, the gradient was not the product of continuous renewal, but rather existed as a holdover from a previous interval.
Tree rings show a different climatic response in a managed and a non-managed plantation of teak (Tectona grandis) in West Africa

Establishing large-scale plantations of teak could reduce the pressure on natural forests and sequester atmospheric carbon into durable wood. Understanding the growth dynamics of this species in plantations, outside its natural distribution area, is crucial for forest management. Stem discs of teak were collected in Ivory Coast at two sites, a non-managed plantation (Gagnoa) and a managed plantation (Seguie). All stem discs were processed using the standard dendrochronological methods in order to unravel the relationships between growth and climate. Results showed that growth is slower in Gagnoa compared to the Seguie plantation that is being thinned regularly. In Gagnoa, trees responded positively to April rainfall, i.e., during the early stage of tree-ring formation, and negatively to September-October rainfall, i.e., during the short dry period. In Seguie, trees responded positively to July rainfall, i.e., during latewood formation, under decreasing rainfall. At both sites, tree growth was influenced by sea-surface temperature anomalies during the summer in the Gulf of Guinea. Teak growth in Seguie could be additionally linked to El Nino events, specifically during three major episodes (1976–77, 1982–83 and 1997–98).
USING GENETIC ANALYSIS AND THE MODEL ORGANISM CAENORHABDITIS ELEGANS TO IDENTIFY BACTERIAL VIRULENCE FACTORS AND INNATE IMMUNE DEFENSES AGAINST PATHOGENS

USING GENETIC ANALYSIS AND THE MODEL ORGANISM CAENORHABDITIS ELEGANS TO IDENTIFY BACTERIAL VIRULENCE FACTORS AND INNATE IMMUNE DEFENSES AGAINST PATHOGENS by Katie Letitia Styer Department of Molecular Genetics and Microbiology Duke University Date: _______________________ Approved: ___________________________ Alejandro Aballay, Supervisor ___________________________ Joseph Heitman ___________________________ Raphael Valdivia ___________________________ Soman Abraham ___________________________ Margarethe Kuehn ___________________________ Richard Frothingham An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2008 Copyright by Katie Letitia Styer 2008
The influence of nutrition on the response of wheat to above-optimal temperature

Wheat plants (Triticum aestivum L. cv. Gabo) were grown at two temperatures (18/13 and 24/19¦C, Day/night), either with full nutrient availability or deprived of nutrients after floral initiation or after anthesis, in order to identify possible interactions between nutrient availability and response to a temperature higher than the optimum for grain dry weight accumulation. Nutrient deprivation reduced levels of nitrogen, potassium and calcium in the vegetative organs of the plant at anthesis and maturity, and levels of nitrogen and calcium, but not potassium, in the grain. Differences in the distribution of nitrogen, potassium and calcium can be explained on the basis of their phloem mobility. An interaction was observed between nutrition and temperature in the time from seedling emergence to anthesis, the number of tillers at anthesis and the number of heads per plant at maturity. Within the main culm ear, high temperature and low nutrition reduced grain number. High temperature, but not low nutrition, reduced individual grain weights. However, there were no interactions between nutrition and temperature in regulating these responses. Therefore, although nutrition may be an important factor when considering the effect of temperature on tillering, there is no evidence from this study that nutritional status will mask the effects of temperature on the later stages of ear and grain development.
IMMUNOLOGICAL AND ULTRASTRUCTURAL CHARACTERIZATION OF THE PHOTOSYNTHETIC COMPLEXES OF THE PROCHLOROPHYTE PROCHLOROCOCCUS (OXYCHLOROBACTERIA)

Ultrastructural features and immunological properties of some thylakoid proteins were examined in two strains of the prochlorophyte Prochlorococcus and compared to those of other photosynthetic prokaryotes and eukaryotes. Both strains exhibited two or three rows of tightly appressed thylakoidal membranes, located at the cell periphery. However, thylakoids were concentrically arranged in the strain from the Sargasso Sea (SARG) and horseshoe‐shaped in the Mediterranean isolate (CCMP 1378). Although lacking phycobilisomes, both cell types shared with cyanobacteria the presence of carboxysome‐like structures and glycogen granules as storage compounds.
Enzymatic evidence for a simultaneous operation of two one-carbon assimilation pathways during growth of Arthrobacter P1 on choline

Assimilation of C~ compounds by aerobic microorganisms may proceed via one of the following cyclic pathways: (I) the ribulose bisphosphate (RuBP) pathway of CO 2 fixation (Calvin cycle), (II) the ribulose monophosphate (RUMP) pathway of formaldehyde fixation, (III) the serine pathway and (IV) the dihydroxyacetone (DHA) pathway of formaldehyde fixation [1,2]. Generally only one pathway is involved in carbon assimilation from one-carbon compounds in a particular organism, although the two variants of the RuMP cycle (the KDPGand FBP-variant) may operate simultaneously in Methylococcus capsulatus and Pseudomonas methanica [3]. However, it has been reported that Methylococcus capsulatus (strain Bath) during growth on methane, in addition to assimilating formaldehyde via the RuMP pathway, has the ability to fix CO 2 via the Calvin cycle [4]. As judged from the low activities of the key enzymes of this cycle it is evident that the Calvin cycle plays only a minor role in the overall synthesis of cell constituents from C~ compounds in this organism. In this communication we wish to report enzymatic evidence for an exception to the general rule that in a certain organism not more than one C~ assimilation pathway operates as the major path of carbon leading to the formation of cell material. Our results suggest that the facultative methylotroph Arthrobacter P1 [5] requires both a serine pathway as well as a RuMP cycle of formaldehyde fixation as indispensable routes during the metabolism of choline.
Systematics and Species Limits of Breadfruit (Artocarpus, Moraceae)

Abstract Breadfruit (Artocarpus, Moraceae) is an important staple in Oceania and throughout much of the tropics. Interpretations of species delimitations among breadfruit and its closest relatives have varied from recognition of one to several species. To better understand the systematics and ultimately the origins of breadfruit, we considered evidence from molecular data. Amplified fragment length polymorphism data for 261 individuals of breadfruit, its closest relatives, putative hybrids, and nine outgroup taxa were analyzed using neighbor joining and parsimony analyses. Three species, A. altilis (domesticated breadfruit), A. camansi, and A. mariannensis, are recognized and the existence of hybrids (A. altilis × A. mariannensis) verified. A revised treatment based on the molecular results, as well as morphological and geographical considerations, is presented.
Two new species of Dactylaria (anamorphic fungi) from Australian rainforests and an update of species in Dacrylaria sensu lato

The new species Dactylaria belliana and D. ficusicola were isolated from leaf litter of an Australian tropical rainforest. Dactylaria belliana differs from other species within this genus in having narrowly fusiform, uniseptate conidia and pigmented, denticulate conidiophores. Dactylaria ficusicola is similar in morphology to D. hemibeltranioidea but differs in producing only cylindrical narrow conidia while the latter species also has fusiform and naviculate conidia. The new species are described and illustrated here. A synopsis of species described in Dactylaria sensu de Hoog since the review by Goh and Hyde (1997) is provided based on the literature.
QTL Analysis of Agronomic Traits and Intracellular Substances Related to Cold Tolerance in Rice (Oryza sativa L.)

Cold acclimation of plants is a highly active process resulting from the expression of a number of physiological and metabolic adaptations to low temperature. Major metabolic changes in carbohydrates, protein, nucleic acids, amino acids, and growth regulators have been documented during the acquisition of cold tolerance. Among these, water-soluble carbohydrate (WSC) and some amino acids were shown to accumulate during cold acclimation of grass species. To determine QTLs associated with agronomic traits and the intracellular substances related to cold tolerance in rice, a molecular map consisted of 106 SSR and 26 AFLP markers has been developed using a recombinant inbred population of F 8 generation derived from a cross between Dasanbyeo, a Tongil type cultivar, and TR22183, a Chinese japonica variety. The total map unit was 1,275 cM with an average dis- tance of 9.6 cM. Most of the traits examined approximately fitted in normal distribution. The number of significant QTLs (LOD ≥ 2.0) affecting each trait ranged from one to five, a total of thirty-nine QTLs were detected from 23 traits. The QTLs derived from 23 traits explained 7.4 to 26.4% of total phenotypic variance.