Miracle-dz/UniFAR-FTUs huggingface dataset:
Collegiality Versus Competition: How Metrics Shape Scientific Communities

There has been a growing focus on the metrics that measure the success of individual researchers, such as the h-index, the number of publications, and the amount of grant money awarded to the researcher (Lawrence 2007, Acuna et al. 2012). Although they can be rapid and convenient indicators of success, the use of such metrics can lead to shifts in the balance of the quantity and the quality of scientific work (Brischoux and Cook 2009, Fischer et al. 2012). Here, we focus on how metrics can cause losses of collegiality and good citizenship and discuss the emerging need to consider scientific values as a broader community. Our point is that a scientific community consisting of researchers who solely maximize their individual success metrics cannot function well. Metrics have the advantage of being objective, but in addition to metrics of the success of individuals, we argue that the scientific community needs metrics that measure collegiality and good citizenship; both of these are vital to the survival of scientific dis ciplines and to the recruitment of new members. Multiple emerging factors—for example, reduced funding and job availability—can decrease collegiality and good citizenship. Many important decisions regarding hiring and promotion in universities are made by individuals with little knowledge of a scientist’s field. In this case, metrics and grants provide a valuable resource for making decisions, because they are objective and quick to reference. Metrics are effective when applied to a field as a passive observation, but we now face a situation in which metrics actively influence the behavior of scientists who are trying to maximize their metrics (Lawrence 2007, Fischer et al. 2012). If we have only metrics of individual success, metric-maximizing scientists may change their behavior in a way that decreases collegiality and teamwork. For example, there is an increasing shift toward big science and big data in ecology, including observatories that involve multiple institutions and investigators, such as the US National Ecological Observatory Network. Such endeavors will work well if the value of teamwork and good citizenship is recognized up front. In practice, however, some scientists often contribute more than others, and credit is traditionally not attributed at the team scale. In a situation in which the excellence of scientists is measured by metrics that are focused solely on individual success, the best strategy for researchers is to be involved in many large endeavors but to contribute only enough to be included as an author. By contrast, team players will invest much time and effort in the projects in which they are involved. As a consequence, the number of publications of a team player can be lower than the number of publications of the metric-maximizing scientist. If we have a community that values team players and gives credit to entire teams when that is appropriate, there are decreased risks of losing scientific efforts that work toward the greater good.
A phylogeny of the North Pacific Sirenia (Dugongidae: Hydrodamalinae) based on a comparative study of endocranial casts

Abstract Comparisons of endocranial casts of the subfamily Hydrodamalinae (Mammalia; Sirenia) reveal some interesting evolutionary trends, especially in the changes to the shape of the cerebrum and olfactory bulbs, and the position of the optic nerve. Endocranial casts of both Hydrodamalis spissa (Furusawa, 1988 and H. gigas (Zimmermann, 1780) reveal several synapomorphies (spherical olfactory bulbs, the optic nerve separate from the trigeminal nerve, and diminished fissura longitudinalis cerebri and transverse sulcus). A revised phylogeny of North Pacific Sirenia based in part on endocranial casts demonstrates that H. spissa and H. gigas are very closely related within the Hydrodamalinae. On the other hand, although they contemporaneously inhabited the North Pacific Ocean, the eastern Pacific H. cuestae differs clearly from the western Pacific H. spissa
Effect of nutrient nitrogen and manganese on manganese peroxidase and laccase production by Pleurotus sajor‐caju

Pleurotus sajor-caju, strain Pl-27, produces manganese-dependent peroxidase (MnP) and laccase, but not lignin peroxidase, when grown on a defined medium with glucose as sole carbon source. MnP activity was detected in fungal cultures supplemented with both high (26 mM-N) and low (2.6 mM-N) nutrient nitrogen although higher specific activity values were recorded under the latter conditions. Conversely, laccase production was not influenced by nutrient nitrogen levels under the growth conditions adopted. Both the titre and time of appearence of MnP were also affected by the concentration of Mn in the culture medium with highest enzyme levels recorded in cultures supplemented with 15 ppm Mn. Two MnP and five laccase isoforms were identified by FPLC and gel electrophoresis.
Association of Grain Fe and Zn Contents with Agronomic Traits in Sorghum

Genetic variability and the association of grain Fe and Zn-contents with other agronomic traits were studied in 1,394 accessions from core germplasm maintained at the ICRISAT gene bank. A large variability for grain Fe and Zn contents were observed. The grain Fe and Zn contents of the accessions with white grains were marginally higher than those with colored grains and these white grain sorghums originated mostly from India and Zimbabwe. The Fe and Zn contents of the accessions with testa and without testa were comparable. However, endosperm texture and grain size appeared to influence grain Fe and Zn contents. Strong positive correlation between grain Fe and Zn contents and their weak association with the agronomic and grain traits indicated possibility to breed simultaneously for high grain Fe and Zn traits in varied plant agronomic backgrounds that might be suitable for different agro-climatic regions across the world.
Aquaphila albicans gen. et sp. nov., a hyphomycete from submerged wood in the tropics

Aquaphila albicans gen. and sp. nov. from submerged wood in the tropics is described and illustrated. It produces hyaline, multiseptate, fusoid or falcate conidia resembling the macroconidia of Fusarium species, but differs by its conidiogenesis and the aquatic habitat. The conidiophores of A. albicans are septate, hyaline, sympodially proliferating with conidiogenous denticles. Conidial development in A. albicans has been studied in culture and results are presented. The genus is compared with similar genera.
Trade‐offs between physical and chemical carbon‐based leaf defence: of intraspecific variation and trait evolution

Despite recent advances in studies on trade‐offs between plant defence traits, little is known about whether trade‐offs reflect (i) evolutionary constraints at the species level or (ii) allocation constraints at the individual level. Here, we asked to which degree physical and chemical carbon‐based leaf defence traits covary within and across species. We assessed leaf toughness, leaf total phenolic and tannin concentrations for 51 subtropical tree species. Species trait means, sample‐specific values and phylogenetically independent contrasts were used in regression analyses. Phylogenetic signals and trait evolution were assessed along the phylogeny. Analyses of species‐level trait means revealed significant negative trait covariations between physical and chemical defence traits in analyses over all species. These covariations were inconsistent at the within‐species level. All three defence aspects showed strong phylogenetic signals, but differed in the degree of conservatism along the phylogeny. Inclusion of intraspecific trait variability significantly decreased the strength of these covariations. Strong negative covariations were detected between physical and chemical defence traits when phylogenetic non‐independence was accounted for. Synthesis. We addressed two sources of variation (allocation and evolution) independently from each other in the context of trait interrelationships. The observed negative covariations hint at the existence of a trade‐off between physical and chemical defence traits. The finding that intraspecific trait variation contributed less to this relationship suggests that the trade‐off is dominated by evolutionary constraints rather than by carbon allocation constraints.
ANTIMICROBIAL AND BRINE SHRIMP LETHALITY OF EXTRACTS OF TERMINALIA MOLLIS LAWS

Using the disc diffusion method it was demonstrated that extracts of the leaves, stem and roots of Terminalia mollis Laws (Combretaceae) have antibacterial activity against Staphylococcus aureus (NCTC 6571), Escherichia coli (NCTC 10418), Pseudomonas aeruginosa (NCTC 10662), Klebsiella pneumoniae (NCTC 9633), Salmonella typhi (NCTC 8385), and Bacillus anthracis (NCTC 10073) and antifungal activity against Candida albicans (Strain HG 392), and local strains of Aspergillus flavus and Cryptococcus neoformans. The root extracts were the most active followed by the stem, and leaf extracts. Extracts of the three parts also exhibited cytotoxicity to brine shrimp larvae with LC50 values ranging from 26.3 to 58.1, l0.4 to 69.5, and 42.9-101. 3µg/ml, for the root, stem, and leaf extracts, respectively. The results support the traditional uses of extracts of this plant for the management of bacterial and fungal infections.
Suppression of Meloidogyne hapla populations by Hirsutella minnesotensis

Abstract The effects of the endoparasitic fungus Hirsutella minnesotensis on populations of Meloidogyne hapla from Michigan (MI), Rhode Island (RI), Connecticut (CT), Lyndonville, New York (NYL), Geneva, New York (NYG), and Wisconsin (WI) were studied in the greenhouse. Twenty-day-old tomato (cv. Rutgers) seedlings were inoculated with either 0 or 600 eggs of each nematode population mixed with either 0, 0.02, or 0.1 g of fresh H. minnesotensis mycelium 0.1 L−1 of soil in pots containing 0.5 L of soil, and maintained at 25±2°C for 2 months. No effect of the fungal treatments and nematode treatments on tomato plant heights and shoot dry weights was observed. While all M. hapla populations were suppressed by H. minnesotensis, the degree to which each population was affected varied slightly. Across fungal treatments and nematode populations, the fungus reduced total number of nematodes in roots by 61–98%, with the highest for NYG and RI, intermediate for NYL and CT, and lowest for MI and WI populations. The study demonstrated that H. minnesotensis may be used as a potential suppressor of M. hapla in vegetable production systems in the Great Lakes Region.
Symbiotic characteristics of subspecies of Trifolium subterraneum L.

An examination was made of the ability of lines of Trifolium subterraneum L. subsp. subterraneum, subsp. yanninicum Katzn. et Morley, and subsp. brachycalycinum Katzn. et Morley to nodulate and fix nitrogen with strains of . Rlzizobium trifolii isolated from habitats dominated by each of the subspecies. Host line x bacterial strain specificity was demonstrated at two levels: (a) some strains nodulated one, or two, host lines ineffectively, yet formed an effective symbiosis with the other host lines; (b) among the symbiotic combinations classed as effective, the degree of effectiveness of the strains was dependent on the host lines. It was found that the lines of a subspecies were not more effectively nodulated by the bacterial strains isolated from a habitat in which that subspecies was the predominant subterranean clover, than they were by strains isolated from habitats in which the other subspecies predominated. For example, lines of T. subterraneum subsp. yanninicum fixed nitrogen as well with strains of R. trifolii isolated from habitats of subsp. subterraneum or subsp. brachycalycinum as they did with strains isolated from its own habitat. Similarly, there was little evidence that the strains from the habitat in which a subspecies predominated were more effective in their symbiosis with the lines of that subspecies than they were with the lines of the other subspecies. The only exception to this latter generalization was that the strains isolated from the subsp. brachycalycinum habitat were slightly more effective with subsp. brachycalycinum than with subspp. yanninicum or subterraneum. Groupings of the strains based on their response with the lines of any subspecies, or with the lines of all subspecies combined, bore no relation to groupings based on the origin of the strains. It was concluded that it was not possible to predict the effectiveness of any symbiotic combination from a consideration of the taxonomy of the host or the habitat from which the bacterium was isolated. The feasibility of using a standard host line for the screening of the general effectiveness of all strains of potential value in subterranean clover inoculants is discussed. The commercial inoculant strain, TA1, was not the most effective strain with all lines, and overall, ranked fifth among the strains examined.
Laboratory evolution of new lactate transporter genes in a jen1Δ mutant of Saccharomyces cerevisiae and their identification as ADY2 alleles by whole-genome resequencing and transcriptome analysis.

Laboratory evolution is a powerful approach in applied and fundamental yeast research, but complete elucidation of the molecular basis of evolved phenotypes remains a challenge. In this study, DNA microarray-based transcriptome analysis and whole-genome resequencing were used to investigate evolution of novel lactate transporters in Saccharomyces cerevisiae that can replace Jen1p, the only documented S. cerevisiae lactate transporter. To this end, a jen1Δ mutant was evolved for growth on lactate in serial batch cultures. Two independent evolution experiments yielded growth on lactate as sole carbon source (0.14 and 0.18 h(-1) , respectively). Transcriptome analysis did not provide leads, but whole-genome resequencing showed different single-nucleotide changes (C755G/Leu219Val and C655G/Ala252Gly) in the acetate transporter gene ADY2. Introduction of these ADY2 alleles in a jen1Δ ady2Δ strain enabled growth on lactate (0.14 h(-1) for Ady2p(Leu219Val) and 0.12 h(-1) for Ady2p(Ala252Gly) ), demonstrating that these alleles of ADY2 encode efficient lactate transporters. Depth of coverage of DNA sequencing, combined with karyotyping, gene deletions and diagnostic PCR, showed that an isochromosome III (c. 475 kb) with two additional copies of ADY2(C755G) had been formed via crossover between retrotransposons YCLWΔ15 and YCRCΔ6. The isochromosome formation shows how even short periods of selective pressure can cause substantial karyotype changes.
AFLP analyses of genetic variation of Eupatorium adenophorum (Asteraceae) populations in China

The Eupatorium adenophorum is one of the most widespread invasive alien species in China. In the present study, the genetic variation and population structure of this species were analyzed using amplified fragment length polymorphism (AFLP) markers. Nine primer pairs were selected for the analysis and 685 bands were produced, among which 474 bands were polymorphic (PPB = 69.2%). Diversity levels within populations were relatively high (mean expected heterozygosity = 0.188, mean Shannon index = 0.296). Regression analysis showed a significant positive relationship between Shannon genetic diversity and altitude (R2 = 0.31). However, there was a negative correlation between Shannon genetic diversity and latitude (R2 = 0.16), as well as between Shannon genetic diversity and longitude (R2 = 0.45). Cluster analysis grouped the majority of the weed populations into three main clusters that corresponded with the geographic regions. At the regional level, the AMOVA indicated that about 70% of the variations in the.
(Z)- and (E)-12-Tetradecenyl Acetates: Sex Pheromone Components of Oriental Corn Borer (Lepidoptera : Pyralidae)

The female sex pheromone of the oriental corn borer, Ostrinia furnacalis Guenee, was presumed to be composed of (Z)-12-tetradecenyl acetate and its geometrical isomer using electroantennogram technique. From the extracts of female moths, the presence of these compounds in a ratio of ca. 3:2 was confirmed by gas-liquid chromatography and gas-liquid chromatography combined with mass spectrometry in selected ion monitoring mode. Since the male moths were not attracted to mixtures of the two synthetic compounds, the presence of minor component(s) was suggested.
A Large Scale Synthesis of Mono- and Di-urethane Derivatives of Lysine

Orthogonally protected diurethane derivatives of lysine are valuable materials for peptide syntheses. An example is ZLys(Boc), which is exploited in the industrial production of certain well-established peptide drugs. 3,4) Another derivative is Fmoc-Lys(Boc), which is in common use in the laboratory synthesis of peptides. 5) The simplest route to these lysine derivatives seems to be using the copper complex for simultaneous protection of the a-amino and a-carboxyl function, N e -tert-butoxycarbonylation and then copper detachment. The obtained Lys(Boc) might be then subjected to N a -benzyloxycarbonylation.
Foraging in a risky environment: a comparison of Bennett's wallabies Macropus rufogriseus rufogriseus (Marsupialia: Macropodidae) and red‐bellied pademelons Thylogale billiardierii (Marsupialia: Macropodidae) in open habitats

This study aimed to establish whether red-bellied pademelons (Thylogale billiardierii) and Bennett's wallabies (Macropus rufogriseus rufogriseus) alter their foraging distribution in open habitat, in response to food availability and distance to protective shelter, the latter used as a measure of predation risk. Scat counts were used as a measure of the presence or absence of these macropods over two plantations (Russell and Dunalley). These plantations differed in both their on-site food and shelter characteristics (the presence or absence of windrows). Logistic regression indicated that at Russell, which had low food availability but the presence of on-site shelter, probability of scats of both species increased with the percentage cover of both edible and inedible vegetation. The probability of both pademelon and wallaby scats decreased with increasing distance from windrows, but increased with increasing distance from forest at the plantation edge. Logistic regression indicated that at Dunalley, which had high food availability but no on-site shelter, the probability of scats of both species increased with an increase in the percentage cover of edible vegetation. In relation to predation risk, however, the two species differed in their response. Pademelons exhibited a decrease in scat probability with increasing distance from the forest at the plantation edge, while wallabies showed an increase in scat probability with distance from the forest at the plantation edge. Results indicated some differences in antipredation strategies of the two species, which may be a function of differences in body size.
Contrasting patterns of genetic differentiation in Macaronesian lineages of Ilex (Aquifoliaceae)

Islands offer an interesting framework in which to study the effect of geographical isolation on population genetic differentiation. For plant species with high dispersal abilities, however, oceanic barriers may not represent a factor promoting strong population structure. In this work, we analysed seven nuclear microsatellite loci in Ilex (Aquifoliaceae), a bird-dispersed plant group, to infer patterns of genetic differentiation among Macaronesian taxa: I. canariensis, I. perado ssp. lopezlilloi, I. perado ssp. platyphylla (Canary Islands) and I. perado ssp. azorica (Azores). In agreement with current taxonomic classification, our results revealed a high genetic differentiation between Ilex lineages (I. canariensis and the I. perado complex), and also supported previous hypotheses that these are the result of independent dispersal events to the islands. In contrast, genetic differentiation between I. perado ssp. azorica and the two subspecies from the Canaries was high, suggesting that taxonomic revision may be necessary. Levels of genetic variation at microsatellite loci in ssp. azorica were, in addition, the lowest reported among Macaronesian bird-dispersed taxa. Lastly, low genetic differentiation was observed between subspecies occurring on the same island (sspp. platyphylla and lopezlilloi). In summary, our results revealed contrasting patterns between Macaronesian Ilex lineages: I. canariensis displayed moderate population structure across islands, whereas the I. perado complex showed strong differentiation among populations sampled on different islands. Thus, the Macaronesian Ilex taxa show that long-distance dispersal syndromes (ornithochory) do not always ensure genetic connectivity across large areas in island systems. Plant groups that successfully colonized the islands on multiple occasions may have found barriers to gene flow within certain lineages. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 258–268.
Red-Breasted Nuthatches (Sitta canadensis) Increase Cavity Excavation in Response to a Mountain Pine Beetle (Dendroctonus ponderosae) Outbreak

Abstract: In cavity-nesting vertebrate species, reproduction is limited by the production and availability of tree cavities. Excavating species may create new cavities to exploit food resource pulses in novel habitats, but availability of nesting resources may be constrained with increases in population densities. Over a 15-y period, we monitored the reproduction of cavity nesters and a large-scale mountain pine beetle (Dendroctonus ponderosae) outbreak that killed all mature lodgepole pine (Pinus contorta var. latifolia), at 30 mixed coniferous—deciduous stands in interior British Columbia, Canada. We examined how the probability of excavation of a bark insectivorous, facultative cavity excavator, the red-breasted nuthatch (Sitta canadensis), was influenced by mountain pine beetle abundance and changes in population densities of conspecific individuals and a nest predator, red squirrel (Tamiasciurus hudsomcus). Nuthatches always chose trembling aspen (Populus tremuloides) for nesting regardless of densities of nuthatch nests and availability of beetle-decayed pine as alternate nest trees. The number of nuthatch nests increased in years of increasing densities of beetle-infected pine, and the proportion of freshly excavated nests varied annually, increasing with the beetle outbreak from 26% of all cavities used in 2001 to 70% in 2002 and then declining after the outbreak to 17% in 2009. For each unit increase in densities per hectare of both nuthatches and beetle-infected pine trees, the odds that individuals would excavate a new cavity rather than use an existing cavity increased by 147 times. With each 10 m farther into the coniferous forest interior, the odds of excavation increased by 10 times. These results suggest that facultative excavators are able to exploit novel habitats during insect outbreaks by adjusting their nest-site selection patterns and increasing excavation, but that resource pulses may lead to limitation of nesting resources.
Theory of Size Distribution in Ecological Communities

Observed regularities in the size composition of pelagic ecosystems are explained by a theoretical model based on trophic processes. The model assumes, in accord with available evidence, that prey and predator sizes are simply related, and that growth and metabolism satisfy similar functions of body (particle) size when averaged over entire trophic levels. The model appears suited to other community types that satisfy these conditions, and suggests that trophic processes are complementary to competitive displacement in determining that particle density is a linear function of the logarithm of particle size.