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Figure 6 from: Pádua DG, Fernandes DRR, Sääksjärvi IE (2020) Pimpla Fabricius, 1804 (Ichneumonidae, Pimplinae) from Uruguay: a replacement name, new records, and an identification key to the species. ZooKeys 1007: 23-47. https://doi.org/10.3897/zookeys.1007.56328
Figure 6 Pimpla patirrufa nom. nov. A ♀, habitus, lateral view B ♂, habitus, lateral view C ♀, face, frontal view D ♀, metasoma, dorsal view E ♀, metasoma, ventral view (arrow pointing to laterotergite V) F ♀, ovipositor apex.
Data from: The socially mediated recovery of a fearful fish paired with periodically replaced calm models
Social learning is an important mechanism for acquiring knowledge about environmental risk. However, little work has explored the learning of safety and how such learning outcomes are shaped by the social environment. Here, we exposed minnows, Pimephales promelas, to a high-risk environment to induce behavioral responses associated with fear (e.g., neophobia). We then used the presence of calm conspecific models (low-risk individuals) to weaken these responses. When observers (individuals from the high-risk environment) and models were paired consistently in a one-on-one setting, the observers showed no recovery (i.e., no weakening of the fear responses), and instead the models indirectly acquired those responses (i.e., a socially-transmitted state of fear). However, observers paired with models that were periodically replaced with new calm models showed a significant recovery, and each new model showed diminished socially-transmitted fear. We argue that our understanding of predation-related fear and social information transfer can prove fruitful in understanding problems with fear and stress across animal taxa, including among humans who experience post-traumatic stress and secondary trauma. Our findings indicate that the periodic replacement of models can promote fear recovery in observers and reduce socially-transmitted fear in models.
Data from: Comparing fitness and drift explanations of Neanderthal replacement
There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40K to 35K YBP. However, the causal mechanism for this replacement continues to be debated. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent, or subject to interpretation. Proposed models have therefore featured either fitness advantages in favor of anatomically modern humans, or invoked neutral drift under various preconditions. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in 1) required initial conditions, 2) reliability, 3) time to replacement, and 4) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find far greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.
Data from: Association of perceived tinnitus with duration of hormone replacement therapy in Korean postmenopausal women: a cross-sectional study
Objective: The purpose of this study was to determine the relationship between hormone replacement therapy and tinnitus in South Korea using data from the Korea National Health and Nutrition Examination Surveys (KNHANES) (2010 ~ 2012). Study Design : Cross-sectional analysis of a nationwide health survey. Methods: KNHANES is a nationally representative cross-sectional survey of South Korea population. Only postmenopausal women aged 19-65 years were included in the study (n = 2736). Auditory function was evaluated using pure-tone audiometric testing according to established KNHANES protocols. Subjects were questioned about their experience with tinnitus. Exogenous hormone-related factors included the starting age and duration of hormone replacement therapy Results: The overall prevalence of tinnitus was 22.2% among postmenopausal women. 1) Tinnitus severity was significantly higher in women using hormone replacement therapy (p = 0.0024) and 2) significantly lower in women who breast-fed their children (p = 0.0386). 3) According to logistic regression models, the longer duration of hormone replacement therapy was significantly associated with increasing tinnitus (OR = 1.323, 95% CI = 1.007-1.737, p = 0.0441). Conclusion: A longer duration of hormone replacement therapy was associated with developing tinnitus in Korean postmenopausal women. Further experimental and epidemiological researches are needed to elucidate the causal relationship between hormone replacement therapy and tinnitus.
Data from: Roles of pathogens on replacement of tree seedlings in heterogeneous light environments in a temperate forest: a reciprocal seed sowing experiment
1. In forest communities, the Janzen–Connell (J-C) hypothesis proposes that species diversity is maintained by non-competitive distance- and/or density-dependent seedling mortality caused by host-specific natural enemies. However, the effects of pathogen associations from nearby conspecifics vs. heterospecifics remain unknown in spatially heterogeneous light environments. 2. Seeds of hardwood species Cornus controversa (Cornus) and Prunus grayana (Prunus) were sown beneath 6–7 Cornus and Prunus adults in both the forest understory (FU) and in gaps (Gap) created by felling all woody vegetation near the focal adults. Seedling growth, mortality, killing agents (e.g. pathogens that cause damping-off and leaf diseases), and root infection by arbuscular mycorrhizal fungi (AMF) were investigated. 3. We found strong habitat effects on the expression of soil fungi beneath both tree species. Seedling mortality caused by soil-borne damping-off pathogens was greater in FU than in Gap, and AMF infection, which enhanced relative seedling growth rate, was greater in Gap than in FU. Seedling mortality caused by damping-off pathogens did not differ between Cornus and Prunus seedlings beneath the adults of conspecific or heterospecific adults in both FU and Gap, suggesting little distance-dependence or host preference in the fungus. 4. Beneath the adults of Cornus and Prunus, the most prevalent leaf diseases were zonate leaf blight and angular leaf spot caused by the airborne pathogenic fungi Haradamyces foliicola and Phaeoisariopsis pruni-grayanae, respectively. Although these pathogens attacked the seedlings of both species, conspecific seedlings (i.e. home) showed more severe leaf damage, earlier leaf shedding and/or less defensive behaviour (cell wall defence) relative to heterospecific seedlings (i.e. away), suggesting negative distance-dependent attack (i.e. host preference) for these leaf diseases. As a result, greater seedling mortality was observed for conspecific seedlings under both FU and Gap treatments. 5. Synthesis. In the temperate forest, the J-C hypothesis is largely mediated through the strong negative influence of airborne leaf diseases rather than through soil-borne damping-off pathogens. We found that airborne diseases demonstrated distance-dependent host preferences, which led to greater conspecific seedling damage regardless of environmental light conditions.
Data from: Ultrasonic-enhanced replacement of lead in lead hydrometallurgy process from lead leaching solution
In this paper, ultrasonic enhanced replacement of lead by zinc in lead leaching solution was studied. The effects of reaction time, rotational speed, temperature, concentration of leaching solution and the ratio of the surface area of the zinc plate immersed in the leaching solution to the volume of leaching solution (S:V) were studied under both conventional and ultrasonic conditions. The optimum ultrasonic assisted replacement conditions were as follows: the S:V of 0.04 (4cm2/100ml), reaction temperature of 30 °C, replacement time of 30 min, and the concentration of leaching solution is 5 g/L, leading to the replacement rate of lead is 94.84%. Compared with conventional replacement process, the reaction time of ultrasonic enhanced substitution could be reduced to one half, and the demand of reaction temperature, leaching solution concentration and other conditions was decreased accordingly. Introducing ultrasonic into the replacement reaction is promising to reduce the energy consumption in hydrometallurgical industry also caters to the demand of environment protection.
Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds
The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.
The 1.1 Å Structure of the Periplasmic Phosphate-Binding Protein from Stenotrophomonas maltophilia - a crystallisation contaminant identified by molecular replacement using the entire protein database (X-ray diffraction images).
<p>During efforts to crystallise the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from <em>Alcaligenes</em> sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this structure as the search model did not give a convincing solution with the original atomic resolution dataset. Hence we considered that these crystals might be due to a protein impurity, although molecular replacement using the structures of common crystallisation contaminants as search models again failed. A script to perform molecular replacement using MOLREP (Vagin, A. & Teplyakov, A. (2010). Acta Crystallogr. D 66, 22-25.) in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron density map at 1.1 Å resolution allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate binding protein from <em>Stenotrophomonas maltophilia</em> (UniProt ID: B4SL31; gene ID: Smal_2208) and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked with the virulence of antibiotic resistant strains of pathogenic bacteria and with biofilm formation. The structure has been refined to an R-factor of 10.15 % and an R-free of 12.46 % at 1.1 Å resolution. The molecule adopts the type-II periplasmic binding protein fold with a number of extensively elaborated loop regions. A fully-dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles. </p>
FIGURE 3 in Gansucossus, a replacement name for Yumenia Hong, 1982 (Insecta, Hemiptera, Palaeontinidae), with description of a new genus
FIGURE 3. Daohugoucossus solutus sp. nov., cameralucida drawing of NIGP141370.
FIGURE 2 in Gansucossus, a replacement name for Yumenia Hong, 1982 (Insecta, Hemiptera, Palaeontinidae), with description of a new genus
FIGURE 2. Gansucossus typicus sp. nov., cameralucida drawing of NIGP141369a.
FIGURE 2. Parapercis rufa Randall, 2001. A. NMMB–P11689, 122.7 in Redescription of Parapercis rufa Randall, 2001, a replacement name for P. r o s e a Fourmanoir, 1985, based on specimens newly collected from southern Taiwan
FIGURE 2. Parapercis rufa Randall, 2001. A. NMMB–P11689, 122.7 mm SL. B. NMMB–P11690, 110.7 mm SL.
FIGURE 1 in Pterostichus (Anilloferonia) diana LaBonte (Coleoptera: Carabidae: Pterostichini), a replacement name for P. (A.) lanei (Hatch, 1935), and validity and redescription of P. (A.) malkini (Hatch, 1953)
FIGURE 1. Habitus of male Pterostichus (Anilloferonia) malkini (Hatch).
FIGURE 2 in Association of the female of Perdita (Xeromacrotera) cephalotes (Cresson), and a replacement name for Perdita bohartorum Parker (Hymenoptera: Andrenidae)
FIGURE 2. Distribution of P. cephalotes (circles) and P. boharti (triangles). Scale bar = 200 km.
FIGURE 3 in Synodus cresseyi Prokofiev, 2008, an unnecessary replacement for S. macrocephalus Cressey, 1981, and a description of a new species from the Western Indian Ocean (Teleostei: Synodontidae)
FIGURE 3. Paratypes of Synodus vityazi sp. nov., USNM 396992, 4 of 6, 77.5-89.1 mm SL.
FIGURE 1 in Synodus cresseyi Prokofiev, 2008, an unnecessary replacement for S. macrocephalus Cressey, 1981, and a description of a new species from the Western Indian Ocean (Teleostei: Synodontidae)
FIGURE 1. Holotype of Synodus macrocephalus Cressey, 1981, USNM 217776, 158.1 mm SL.
Figure 1 from: Nelson EC, Oliver EGH, Pirie MD (2023) Erica L. (Ericaceae): homonyms amongst published names for African species and proposed replacement names. PhytoKeys 236: 157-178. https://doi.org/10.3897/phytokeys.236.110498
Figure 1 Erica oliveranthus E.C. Nelson and Pirie, renamed in honour of E.G.H. (Ted) Oliver and Inge M. Oliver (photo: MDP; https://www.inaturalist.org/observations/19098927).
Figure 1 from: Babcock LE (2024) Replacement names for two species of Orthacanthus Agassiz, 1843 (Chondrichthyes, Xenacanthiformes), and discussion of Giebelodus Whitley, 1940, replacement name for Chilodus Giebel, 1848 (Chondrichthyes, Xenacanthiformes), preoccupied by Chilodus Müller & Troschel, 1844 (Actinopterygii, Characiformes). ZooKeys 1188: 219-226. https://doi.org/10.3897/zookeys.1188.108571
Figure 1 Original 19th century figures of Carboniferous-age xenacanthiform shark fossils from Saxony-Anhalt, Germany, and Ohio, USA AOrthacanthus gracilis (Giebel, 1848), tooth, holotype (Geiseltalmuseum Halle, GTM 1095), two views; reproduced from Giebel (1849: pl. XXIX, fig. 2a, b), 7.7 mm long. Wettin-Schichten, Wettin/Saalegebiet, Saxony-Anhalt, Germany BOrthacanthus lintonensis nom. nov., replacement name for Diplodus gracilis Newberry, 1857a, two teeth, syntypes (repository unknown); reproduced from Newberry (1875a: pl. LVIII, figs. 3, 3a), ca 5 and 13 mm long. Upper Freeport Coal, Allegheny Group, Diamond Coal Mine, Linton, Ohio, USA COrthacanthus adamas nom. nov., replacement name for Orthacanthus gracilis Newberry, 1875a, dorsal spine, illustration is a composite based on syntypes (Orton Geological Museum, OSU 4467A, 4467B); reproduced from Newberry (1875a, pl. LIX, fig. 7), ca 71 mm long. Upper Freeport Coal, Allegheny Group, Diamond Coal Mine, Linton, Ohio, USA DOrthacanthus carbonarius (Germar, 1844), two teeth, syntypes (repository unknown) of Chilodus tuberosus Giebel, 1848; reproduction of Giebel (1849: pl. XXIX, figs. 1, 1a, 1b as), length unknown. Wettin-Löbejun, Saxony-Anhalt, Germany EOrthacanthus carbonarius (Germar, 1844), tooth, syntype (repository unknown) of Lamna carbonaria Germar, 1844; reproduced from Germar (1844: pl. 1, fig. 1), ca 20 mm long. Presumably from Saxony-Anhalt, Germany.
Minimally invasive Aortic Valve and Ascending Aorta Replacement
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Supplementary material 3 from: Liao M, Zeng S-J, Zeng L-Y, Yin H-J, Yan M-L, Zhang C-F, Tang G-D (2024) A new species and a replacement name in Cynanchum (Apocynaceae, Asclepiadeae) from China. PhytoKeys 241: 49-63. https://doi.org/10.3897/phytokeys.241.111499
Maximum likelihood tree of Cynanchum
Supplementary material 2 from: Liao M, Zeng S-J, Zeng L-Y, Yin H-J, Yan M-L, Zhang C-F, Tang G-D (2024) A new species and a replacement name in Cynanchum (Apocynaceae, Asclepiadeae) from China. PhytoKeys 241: 49-63. https://doi.org/10.3897/phytokeys.241.111499
List of ingroup and outgroup taxa used in the phylogenetic analyses
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