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To evaluate how the certification of specialised Oncology Centres in Germany affects the relative survival of patients with colorectal cancer (CRC) by means of national and international comparison.

Abstract Introduction Painful temporomandibular disorders (TMDs) are usually treated with physiotherapy, self-exercises, medication-based therapy and splint therapy. For splint therapy different types of splints are available. Therefore this randomized controlled study compared the effectiveness of a semi-finished occlusal appliance (SB) with a laboratory-made occlusal appliance (SS) in myofascial pain patients. Method The trial subjects allocated to the experimental groups with the (SB) occlusal appliance and those provided with a laboratory-made occlusal appliance (SS) did, in addition, receive conservative treatment (self-exercises, drug-based and manual therapy). The control group was given conservative therapy (CO) only. Overall, a total of 63 patients participated in the study with each group consisting of 21 subjects. Results When the first follow-up examination took place (14 days after splint insertion) mouth opening within the SB group was significantly enlarged. When the second examination was conducted (2.5 months after splint insertion) mouth opening was significantly enlarged in both splint groups when compared with the initial value. In the control group, no significant enlargement of mouth opening was detected. At no point there was a significant reduction in the number of pressure-sensitive areas of the TMJ. On palpation of the masticatory muscles however, a significant reduction in the number of pressure-sensitive areas could be observed within the CO group and the SS group after 2.5 months. When comparing pain reduction (muscle/joint pain) and mouth opening, no significant differences could be detected between the treatments. Conclusion The results suggest that TMD should be treated conservatively. In cases of restricted mouth opening, the additional use of occlusal appliances can eliminate the patient’s discomfort more quickly. In this context, the tested, semi-finished occlusal appliance appears to offer an immediately available, temporary alternative to laboratory-made splints.

Abstract Background To perform a systematic review about the effect of using clinical pathways on length of stay (LOS), hospital costs and patient outcomes. To provide a framework for local healthcare organisations considering the effectiveness of clinical pathways as a patient management strategy. Methods As participants, we considered hospitalized children and adults of every age and indication whose treatment involved the management strategy "clinical pathways". We include only randomised controlled trials (RCT) and controlled clinical trials (CCT), not restricted by language or country of publication. Single measures of continuous and dichotomous study outcomes were extracted from each study. Separate analyses were done in order to compare effects of clinical pathways on length of stay (LOS), hospital costs and patient outcomes. A random effects meta-analysis was performed with untransformed and log transformed outcomes. Results In total 17 trials met inclusion criteria, representing 4,070 patients. The quality of the included studies was moderate and studies reporting economic data can be described by a very limited scope of evaluation. In general, the majority of studies reporting economic data (LOS and hospital costs) showed a positive impact. Out of 16 reporting effects on LOS, 12 found significant shortening. Furthermore, in a subgroup-analysis, clinical pathways for invasive procedures showed a stronger LOS reduction (weighted mean difference (WMD) -2.5 days versus -0.8 days)). There was no evidence of differences in readmission to hospitals or in-hospital complications. The overall Odds Ratio (OR) for re-admission was 1.1 (95% CI: 0.57 to 2.08) and for in-hospital complications, the overall OR was 0.7 (95% CI: 0.49 to 1.0). Six studies examined costs, and four showed significantly lower costs for the pathway group. However, heterogeneity between studies reporting on LOS and cost effects was substantial. Conclusion As a result of the relatively small number of studies meeting inclusion criteria, this evidence base is not conclusive enough to provide a replicable framework for all pathway strategies. Considering the clinical areas for implementation, clinical pathways seem to be effective especially for invasive care. When implementing clinical pathways, the decision makers need to consider the benefits and costs under different circumstances (e.g. market forces).

Purpose: The in vitro clonogenic assay (IVCA) is the mainstay of quantitative radiobiology. Here, we investigate the benefit of a time-resolved IVCA version (trIVCA) to improve the quantification of clonogenic survival and relative biological effectiveness (RBE) by analyzing cell colony growth behavior., Materials & Methods: In the IVCA, clonogenicity classification of cell colonies is performed based on a fixed colony size threshold after incubation. In contrast, using trIVCA, we acquire time-lapse microscopy images during incubation and track the growth of each colony using neural-net-based image segmentation. Attributes of the resulting growth curves are then used as predictors for a decision tree classifier to determine clonogenicity of each colony. The method was applied to three cell lines, each irradiated with 250 kV X-rays in the range 0-8 Gy and carbon ions of high LET (100 keV/μm, dose-averaged) in the range 0-2 Gy. We compared the cell survival curves determined by trIVCA to those from the classical IVCA across different size thresholds and incubation times. Further, we investigated the impact of the assaying method on RBE determination., Results: Size distributions of abortive and clonogenic colonies overlap consistently, rendering perfect separation via size threshold unfeasible at any readout time. This effect is dose-dependent, systematically inflating the steepness and curvature of cell survival curves. Consequently, resulting cell survival estimates show variability between 3% and 105%. This uncertainty propagates into RBE calculation with variability between 8% and 25% at 2 Gy.Determining clonogenicity based on growth curves has an accuracy of 95% on average., Conclusion: The IVCA suffers from substantial uncertainty caused by the overlap of size distributions of delayed abortive and clonogenic colonies. This impairs precise quantification of cell survival and RBE. By considering colony growth over time, our method improves assaying clonogenicity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors. Published by Elsevier B.V. on behalf of European Society for Radiotherapy and Oncology.)

Synovial sarcoma is a rare soft tissue sarcoma which frequently involves the upper or lower extremities. Soft tissue sarcomas including synovial sarcoma have a propensity to metastasize to the lungs, and there are very few reports of metastatic lesions in other locations.Here, we report a case of a 49-year-old patient who underwent neoadjuvant chemoradiation for an upper extremity synovial sarcoma and presented approximately 4 years later with abdominal pain and hemoperitoneum and was ultimately found to have metastatic synovial sarcoma involving the greater curvature of the stomach and surrounding peri-gastric soft tissue. We describe the multidisciplinary management of this complex patient presentation and propose that expanded surveillance imaging beyond that of the local tumor resection bed and the chest may be beneficial especially in tumors with high-risk features., (© 2023. The Author(s).)

The tropics were long considered to have few ectomycorrhizal fungi, presumably due to a paucity of ectomycorrhizal host plants relative to higher-latitude ecosystems. However, an increase in research in tropical regions over the past 30 years has greatly expanded knowledge about the occurrence of tropical ectomycorrhizal fungi. To assess their broad biogeographic and diversity patterns, we conducted a comprehensive review and quantitative data analysis of 49 studies with 80 individual data sets along with additional data from GlobalFungi to elucidate tropical diversity patterns and biogeography of ectomycorrhizal fungi across the four main tropical regions: the Afrotropics, the Neotropics, Southeast Asia, and Oceania. Generalized linear models were used to explore biotic and abiotic influences on the relative abundance of the 10 most frequently occurring lineages. We also reviewed the available literature and synthesized current knowledge about responses of fungi to anthropogenic disturbances, and their conservation status and threats. We found that /russula-lactarius and /tomentella-thelephora were the most abundant lineages in the Afrotropics, the Neotropics, and Southeast Asia, whereas /cortinarius was the most abundant lineage in Oceania, and that /russula-lactarius, /inocybe, and /tomentella-thelephora were the most species-rich lineages across all of the tropical regions. Based on these analyses, we highlight knowledge gaps for each tropical region. Increased sampling of tropical regions, collaborative efforts, and use of molecular methodologies are needed for a more comprehensive view of the ecology and diversity of tropical ectomycorrhizal fungi.

Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix .

Here, we report the draft genome sequence of Pseudotulostoma volvatum, an unusual ectomycorrhizal fungus in the "mold" order Eurotiales (Ascomycota, Pezizomycotina). The assembled genome is 60.4 Mbp and contains an estimated 5,492 genes. Compared with closely related species, the P. volvatum genome is depauperate in secondary metabolite gene clusters.

There has been a steady rise in the use of dormant propagules to study biotic responses to environmental change over time. This is particularly important for organisms that strongly mediate ecosystem processes, as changes in their traits over time can provide a unique snapshot into the structure and function of ecosystems from decades to millennia in the past. Understanding sources of bias and variation is a challenge in the field of resurrection ecology, including those that arise because often-used measurements like seed germination success are imperfect indicators of propagule viability. Using a Bayesian statistical framework, we evaluated sources of variability and tested for zero-inflation and overdispersion in data from 13 germination trials of soil-stored seeds of Schoenoplectus americanus , an ecosystem engineer in coastal salt marshes in the Chesapeake Bay. We hypothesized that these two model structures align with an ecological understanding of dormancy and revival: zero-inflation could arise due to failed germinations resulting from inviability or failed attempts to break dormancy, and overdispersion could arise by failing to measure important seed traits. A model that accounted for overdispersion, but not zero-inflation, was the best fit to our data. Tetrazolium viability tests corroborated this result: most seeds that failed to germinate did so because they were inviable, not because experimental methods failed to break their dormancy. Seed viability declined exponentially with seed age and was mediated by seed provenance and experimental conditions. Our results provide a framework for accounting for and explaining variability when estimating propagule viability from soil-stored natural archives which is a key aspect of using dormant propagules in eco-evolutionary studies., Competing Interests: The authors declare no conflict of interest., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. This article has been contributed to by US Government employees and their work is in the public domain in the USA.)

Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria , we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well as ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Koch and Herr.)

During mycoparasitism, a fungus-the host-is parasitized by another fungus-the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria , where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum , supporting the hypothesis that this species is parasitizing Armillaria . Most notably, we identified differentially upregulated E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most differentially upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases-enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species; however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome was reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction. IMPORTANCE By studying fungi that parasitize other fungi, we can understand the basic biology of these unique interactions. Studies focused on the genetic mechanisms regulating mycoparasitism between host and parasite have thus far concentrated on a single fungal lineage within the Ascomycota. The work presented here expands our understanding of mycoparasitic relationships to the Basidiomycota and represents the first transcriptomic study to our knowledge that examines fungal-fungal relationships in their natural setting. The results presented here suggest that even distantly related mycoparasites utilize similar mechanisms to parasitize their host. Given that species of the mushroom-forming pathogen Armillaria cause plant root-rot diseases in many agroecosystems, an enhanced understanding of this interaction may contribute to better control of these diseases through biocontrol applications.

Nitrogen (N) fixation is a driving force for the formation of symbiotic associations between N 2 -fixing bacteria and eukaryotes. 1 Limited examples of these associations are known in fungi, and none with sexual structures of non-lichenized species. 2-6 The basidiomycete Guyanagaster necrorhizus is a sequestrate fungus endemic to the Guiana Shield. 7 Like the root rot-causing species in its sister genera Armillaria and Desarmillaria, G. necrorhizus sporocarps fruit from roots of decaying trees (Figures 1A-1C), 8 and genome sequencing is consistent with observations that G. necrorhizus is a white-rotting decomposer. This species also represents the first documentation of an arthropod-dispersed sequestrate fungus. Numerous species of distantly related wood-feeding termites, which scavenge for N-rich food, feed on the mature spore-bearing tissue, or gleba, of G. necrorhizus. During feeding, mature spores adhere to termites for subsequent dispersal. 9 Using chemical assays, isotope analysis, and high-throughput sequencing, we show that the sporocarps harbor actively N 2 -fixing Enterobacteriaceae species and that the N content within fungal tissue increases with maturation. Untargeted proteomic profiling suggests that ATP generation in the gleba is accomplished via fermentation. The use of fermentation-an anaerobic process-indicates that the sporocarp environment is anoxic, likely an adaptation to protect the oxygen-sensitive nitrogenase enzyme. Sporocarps also have a thick outer covering, possibly to limit oxygen diffusion. The enriched N content within mature sporocarps may offer a dietary inducement for termites in exchange for spore dispersal. These results show that the flexible metabolic capacity of fungi may facilitate N 2 -fixing associations, as well as higher-level organismal associations., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Understanding dose-dependent survival of irradiated cells is a pivotal goal in radiotherapy and radiobiology. To this end, the clonogenic assay is the standard in vitro method, classifying colonies into either clonogenic or non-clonogenic based on a size threshold at a fixed time. Here we developed a methodological framework for the automated analysis of time course live-cell image data to examine in detail the growth dynamics of large numbers of colonies that occur during such an experiment. We developed a segmentation procedure that exploits the characteristic composition of phase-contrast images to identify individual colonies. Colony tracking allowed us to characterize colony growth dynamics as a function of dose by extracting essential information: (a) colony size distributions across time; (b) fractions of differential growth behavior; and (c) distributions of colony growth rates across all tested doses. We analyzed three data sets from two cell lines (H3122 and RENCA) and made consistent observations in line with already published results: (i) colony growth rates are normally distributed with a large variance; (ii) with increasing dose, the fraction of exponentially growing colonies decreases, whereas the fraction of delayed abortive colonies increases; as a novel finding, we observed that (iii) mean exponential growth rates decrease linearly with increasing dose across the tested range (0-10 Gy). The presented method is a powerful tool to examine live colony growth on a large scale and will help to deepen our understanding of the dynamic, stochastic processes underlying the radiation response in vitro.

Four epitypes and three new species of Amanita (Amanitaceae, Agaricales, Agaricomycetes, Basidiomycota) are described from Guineo-Congolian rainforests of Cameroon. Amanita echinulata, A. fulvopulverulenta, A. robusta , and A. bingensis are epitypified based on collections that are the first since the species were described nearly a century ago. Morphological features of the epitypes are described and enumerated. Amanita minima, Amanita luteolamellata , and A. goossensfontanae are described as new and added to the known macromycota of tropical Africa. Habit, habitat, and known distribution are provided for each species. Sequence data for the internal transcribed spacer (ITS) locus are provided for types and other collections of all taxa, and a molecular phylogenetic analysis across the genus Amanita corroborates morphology-based infrageneric placement for each.

In tropical and subtropical rainforests, vegetative fungal rhizomorphs from the Marasmiineae are routinely used as construction material in bird nests. Because rhizomorphs seldom produce mushrooms within nests, the fungal species involved remain largely unknown. In turn, this limitation has prevented us from resolving broader questions such as whether specific fungal species are selected by birds for different functional roles (i.e., attachment, or parasite control). To fill some of these gaps, we collected 74 rhizomorph-containing bird nests from the Neo- and Afrotropics and used nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) sequences to discriminate between rhizomorph-forming species. In total we recovered 25 Marasmiineae species used by birds in nest construction, none of which were shared between the Neotropics and the Afrotropics. We also collected Marasmiineae basidiomes in the vicinity of nests and used ITS sequences to match these sporulating morphs with nest rhizomorphs for nine species. Basidiomes from an additional five species were found fruiting from rhizomorphs incorporated within bird nests. Finally, an additional six species were putatively identified based on publicly available sequence data. Rhizomorphs of five species were found to be utilized almost exclusively as lining material in nests. Lining material comes in direct contact with nestlings and is hypothesized to play a role in parasite control. Rhizomorphs from 10 species were used to attach and anchor nests to substrates; we matched six of those to fruiting litter trap-forming species collected in the understory. Litter traps hold large quantities of fallen litter material, suggesting that birds may preferentially use rhizomorphs that are adapted to bearing heavy loads for nest attachment. Finally, we describe two species of Marasmius-M. neocrinis-equi , sp. nov., and M. nidus-avis , sp. nov.-that are commonly found associated with bird nests and show that rhizomorph production is common across the genus.

Six species of Entoloma ( Entolomataceae , Agaricales , Basidiomycota ) are described from recent Cameroonian collections: E. bisterigmatum , E. brunneoloaurantiacum , E. djaense , E. intricatum , E. versiforme , and E. parvistellatum .These species occur in tropical rainforests dominated by ectomycorrhizal trees in the genera Gilbertiodendron and Uapaca. Data on macromorphology, micromorphology, DNA sequences, habitat and comparisons with similar taxa are provided for each. This is the first contemporary taxonomic work on the Entolomataceae from Cameroon., (© 2020 Westerdijk Fungal Biodiversity Institute.)

We report on the discovery and characterization of a novel Fusarium species that produced yellow-orange pseudoflowers on Xyris spp. (yellow-eyed grass; Xyridaceae) growing in the savannas of the Pakaraima Mountains of western Guyana. The petaloid fungal structures produced on infected plants mimic host flowers in gross morphology. Molecular phylogenetic analyses of full-length RPB1 (RNA polymerase largest subunit), RPB2 (RNA polymerase second largest subunit), and TEF1 (elongation factor 1-α) DNA sequences mined from genome sequences resolved the fungus, described herein as F. xyrophilum , sp. nov., as sister to F. pseudocircinatum within the African clade of the F. fujikuroi species complex. Results of a polymerase chain reaction (PCR) assay for mating type idiomorph revealed that single-conidial isolates of F. xyrophilum had only one of the MAT idiomorphs ( MAT1-1 or MAT1-2 ), which suggests that the fungus may have a heterothallic sexual reproductive mode. BLASTn searches of whole-genome sequence of three strains of F. xyrophilum indicated that it has the genetic potential to produce secondary metabolites, including phytohormones, pigments, and mycotoxins. However, a polyketide-derived pigment, 8- O -methylbostrycoidin, was the only metabolite detected in cracked maize kernel cultures. When grown on carnation leaf agar, F. xyrophilum is phenotypically distinct from other described Fusarium species in that it produces aseptate microconidia on erect indeterminate synnemata that are up to 2 mm tall and it does not produce multiseptate macroconidia.

New species of Amanita subgen. Lepidella are described from Guyana. Amanita cyanochlorinosma sp. nov. , Amanita fulvoalba sp. nov. , and Amanita guyanensis sp. nov. represent the latest additions to the growing body of newly described ectomycorrhizal fungi native to Dicymbe -dominated tropical rainforests. Macro- and micromorphological characters, habitat, and DNA sequence data for the ITS, nrLSU, rpb2 , and ef1-α are provided for each taxon, and β- tubulin for most. Distinctive morphological features warrant the recognition of the three new species and a molecular phylogenetic analysis of taxa across Amanita subgen. Lepidella corroborates their infrageneric placements., (© 2019 Westerdijk Fungal Biodiversity Institute.)

Understanding how species accomplish dispersal of their propagules can shed light on how they are adapted for their ecosystem. Guyanagaster necrorhizus is a sequestrate fungus, meaning its dispersal propagules, or spores, are entirely enclosed within a fruiting body, termed a sporocarp. This fungus is most closely related to Armillaria and its allies. While Armillaria species form mushrooms and have forcibly discharged spores, G. necrorhizus spores have lost this ability, and by necessity, must be passively dispersed. However, G. necrorhizus does not possess characteristics of other sequestrate fungi with known dispersal mechanisms. Repeated observations of termites feeding on G. necrorhizus sporocarps, and spores subsequently adhering to their exoskeletons, led to the hypothesis that termites disperse G. necrorhizus spores. To test this hypothesis, we used microsatellite markers and population genetics analyses to understand patterns of clonality and population structure of G. necrorhizus. While Armillaria individuals can spread vegetatively over large areas, high genotypic diversity in G. necrorhizus populations suggests spores are the primary mode of dispersal. Spatial genetic structure analyses show that G. necrorhizus sporocarps within 238 m of each other are more closely related than would be expected by chance and conservative estimates from population assignment tests suggest gene flow no longer occurs between sporocarps separated by 2 km. These distances are consistent with previous studies analysing foraging distances of the termites found associated with G. necrorhizus sporocarps. Termites have rarely been recorded to specifically target fungal sporocarps, making this a potentially novel fungal-insect interaction., (© 2018 John Wiley & Sons Ltd.)

In this paper an approach is presented to estimate the constraint required to apply maximum entropy (ME) for statistical inference with underwater acoustic data from a single track segment. Previous algorithms for estimating the ME constraint require multiple source track segments to determine the constraint. The approach is relevant for addressing model mismatch effects, i.e., inaccuracies in parameter values determined from inversions because the propagation model does not account for all acoustic processes that contribute to the measured data. One effect of model mismatch is that the lowest cost inversion solution may be well outside a relatively well-known parameter value's uncertainty interval (prior), e.g., source speed from track reconstruction or towed source levels. The approach requires, for some particular parameter value, the ME constraint to produce an inferred uncertainty interval that encompasses the prior. Motivating this approach is the hypothesis that the proposed constraint determination procedure would produce a posterior probability density that accounts for the effect of model mismatch on inferred values of other inversion parameters for which the priors might be quite broad. Applications to both measured and simulated data are presented for model mismatch that produces minimum cost solutions either inside or outside some priors.

Background: Armillaria is a globally distributed mushroom-forming genus composed primarily of plant pathogens. Species in this genus are prolific producers of rhizomorphs, or vegetative structures, which, when found, are often associated with infection. Because of their importance as plant pathogens, understanding the evolutionary origins of this genus and how it gained a worldwide distribution is of interest. The first gasteroid fungus with close affinities to Armillaria-Guyanagaster necrorhizus-was described from the Neotropical rainforests of Guyana. In this study, we conducted phylogenetic analyses to fully resolve the relationship of G. necrorhizus with Armillaria. Data sets containing Guyanagaster from two collecting localities, along with a global sampling of 21 Armillaria species-including newly collected specimens from Guyana and Africa-at six loci (28S, EF1α, RPB2, TUB, actin-1 and gpd) were used. Three loci-28S, EF1α and RPB2-were analyzed in a partitioned nucleotide data set to infer divergence dates and ancestral range estimations for well-supported, monophyletic lineages., Results: The six-locus phylogenetic analysis resolves Guyanagaster as the earliest diverging lineage in the armillarioid clade. The next lineage to diverge is that composed of species in Armillaria subgenus Desarmillaria. This subgenus is elevated to genus level to accommodate the exannulate mushroom-forming armillarioid species. The final lineage to diverge is that composed of annulate mushroom-forming armillarioid species, in what is now Armillaria sensu stricto. The molecular clock analysis and ancestral range estimation suggest the most recent common ancestor to the armillarioid lineage arose 51 million years ago in Eurasia. A new species, Guyanagaster lucianii sp. nov. from Guyana, is described., Conclusions: The armillarioid lineage evolved in Eurasia during the height of tropical rainforest expansion about 51 million years ago, a time marked by a warm and wet global climate. Species of Guyanagaster and Desarmillaria represent extant taxa of these early diverging lineages. Desarmillaria represents an armillarioid lineage that was likely much more widespread in the past. Guyanagaster likely evolved from a gilled mushroom ancestor and could represent a highly specialized endemic in the Guiana Shield. Armillaria species represent those that evolved after the shift in climate from warm and tropical to cool and arid during the late Eocene. No species in either Desarmillaria or Guyanagaster are known to produce melanized rhizomorphs in nature, whereas almost all Armillaria species are known to produce them. The production of rhizomorphs is an adaptation to harsh environments, and could be a driver of diversification in Armillaria by conferring a competitive advantage to the species that produce them.

This paper shows that energy conservation and the derivation of the two-way coupled mode range equations can be extended in three dimensions to complex mode functions and eigenvalues. Furthermore, the energy in the coupled mode formulation is conserved for finite thickness fluid ocean waveguides with a penetrable bottom boundary beneath any range dependence. The derivations rely on completeness and a modified orthonormality statement. The mode coupling coefficients are specified solely and explicitly by the waveguide range dependence. The statement of energy conservation is applied to a numerical coupled mode calculation.

Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post-Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate-n and ∂a∂i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system., (© 2013 John Wiley & Sons Ltd.)

A conditional probability distribution suitable for estimating the statistical properties of ocean seabed parameter values inferred from acoustic measurements is derived from a maximum entropy principle. The specification of the expectation value for an error function constrains the maximization of an entropy functional. This constraint determines the sensitivity factor (β) to the error function of the resulting probability distribution, which is a canonical form that provides a conservative estimate of the uncertainty of the parameter values. From the conditional distribution, marginal distributions for individual parameters can be determined from integration over the other parameters. The approach is an alternative to obtaining the posterior probability distribution without an intermediary determination of the likelihood function followed by an application of Bayes' rule. In this paper the expectation value that specifies the constraint is determined from the values of the error function for the model solutions obtained from a sparse number of data samples. The method is applied to ocean acoustic measurements taken on the New Jersey continental shelf. The marginal probability distribution for the values of the sound speed ratio at the surface of the seabed and the source levels of a towed source are examined for different geoacoustic model representations., (© 2012 Acoustical Society of America)

Scattering from a rough ocean bottom is described numerically with a two-way coupled-mode formalism that contains scattering effects to all orders and provides an exact solution to the wave equation. Both scattered field and direct blast components are computed within the formalism framework. A comparison of the scattered component solution from the coupled mode with the Born approximation (BA) solution for scattering from a rough bottom Pekeris waveguide shows that the BA predicts correctly the scattered field levels but not detailed structure. The transition from direct blast to scattered field dominance is identified in the total field time series.

Acoustic data collected from a 22 m long horizontal line array with elements comprised of omni-directional hydrophone sensors co-located with acceleration vector sensor triplets are analyzed for seabed geo-acoustic information. Broadband and continuous wave tone data were recorded from the passage of a surface vessel source, the R/V Montague, in an August 2006 experiment conducted in Monterey Bay. The water depth at the array and along the source track was approximately 85 m. Simultaneous inversions for source track and geo-acoustic parameters were performed with 18 tones from the 62-415 Hz tone data for source ranges 0.5-2.0 km. The efficacy of inversions with vector sensor data is demonstrated by the fact that data from vector sensor acceleration components parallel to the array line of bearing produced inversion solutions approximately identical to the solutions obtained from the inversion of data for the same tones from the hydrophone array components. In addition the source spectra derived from these inversions are in nominal agreement with the source spectra obtained from an independent measurement.

A technique has been developed for incorporating adaptively beamformed (ABF) data into geoacoustic inversions and source localizations based on matched-field processing. Rather than adaptively adjusting matched-field weights, for this paper ABF processing is applied to construct subaperture beam data from which the inversions and localizations are derived. This application of ABF processing to inversion and localization is successfully demonstrated with data collected on a horizontal line array from a surface ship of opportunity source (SSOS). When measured data representing noise from one or more interfering sources at various levels are injected into the data collected from the SSOS, the inversion processing with ABF subaperture data is successful at interferer noise levels exceeding the SSOS levels by 10-13 dB and for which the inversion processing with conventionally beamformed data fails.

Scattering from a rough surface in an ocean waveguide is described in a new derivation from a two-way coupled-mode representation. The general formalism, which contains scattering effects to all orders, is truncated to the first-order terms of an iterative (Born) expansion. Both two- and three-dimensional ocean waveguide geometries are discussed. By reducing the mode functions in terms of plane wave reflection coefficients, the off-diagonal components of the scattering kernel that is derived are shown to be consistent with a standard solution, but the diagonal components are different from the standard solution.

Sound propagation in a wedge-shaped environment with a penetrable bottom is simulated with broadband adiabatic mode, coupled mode, and parabolic equation model computations. Simulated results are compared to measured data taken in a tank experiment by Tindle et al. The coupled mode formalism is shown to predict, in agreement with that experiment, that modal wave fronts in penetrable wedges are approximately circular arcs centered at the apex of the wedge for a source near the apex. It is also shown that for wedge angles up to 6 degrees, the received waveforms are well approximated by the adiabatic waveforms time-shifted by a depth-dependent interval to account for the curvature of the modal wave fronts. A small deviation from circularity in the modal wave fronts is possibly observed in the 6 degrees case.

Estimation of geoacoustic parameters using acoustic data from a surface ship was performed for a shallow water region in the Gulf of Mexico. The data were recorded from hydrophones in a bottom mounted, horizontal line array (HLA). The techniques developed to produce the geoacoustic inversion are described, and an efficient method for geoacoustic inversion with broadband beam cross-spectral data is demonstrated. The performance of cost functions that involve coherent or incoherent sums over frequency and one or multiple time segments is discussed. Successful inversions for the first sediment layer sound speed and thickness and some of the parameters for the deeper layers were obtained with the surface ship at nominal ranges of 20, 30, or 50 water depths. The data for these inversions were beam cross-spectra from four subapertures of the HLA spanning a little more than two water depths. The subaperture beams included ten frequencies equally spaced in the 120-200 Hz band. The values of the geoacoustic parameters from the inversions are validated by comparisons with geophysical observations and with the parameter values from previous inversions by other invesigators, and by comparing transmission loss (TL) measured in the experiment with modeled TL based on the inverted geoacoustic parameters.

A two-way integral equation coupled mode method is applied to a continental shelf ocean waveguide proposed for a special session devoted to range-dependent acoustic modeling at the 141st meeting of the Acoustical Society of America. The coupled mode solution includes both sediment trapped and continuum modes. The continuum is approximated by a finite number of leaky modes but neglects the branch cut contribution. Mode coupling matrix elements and the range evolution of the modal amplitudes show the nature of the mode coupling. Transmission loss versus range at 100 Hz predicted by the integral equation approach is compared to the transmission loss predicted by a wide angle parabolic equation method. While there is very good agreement, one observes small differences that can be interpreted as backscattering predicted by the integral equation solution.

Part of an experiment to test a measurement package in a shallow water region in the Gulf of Mexico was designed to gather broadband acoustic data suitable for inversion to estimate seabed geoacoustic parameters. Continuous wave tow acoustic signals at multiple frequencies and broadband impulsive source signals were recorded on a horizontal line array in a high-noise environment. Simulated annealing with a normal mode forward propagation model is utilized to invert for a geoacoustic representation of the seabed. Several inversions are made from different data samples of two light bulb implosions, the measured sound speed profiles at the HLA and at the positions of the light bulb deployments, and for two different cost functions. The different cost functions, measured sound speed profiles, and measured time series result in different inverted geoacoustic profiles from which transmission loss is generated for comparison with measurements. On the basis of physical consistency and from the comparison of the transmission loss and time series, a best estimate geoacoustic profile is selected and compared to those obtained from previously reported inversions. Uncertainties in the sound speed profile are shown to affect the uncertainties of the estimated seabed parameters.

A rise in intracellular free Ca(2+) concentration ([Ca(2+)](i)) is required to activate sperm of all organisms studied. Such elevation of [Ca(2+)](i) can occur either by influx of extracellular Ca(2+) or by release of Ca(2+) from intracellular stores. We have examined these sources of Ca(2+) in sperm from the sea squirt Ascidia ceratodes using mitochondrial translocation to evaluate activation and the Ca(2+)-sensitive dye fura-2 to monitor [Ca(2+)](i) by bulk spectrofluorometry. Sperm activation artificially evoked by incubation in high-pH seawater was inhibited by reducing seawater [Ca(2+)], as well as by the presence of high [K(+)](o) or the Ca channel blockers pimozide, penfluridol, or Ni(2+), but not nifedipine or Co(2+). The accompanying rise in [Ca(2+)](i) was also blocked by pimozide or penfluridol. These results indicate that activation produced by alkaline incubation involves opening of plasmalemmal voltage-dependent Ca channels and Ca(2+) entry to initiate mitochondrial translocation. Incubation in thimerosal or thapsigargin, but not ryanodine (even if combined with caffeine pretreatment), evoked sperm activation. Activation by thimerosal was insensitive to reduced external calcium and to Ca channel blockers. Sperm [Ca(2+)](i) increased upon incubation in high-pH or thimerosal-containing seawater, but only the high-pH-dependent elevation in [Ca(2+)](i) could be inhibited by pimozide or penfluridol. Treatment with the protonophore CCCP indicated that only a small percentage of sperm could release enough Ca(2+) from mitochondria to cause activation. Inositol 1,4,5-trisphosphate (IP(3)) delivered by liposomes or by permeabilization increased sperm activation. Both of these effects were blocked by heparin. We conclude that high external pH induces intracellular alkalization that directly or indirectly activates plasma membrane voltage-dependent Ca channels allowing entry of external Ca(2+) and that thimerosal stimulates release of Ca(2+) from IP(3)-sensitive intracellular stores., (Copyright 1999 Academic Press.)

Sperm cell activation is a critical step in fertilization. To directly investigate the cell signaling events leading to sperm activation it is necessary to deliver membrane impermeant agents into the cytoplasm. In this study, the use of liposomes as possible agent-loading vectors was examined using (1) the octadecylrhodamine B (R18) and NBD phosphatidylethanolamine (NBD DHPE)/rhodamine phosphatidylethanolamine (rhod DHPE) fusion assays in bulk samples, (2) membrane transfer of fluorescence from liposome membranes labeled with R18 and rhodamine-tagged phosphatidylethanolamine (TRITC DHPE), and (3) lumenal transfer of impermeant calcium ions from liposomes to sperm cells, a process that stimulated sperm cell activation. Intermediate-sized unilamellar liposomes (98.17+/-15.34 nm) were prepared by the detergent-removal technique using sodium cholate as the detergent and a phosphatidylcholine/phosphatidylethanolamine/cholesterol (2:1:1 mole ratio) lipid composition. In the R18 fusion assays, self-quenching increased logarithmically with increasing concentrations of R18 in the liposome membranes; addition of unlabeled sperm to R18-labeled liposomes lead to a rapid release of self-quenching. In the NBD DHPE/rhod DHPE resonance energy transfer (RET) fusion assay, RET was rapidly reduced under similar conditions. In addition, individual sperm became fluorescent when TRITC DHPE-labeled liposomes were incubated with unlabeled sperm cells. Incubation of sperm cells with empty liposomes did not significantly affect sperm cell activation and did not alter cell morphology. However, incubation with Ca (10 mM)-loaded liposomes resulted in a time-dependent increase in sperm cell activation (7.5-fold over controls after 15 min). We conclude that liposomes can be used for direct loading of membrane-impermeant agents into sea squirt sperm cell cytoplasm, and that delivery occurs via fusion and content intermixing.

During fertilization, species-specific gamete binding must be followed by sperm penetration of egg vestments before gamete fusion can occur. Sperm proteases, called lysins, aid this process. Sperm from Ascidia ceratodes, Ascidia callosa, and Ascidia paratropa were found to have a surface-mounted chymotrypsin-like protease when studied by enzymology, biotinylated, immunolabeling, and histochemistry. Chymotrypsin substrates and inhibitors blocked fertilization in a concentration-dependent manner in A. ceratodes and decreased the number of sperm heads which penetrated the egg's vitelline coat, but had no effect on sperm binding to follicle cells. Sperm bound to agarose beads coated with the chymotrypsin inhibitor alpha 2-macroglobulin. Chymotrypsin-like enzyme activity, assayed fluorimetrically using N-succinyl-leucinyl-leucinyl-valinyl-tyrosinyl-7 -amido-4-methyl-coumarin as the substrate, was associated with head fractions prepared by differential centrifugation. Biotinylation of live sperm followed by detergent extraction showed that chymotrypsin-like activity could be removed from the detergent extract using avidin-agarose beads. Indirect immunofluorescence of unreacted and reacted sperm heavily labeled membrane domains overlying the mitochondrion and at the base of the head with occasional labeling of the sperm tip. Histochemical studies, which used N-succinyl-alanyl-alanyl-prolyl-phenylalanyl-beta-naphthylamide as the substrate, colocalized enzyme activity in head regions of unreacted and near the mitochondrion of reacted sperm. Thus, we conclude that in ascidian sperm a chymotrypsin-like protease is exposed on the external surface of the plasma membrane of the head, is required for fertilization, and plays a role in sperm penetration but not binding.

Serotonin immunoreactivity was localized in hearts of the opisthobranch gastropod, Aplysia californica (sea hare) and several species of bivalve mollusks, the heterodonts, Mercenaria mercenaria (quahog or cherry stone clam), Protothaca staminea (little neck clam), and the pteriomorphs, Hinnites multirugosus (rock scallop), Crassostrea virginica (eastern oyster), Mytilus edulis (eastern mussel), and Geukensia demissa (ribbed mussel). In addition, serotonin was assayed in the ventricles, auricles and heart-associated tissues in A. californica, M. mercenaria, H. multirugosus, and G. demissa with a sensitive radioenzymatic assay. Serotonin concentrations and the density of innervation were significantly higher in members of the subclass Heterodonta compared to the subclass Pteriomorpha. Serotonin immunoreactivity was observed in all species surveyed except G. demissa, which also contained relatively low concentrations of serotonin. Varicose fibers presumably corresponding to release sites were localized in the ventricles, auricles, and the auricular-ventricular valves. We hypothesize that in the species where serotonin-immunoreactive fibers are present, serotonin serves to modulate cardiac myogenic activity. The significance of the observed distribution and concentration of serotonin to the physiological effects of serotonin on cardiac function in these species is discussed.

This review discusses the ultrastructure of sperm with reference to their development, the surface morphology of the egg, and the processes of sperm binding and penetration during fertilization. These topics are treated for selected invertebrates and lower vertebrates which live in aquatic environments and fertilize their eggs externally. Specifically, sperm eggs from cnidarians, echinoderms, decapod crustaceans, ascidians, lampreys, bony fishes, and amphibians are discussed. Sperm from the majority of these groups exhibit the classical head-midregion-tail configuration characteristic of primitive sperm. Specific variations within this general morphology have been described. The notable exceptions to the primitive-sperm paradigm are the sperm of decapod crustaceans and amphibians. Eggs from all of the animals considered are covered by complex vitelline envelopes except those of cnidarians. In general, the ultrastructural analysis of these egg envelopes shows that they are composed of fibrous subunits. Sperm bind to the vitelline envelope and then penetrate through it to fertilize the egg in all groups reviewed except fishes. In sperm ultrastructure which occur during penetration of the egg envelopes in both flagellated and non-flagellated sperm. These changes, which involve membrane fusion and reorganization as well as movement of membranous organelles, aid the sperm in reaching the actual site of gamete fusion.

A device capable of quantitative measurement of intestinal ischemic damage has been designed. The device is called the electrical contractility meter and employs a clip-on strain gauge transducer that delivers a precisely controlled electrical stimulus to the bowel. Threshold stimulus level (TSL) is the stimulus current in milliamperes (mA) that is necessary to produce a clearly defined smooth-muscle contraction. In 30 dogs, TSL was used to establish viability boundaries in 40 cm ischemic bowel segments. Bowel viability was assessed with the use of TSL in comparison with gross features (color, peristalsis) and blood flow measured by means of Doppler ultrasound at 2 cm intervals in the ischemic small-bowel segments. The TSL scale ranges to 100 mA and varied from a low of 22 +/- 2 mA in normal bowel outside the ischemic segment to 97 +/- 4 mA in grossly gangrenous bowel. There was a consistent correlation between rising TSL and worsening bowel color, disappearance of visible peristalsis, and progressive disappearance of audible Doppler signals. Resection and anastomosis were performed in three groups of 10 dogs at TSL measurements of 30 mA, 40 mA, and 50 mA, respectively. Dogs were killed and anastomoses were inspected on the tenth postoperative day. There were no leaks at TSL = 30 mA, one leak at TSL = 40 mA, and four leaks at TSL = 50 mA. The number of leaks at TSL = 50 mA was significantly greater than at TSL = 30 mA (p less than 0.04, Fisher's exact test). These results show that the quantitative myoelectric parameters established by this device provide a reliable in vivo assessment of bowel viability. The electrical contractility meter is easy to use and may have clinical applicability.