Geographical gradient of the <em>eIF4E</em> alleles conferring resistance to potyviruses in pea (<em>Pisum</em>) germplasm

<div><p>Background</p><p>The eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the <i>eIF4E</i> gene to identify novel genetic diversity.</p><p>Methodology/Principal findings</p><p>Germplasm of 2803 pea accessions was screened for <i>eIF4E</i> intron 3 length polymorphism, resulting in the detection of four <i>eIF4E^A-B-C-S</i> variants, whose distribution was geographically structured. The <i>eIF4E^A</i> variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, <i>eIF4E^B</i>, was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The <i>eIF4E^C</i> variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The <i>eIF4E^S</i> variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (<i>eIF4E^{A-1-2-3-4-5-6-7}</i>, <i>eIF4E^B-1</i>, <i>eIF4E^C-2</i>) conferred resistance to the P1 PSbMV pathotype.</p><p>Conclusions/Significance</p><p>This work identified novel <i>eIF4E</i> alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible <i>eIF4E^S1</i> allele. Despite high variation present in wild <i>Pisum</i> accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis to study the co-evolution of potyviruses and the pea host.</p></div

The gene normalization task in BioCreative III

BACKGROUND: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k). RESULTS: We received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively. CONCLUSIONS: By using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance

Factors driving patterns and trends in strandings of small cetaceans

The incidence of cetacean strandings is expected to depend on a combination of factors, including the dis- tribution and abundance of the cetaceans, their prey, and causes of mortality (e.g. natural, fishery bycatch), as well as currents and winds which affect whether carcasses reach the shore. We investigated spatiotemporal patterns and trends in the numbers of strandings of three species of small cetacean in Galicia (NW Spain) and their relationships with meteoro- logical, oceanographic, prey abundance and fishing-related variables, aiming to disentangle the relationship that may exist between these factors, cetacean abundance and mor- tality off the coast. Strandings of 1166 common dolphins (Delphinus delphis), 118 bottlenose dolphins (Tursiops truncatus) and 90 harbour porpoises (Phocoena phocoena) during 2000–2013 were analysed. Generalised additive and generalised additive-mixed model results showed that the variables which best explained the pattern of strandings of the three cetacean species were those related with local ocean meteorology (strength and direction of the North– South component of the winds and the number of days with South-West winds) and the winter North Atlantic Oscil- lation Index. There were no significant relationships with indices of fishing effort or landings. Only bottlenose dolphin showed possible fluctuations in local abundance over the study period. There was no evidence of long-term trends in number of strandings in any of the species and their abun- dances were, therefore, considered to have been relatively stable during the study period.Versión del editor2,01

A TECHNIQUE OF MULTIDETECTOR COMPUTED TOMOGRAPHY FOR OPTIC CEREBRAL OXYMETRY

Aim: To assess geometric parameters of the human head based on X-ray computed tomography for construction of the first Russian optical cerebral oxymeter.Materials and methods: Based on the data obtained by multidetector computed tomography, we retrospectively assessed thickness of the frontal bone squame, adjacent soft tissues and calculated their sum in 100 patients above 50 years of age (50 male and 50 female, mean age 64 ± 8 years). The supraorbital edge of the orbit and the middle line were chosen as the reference points.Results: The mean frontal squame thickness was6.28 mm (± 1.58) on the right side and6.38 mm (± 1.62) on the left side. The mean thickness of the soft tissues covering the bone at this level was4.39 mm (± 1.21) on the right side and4.41 mm (± 1.22) on the left side. The mean total thickness of the frontal squame bone and soft tissue was11.76 mm (± 2.25) on the right side and11.89 mm (± 2.31) on the left side.Conclusion: For reliable reproducibility of cerebral oxymetry, geometric characteristics of the area where the sensor will be placed, taking the supraorbital edge and the middle line as reference points. Minimal sums of the mean values and their standard deviations for the frontal bone thickness and soft tissues were measured at the intersection points of3 cm lines perpendicular to these reference points

RARE NON-TUMOR DISEASES OF THE PHARYNX AND LARYNX

A number of inflammatory systemic and non-systemic pharyngel and laryngeal diseases may clinically imitate a tumor. In these cases, computed tomography provides rapid assessment and significant additional information to that obtained from endoscopy. We present 4 clinical observations with certain common features. These are a suspicion of a neoplasm and absence of typical computed tomography symptoms characteristic of tumor lesions. IgG4-related systemic disease, rheumatoid arthritis, amyloidosis, and actinomycosis are rare disorders, however, they should be considered in the differential diagnosis. In this context, the knowledge of the radiation diagnostic characteristics of these rare nosologies will be useful for a practitioner

Polarized Macrophages As Potential Anti-Endometrioid agent

Endometriosis is an estrogen-dependent chronic inflammatory disease characterized by the presence of endometrial stroma and glands outside the endometrium. The gold standard in the treatment of endometriosis is laparoscopy but after that, the relapse rate is about 50%. Thus, the search for new effective non-invasive methods of endometriosis therapy is an actual problem. Endometriosis has many properties similar to tumors including the fact that macrophages with an anti-inflammatory phenotype (M2) prevail in the foci of endometriosis. It is already known that activated macrophages with a pro-inflammatory phenotype (M1) have an antitumor effect. In this regard, we hypothesized that increasing the proportion of M1 macrophages could help in the treatment of endometriosis. The objectives of our work were (1) to assess the expression profile of macrophages in the foci of endometriosis in mice model of endometriosis; (2) to test the efficacy of administration of reprogrammed M1 macrophages as a possible anti-endometrioid agent in the mouse. We studied the phenotypic profile of macrophages in the foci of endometriosis and the anti-endometrioid activity of M1 macrophages on in vivoallogeneic model of mouse endometriosis induced in ovariectomized mice after intraperitoneal transplantation of the mouse uterus accompanied by 17β-estradiol therapy. Analysis of the phenotypic profile of macrophages in the foci of endometriosis was carried out using immunohistochemical staining, western blot analysis, and qPCR. We obtained a reproducible model with lesions that had characteristic morphology. It was shown that macrophages with an anti-inflammatory arginase1+ phenotype prevail in the foci of endometriosis compared with the intact endometrium. After verifying endometriosis development in mice, the experimental group was injected with M1-polarized macrophages, while the control group was injected with unpolarized macrophages, and then the animals were monitored for two weeks. Macrophage cell line RAW264 was incubated with lipopolysaccharide (100 ng/ml) for 24 h to obtain M1-polarized macrophages. M1-polarization was verified by significant up-regulation of MARCO, iNOS markers using western blot and qPCR analysis. After treatment of animals with M1 macrophages, we found that the number of foci and their sizes significantly decreased (p<0.05) in comparison with control animals. In our work, we proved the predominance of anti-inflammatory macrophages in the foci of endometriosis and obtained the first results of a positive effect of M1 macrophages on the regression of foci of endometriosis. © FASEB

VOSTOCHNO-VERKHOTURSKY GABBRO-DIORITE-GRANODIORITE MASSIF (MIDDLE URALS): NEW DATA ON COMPOSITION, FORMATION CONDITIONS, AGE AND METALLOGENY

Relevance of the problem. In the Urals, in connection with the solution of the problem of supplying the operating non-ferrous metallurgy enterprises with local raw materials, a number of copper-porphyry ore-bearing deposits have been involved in the industrial development in the last decade; low-sulfidation mineralization is localized mainly in dioritic intrusive massifs. The presence of large-scale mineralization of native copper in the diorites of the Vostochno-Verkhotursky massif testifies to the need for its comprehensive study and determination of ore-forming appurtenances. Purpose of the paper is to determine the formation and age appurtenances, as well as the metallogenic specialization of the eastern part of Verkhotursko-Isetskaya zone (Middle Urals) of the Vostochno-Verkhotursky massif within which mineralization of native copper was previously identified. Results. Petrographic, geochemical, and isotope-geochronological studies of the gabbro, diorite and granodiorite massifs were carried out (SiO2–53.97–67.32%, K2O – 1.04–2.65%) and gabbro-diorite dikes occurring among them SiO2 – 54.50-56.50%, K2O – 0.96–1.50%). The predominantly corniferous rocks of the massif belong to a single homodromous calci-alkalic normal-alkalic series of a moderately potassic type. Dyorites of dikes are comagmatic to enclosing rocks. The massif is formed in the abyssal-mesoabyssal conditions of the supra-subduction situation at the continental margin of the zone development. The U-Pb age of the investigated rocks of the massif is determined by zircon (the method of laser ablation) in 339.2 2.8 million years (Carbonic period). The formation of the massif occurred within the tectonic block with the basement of the Proterozoic age of the sialic composition. The presence of high concentrations of F in accessory apatites (up to 3.5–4.2%) at relatively low Cl (up to 0.5%) and SO3 (up to 0.4-0.9%) indicates a possible gold-rare metal specialization of formations. Conclusion. To determine conditions for the formation of the mineralization of native copper among the supra-subduction dioritoids of the Middle Carbonic period, its age, ore-bearing belonging, and scale, it is necessary to further study both the formations of the Vostochno-Verkhotursky massif (including those that underwent secondary alterations) and other dioritoid massifs in the eastern part of the Verkhoturskaya-Isetskaya zon