Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx

Background: The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1.6 million SNPs, of which 1536 were selected and genotyped in an extended Iberian lynx sample. Methods: We validated 1492 SNPs and analysed their heterozygosity, Hardy-Weinberg equilibrium, and linkage disequilibrium. We then selected a panel of 343 minimally linked autosomal SNPs from which we extracted subsets optimized for four different typical tasks in conservation applications: individual identification, parentage assignment, relatedness estimation, and admixture classification, and compared their power to currently used STR panels. Results: We ascribed 21 SNPs to chromosome X based on their segregation patterns, and identified one additional marker that showed significant differentiation between sexes. For all applications considered, panels of autosomal SNPs showed higher power than the currently used STR set with only a very modest increase in the number of markers. Conclusions: These novel panels of highly informative genome-wide SNPs provide more powerful, efficient, and flexible tools for the genetic management and non-invasive monitoring of Iberian lynx populations. This example highlights an important outcome of whole-genome studies in genetically threatened species

A Study of Archiving Strategies in Multi-Objective PSO for Molecular Docking

Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Morphometry And Histology Of Gonads From 13 Children With Dysgenetic Male Pseudohermaphroditism

Background. - Dysgenetic male pseudohermaphroditism (DMP) is a sexual differentiation disorder characterized by bilateral dysgenetic testes, persistent müllerian structures, and cryptorchidism in individuals with a 46,XY karyotype. However, the histologic criteria for the diagnosis of DMP are poorly established. Objective. - To determine gonadal histology in children with DMP. Patients and Methods. - Between 1996 and 1998, 13 patients with DMP were evaluated on our service. The clinical diagnosis of DMP was based on a 46,XY karyotype, sex ambiguity, high levels of follicle-stimulating hormone and low levels Of antimüllerian hormone, a decreased testosterone response to human chorionic gonadotropin stimulation without accumulation of testosterone precursors, and the presence of müllerian structures. Molecular sequencing the HMGbox region of the SRY gene did not reveal any mutations. Biopsies were performed for 22 of 26 gonads (patient age at the time of biopsy, 16 months to 10 years). Conventional microscopy was used to evaluate mean tubular diameter, tubular fertility index, and number of Sertoli cells per tubular profile. Results. - All 26 gonads were located outside of the labioscrotal folds. Their histologic features varied from only a reduction in tubular size to features of a streak gonad. Five of the 22 gonads grossly resembled a streak gonad. The mean tubular diameter was severely reduced (>30% reduction relative to the normal tubular diameter for the patient's age) in 4 gonads, markedly reduced (10%-30%) in 11 gonads, slightly reduced (<10%) in one gonad, and normal in one gonad. The tubular fertililty index, expressed as the percentage of tubular profiles containing germ cells, was severely reduced (<30% of normal values) in 9 gonads, markedly reduced (50%-30%) in 2 gonads, and normal in 6 gonads. The number of Sertoli cells per tubular profile was elevated in 16 gonads and normal in one gonad. Thin tubules surrounded by fibrous tissue were occasionally observed. Conclusion. - The histologic findings confirmed the clinical diagnosis of DMP in every patient in the present series. However, gonadal histology was variable, and careful morphometric evaluation may be necessary to establish the diagnosis.1255652656Robboy, S.J., Miller, T., Donahoe, P.K., Dysgenesis of testicular and streak gonads in the syndrome of mixed gonadal dysgenesis: Perspective derived from clinicopathologic analysis of twenty-one cases (1982) Hum Pathol, 13, pp. 700-716Troche, V., Hernandez, E., Neoplasia arising in dysgenetic gonads (1986) Obstet Gynecol Surv, 41, pp. 74-79Krasna, I.H., Lee, M.L., Smilow, P., Sciorra, L., Eierman, L., Risk of malignancy in bilateral streak gonads: The role of the Y chromosome (1992) J Pediatr Surg, 27, pp. 1376-1380Rohatgi, M., Gupta, D.K., Menon, P.S., Verma, I.C., Mathur, M., Mixed gonadal dysgenesis and dysgenetic male pseudohermaphroditism - A critical analysis (1992) Indian J Pediatr, 59, pp. 487-500Rey, R.A., Belville, C., Nhou-Fékété, C., Evaluation of gonadal function in 107 intersex patients by means of serum antimüllerian hormone measurement (1999) J Clin Endocrinol Metab, 84, pp. 627-631Stuchi-Perez, E.G., Lukas-Croisier, C., Castro, M., Evaluation of the tubular and interstitial functions of the testis in 46,XY patients with ambiguous genitalia (2000) J Pediatr Endocrinol Metab, 13, pp. 605-612Chang, H.J., Clark, R.D., Bachman, H., The phenotype of 45,X/46,XY mosaicism: An analysis of 92 prenatally diagnosed cases (1990) Am J Hum Genet, 46, pp. 156-167Rajfer, J., Walsh, P.C., Mixed gonadal dysgenesis: Dysgenetic male pseudoher-maphroditism (1981) The Intersex Child: Pediatric and Adolescent Endocrinology, pp. 103-115. , Josso N, ed. Basel, Switzerland: S. KargerBorer, J.G., Nitti, V.W., Glassberg, K.I., Mixed gonadal dysgenesis and dysgenetic male pseudohermaphroditism (1995) J Urol, 153, pp. 1267-1273Donahoe, P.K., Crawford, J.D., Hendren, W.H., Mixed gonadal dysgenesis: Pathogenesis and management (1979) J Pediatr Surg, 14, pp. 287-300Pelletier, J., Bruening, W., Kashtan, C.E., Germline mutations in the Wilms' tumor supressor gene are associated with abnormal urogenital development in Denys-Drash syndrome (1991) Cell, 67, pp. 437-1147Carré-Éusebe, D., Imbeaud, S., Harbison, M., New, M.I., Josso, N., Picard, J.Y., Variants of the anti-Müllerian hormone gene in a compound heterozygote with the persistent Müllerian duct syndrome and his family (1992) Hum Genet, 90, pp. 389-394Nistal, M., Paniagua, R., Non-neoplastic diseases of the testis (1996) Urologic Surgical Pathology, pp. 458-565. , Bostiwick DG, Eble JN, eds. St Louis, Mo: MosbyLennox, B., Ahmad, K.M., Mack, W.S., A method for determining the relative total length of the tubules in the testis (1970) J Pathol, 102, pp. 229-238Jimenez, R., Sanchez, A., Burgos, M., Dias De La Guardia, R.C., Puzzling out the genetics of mammalian sex determination (1996) Trends Genet, 12, pp. 164-166Müller, J., Skakkebaek, N.F., Quantification of germ cells and seminiferous tubules by stereological examination of testicles from 50 boys who suffered from sudden death (1983) Int J Androl, 6, pp. 143-156Cortes, D., Müller, J., Skakkebaek, N.E., Proliferation of Sertoli cells during development of the human testis assessed by stereological methods (1987) Int J Androl, 10, pp. 589-596Nistal, M., Abaurrea, M.A., Paniagua, R., Morphological and histometric study on the human Sertoli cell from birth to the onset of puberty (1982) J Anat, 14, pp. 351-363Van Niekerk, W.A., Retief, A.E., The gonads of human true hermaphrodites (1981) Hum Genet, 58, pp. 117-122Guerra Jr., G., De Mello, M.P., Assumpção, J.G., True hermaphrodites in the southeastern region of Brazil: A different cytogenetic and gonadal profile (1998) J Pediatr Endocrinol Metab, 11, pp. 519-524Quigley, C.A., De Bellis, A., Marschke, K.B., El-Awady, M.K., Wilson, E.M., French, F.S., Androgen receptor defects: Historical, clinical and molecular perspectives (1995) Endocr Rev, 16, pp. 271-32

Anatomical targets and expected outcomes of catheter-based ablation of atrial fibrillation in 2020.

Anatomical-based approaches, targeting either pulmonary vein isolation (PVI) or additional extra PV regions, represent the most commonly used ablation treatments in symptomatic patients with atrial fibrillation (AF) recurrences despite antiarrhythmic drug therapy. PVI remains the main anatomical target during catheter-based AF ablation, with the aid of new technological advances as contact force monitoring to increase safety and effective radiofrequency (RF) lesions. Nowadays, cryoballoon ablation has also achieved the same level of scientific evidence in patients with paroxysmal AF undergoing PVI. In parallel, electrical isolation of extra PV targets has progressively increased, which is associated with a steady increase in complex cases undergoing ablation. Several atrial regions as the left atrial posterior wall, the vein of Marshall, the left atrial appendage, or the coronary sinus have been described in different series as locations potentially involved in AF initiation and maintenance. Targeting these regions may be challenging using conventional point-by-point RF delivery, which has opened new opportunities for coadjuvant alternatives as balloon ablation or selective ethanol injection. Although more extensive ablation may increase intraprocedural AF termination and freedom from arrhythmias during the follow-up, some of the targets to achieve such outcomes are not exempt of potential severe complications. Here, we review and discuss current anatomical approaches and the main ablation technologies to target atrial regions associated with AF initiation and maintenance.This work was supported by the European Regional Development Fund, the Spanish Ministry of Science and Innovation (SAF2016- 80324-R), and the Fundación Interhospitalaria para la Investigación Cardiovascular (FIC). The Centro Nacional de Investigaciones Cardiovasculares (CNIC) is supported by the Spanish Ministry of Science and Innovation and the Pro-CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505). Giulio La Rosa has received a fellowship grant from the joint program between the Heart Rhythm Association of the Spanish Society of Cardiology (ARC) and CNIC.S

Melioidosis in Tsunami Survivors

Eugene Athan, Anthony M. Allworth, Catherine Engler, Ivan Bastian, and Allen C. Chen

Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: current actions and indicators are insufficient

20openInternationalInternational coauthor/editorInternational agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on progress. However, the CBD and similar policy agreements have often neglected genetic diversity.openHoban, Sean; Campbell, Catriona D.; da Silva, Jessica M.; Ekblom, Robert; Funk, W. Chris; Garner, Brittany A.; Godoy, José A.; Kershaw, Francine; MacDonald, Anna J.; Mergeay, Joachim; Minter, Melissa; O'Brien, David; Vinas, Ivan Paz; Pearson, Sarah K.; Pérez-Espona, Sílvia; Potter, Kevin M.; Russo, Isa-Rita M.; Segelbacher, Gernot; Vernesi, Cristiano; Hunter, Margaret E.Hoban, S.; Campbell, C.D.; da Silva, J.M.; Ekblom, R.; Funk, W.C.; Garner, B.A.; Godoy, J.A.; Kershaw, F.; Macdonald, A.J.; Mergeay, J.; Minter, M.; O'Brien, D.; Vinas, I.P.; Pearson, S.K.; Pérez-Espona, S.; Potter, K.M.; Russo, I.M.; Segelbacher, G.; Vernesi, C.; Hunter, M.E

Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016

In addition to outbreaks of nosocomial influenza, sporadic nosocomial influenza infections also occur but are generally not reported in the literature. This study aimed to determine the epidemiologic characteristics of cases of nosocomial influenza compared with the remaining severe cases of severe influenza in acute hospitals in Catalonia (Spain) which were identified by surveillance. An observational case-case epidemiological study was carried out in patients aged ≥18 years from Catalan 12 hospitals between 2010 and 2016. For each laboratory-confirmed influenza case (nosocomial or not) we collected demographic, virological and clinical characteristics. We defined patients with nosocomial influenza as those admitted to a hospital for a reason other than acute respiratory infection in whom ILI symptoms developed ≥48 h after admission and influenza virus infection was confirmed using RT-PCR. Mixed-effects regression was used to estimate the crude and adjusted OR. One thousand seven hundred twenty-two hospitalized patients with severe laboratory-confirmed influenza virus infection were included: 96 (5.6%) were classified as nosocomial influenza and more frequently had > 14 days of hospital stay (42.7% vs. 27.7%, P <.001) and higher mortality (18.8% vs. 12.6%, P <.02). The variables associated with nosocomial influenza cases in acute-care hospital settings were chronic renal disease (aOR 2.44 95% CI 1.44-4.15) and immunodeficiency (aOR 1.79 95% CI 1.04-3.06). Nosocomial infections are a recurring problem associated with high rates of chronic diseases and death. These findings underline the need for adherence to infection control guidelines

Charge separation relative to the reaction plane in Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}}= 2.76 TeV

Measurements of charge dependent azimuthal correlations with the ALICE detector at the LHC are reported for Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV. Two- and three-particle charge-dependent azimuthal correlations in the pseudo-rapidity range $|\eta| < 0.8$ are presented as a function of the collision centrality, particle separation in pseudo-rapidity, and transverse momentum. A clear signal compatible with a charge-dependent separation relative to the reaction plane is observed, which shows little or no collision energy dependence when compared to measurements at RHIC energies. This provides a new insight for understanding the nature of the charge dependent azimuthal correlations observed at RHIC and LHC energies.Comment: 12 pages, 3 captioned figures, authors from page 2 to 6, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/286

A note on comonotonicity and positivity of the control components of decoupled quadratic FBSDE

In this small note we are concerned with the solution of Forward-Backward Stochastic Differential Equations (FBSDE) with drivers that grow quadratically in the control component (quadratic growth FBSDE or qgFBSDE). The main theorem is a comparison result that allows comparing componentwise the signs of the control processes of two different qgFBSDE. As a byproduct one obtains conditions that allow establishing the positivity of the control process.Comment: accepted for publicatio

Transverse sphericity of primary charged particles in minimum bias proton-proton collisions at s=0.9\sqrt{s}=0.9, 2.76 and 7 TeV

Measurements of the sphericity of primary charged particles in minimum bias proton--proton collisions at $\sqrt{s}=0.9$, 2.76 and 7 TeV with the ALICE detector at the LHC are presented. The observable is linearized to be collinear safe and is measured in the plane perpendicular to the beam direction using primary charged tracks with $p_{\rm T}\geq0.5$ GeV/c in $|\eta|\leq0.8$. The mean sphericity as a function of the charged particle multiplicity at mid-rapidity ($N_{\rm ch}$) is reported for events with different $p_{\rm T}$ scales ("soft" and "hard") defined by the transverse momentum of the leading particle. In addition, the mean charged particle transverse momentum versus multiplicity is presented for the different event classes, and the sphericity distributions in bins of multiplicity are presented. The data are compared with calculations of standard Monte Carlo event generators. The transverse sphericity is found to grow with multiplicity at all collision energies, with a steeper rise at low $N_{\rm ch}$, whereas the event generators show the opposite tendency. The combined study of the sphericity and the mean $p_{\rm T}$ with multiplicity indicates that most of the tested event generators produce events with higher multiplicity by generating more back-to-back jets resulting in decreased sphericity (and isotropy). The PYTHIA6 generator with tune PERUGIA-2011 exhibits a noticeable improvement in describing the data, compared to the other tested generators.Comment: 21 pages, 9 captioned figures, 3 tables, authors from page 16, published version, figures from http://aliceinfo.cern.ch/ArtSubmission/node/308