Auricular mild errors of morphogenesis: epidemiological analysis, local correlations and clinical significance

BACKGROUND: The mild errors or morphogenesis (MEMs) are well known and accepted markers of alterations in embryonic development with predictive value in identification of major malformations, specific genetic syndromes, metabolic and psychiatric disease and childhood malignancy. OBJECTIVE: The goal of this study was to assess the contribution of auricular MEMs as part of total MEMs in an effort to study the factors influencing the different potential informative value of different types of MEMs and their variability with perinatal factors. METHOD: Three thousand one hundred and seven consecutive born neonates were screened for auricular and non-auricular MEMs, inregistered concomitantly with major malformations and postural defects. The study was accomplished by our specially designed computerized program in a relatively large nonhomogeneous ethnic population, in the metropolitan area of Haifa, Israel. RESULTS: The general prevalence of auricular MEMs was 43.1%; the most frequent pathogenetic type was the postural one. Significantly higher rates of auricular MEMs were associated with male sex, small- and large-for-gestational age, IVF pregnancy, triplet pregnancy, maternal diabetes and parental consanguinity. CONCLUSION: We conclude that the presence, number, and association or concomitance of auricular MEMs in the same neonate may have important clinical, diagnostic, pathogenetic, screening, and therapeutic value.     

Gclust:A Parallel Clustering Tool for Microbial Genomic Data

The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources.Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential.However,existing clustering algorithms perform poorly on long genomic sequences.In this article,we present Gclust,a parallel program for clustering complete or draft genomic sequences,where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays(SSAs).Moreover,genome identity measures between two sequences are calculated based on their maximal exact matches(MEMs).In this paper,we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets.Gclust is freely available for non-commercial use at https://github.com/niu-lab/gclust.We also introduce a web server for clustering user-uploaded genomes at http://niulab.scgrid.cn/gclust.     

Are stacked species distribution models accurate at predicting multiple levels of diversity along a rainfall gradient?

We use observed patterns of species richness and composition of ant communities along a 1000 mm rainfall gradient in northern Australian savanna to assess the accuracy of species richness and turnover predictions derived from stacked species distribution models (S‐SDMs) and constrained by macroecological models (MEMs). We systematically sampled ants at 15 sites at 50 km intervals along the rainfall gradient in 2012 and 2013. Using the observed data, we created MEMs of species richness, composition and turnover. We built distribution models for 135 of the observed species using data from museum collections and online databases. We compared two approaches of stacking SDMs and three modelling algorithms to identify the most accurate way of predicting richness and composition. We then applied the same beta diversity metrics to compare the observed versus predicted patterns. Stacked SDMs consistently over‐predicted local species richness, and there was a mismatch between the observed pattern of richness estimated from the MEM, and the pattern predicted by S‐SDMs. The most accurate richness and turnover predictions occurred when the stacked models were rank‐ordered by their habitat suitability and constrained by the observed MEM richness predictions. In contrast with species richness, the predictions obtained by the MEM of community similarity, composition and turnover matched those predicted by the S‐SDMs. S‐SDMs regulated by MEMs may therefore be a useful tool in predicting compositional patterns despite being unreliable estimators of species richness. Our results highlight that the choice of species distribution model, the stacking method used, and underlying macroecological patterns all influence the accuracy of community assembly predictions derived from S‐SDMS.     

Survey of rotavirus infection in a Hungarian paediatric hospital. A short communication

In anticipation of a future vaccination program against rotavirus disease, a longitudinal survey has been set up to evaluate the epidemiologic features of rotavirus infections. In this report hospitalisation data and serotyping results are compiled from an epidemiologic survey conducted in Baranya County, Hungary. It was found that rotavirus-associated hospitalisation constituted a major part of infectious gastroenteritis cases (range, 14.9% to 28.5%). A higher proportion of rotavirus-positive cases was recorded when the serotype of predominant strains changed from G1 (1996-1999) to G4 (1999-2000), however, due to the short time period it was not possible to demonstrate a firm association between serotype prevalence and rotavirus-associated hospitalisation rate. In the future, such studies might help to understand if serotype-specific immunity against rotavirus infection plays an important role at the population level and if (re-)emerging rotavirus strains make an impact on the annual disease burden.     

Prevalence of drug-resistant human immunodeficiency virus type 1 in therapy-naive patients and usefulness of genotype testing

In the present study, we performed genotypic drug-resistance testing in 116 therapy-naive human immunodeficiency virus type 1 (HIV-1)-infected patients between 1999 and 2002 at Nagoya National Hospital, Japan. The prevalence of drug-resistant HIV-1 with one or more major mutations significantly increased from 5.3% (4/75) in 1999-2001 to 17.1% (7/41) in 2002 (P=0.05), suggesting the spread of drug-resistant HIV-1. We identified a patient who possessed a protease (PR) inhibitor-resistant HIV-1 with a major mutation consisting of L90M before the initiation of therapy. The patient was administered zidovudine, lamivudine, and efavirenz as highly active antiretroviral therapy (HAART), as PR inhibitors were excluded based on the result of the drug-resistance testing. The treatment succeeded in strongly suppressing the proliferation of drug-resistant HIV-1 and concomitantly increased CD4 cell counts. Thus, we conclude that drug-resistance testing prior to the initiation of therapy is important for therapy-naive patients to devise the optimum therapy regimen for each individual.     

Morphometry of auricular feathers of barn owls (Tyto alba)

In all owl species, the facial plumage forms a parabolic dish, the facial ruff, which is most conspicuous in the the barn owl (Tyto alba). The center of the ruff is formed by auricular feathers. Such feathers are also found on the preaural flaps which cover the ear openings, and in the region of the beak. In this study, we compare the different types of auricular feathers of the barn owl with contour feathers from the neck. Auricular feathers are characterised by an open vane structure and fewer barbs as compared to contour feathers. Auricular feathers also have fewer distal and proximal barbules than contour feathers. The open vane of the auricular feather results from an acute angle between the barb and the basis of the barbules, and from the extension of the pennula parallel to the barbs. These reductions are differently expressed in the three different types of auricular feathers investigated here and correspond with their function (protecting the ruff from dust).     

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.

We propose a framework for modeling sequence motifs based on the maximum entropy principle (MEP). We recommend approximating short sequence motif distributions with the maximum entropy distribution (MED) consistent with low-order marginal constraints estimated from available data, which may include dependencies between nonadjacent as well as adjacent positions. Many maximum entropy models (MEMs) are specified by simply changing the set of constraints. Such models can be utilized to discriminate between signals and decoys. Classification performance using different MEMs gives insight into the relative importance of dependencies between different positions. We apply our framework to large datasets of RNA splicing signals. Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models.     

Tension lines of the auricular cartilage

Utilizing Langer's technique for skin tension lines, we punctured the auricular cartilage of 10 human cadavers and 2 mature rabbits and 24 immature rabbits with a conical awl to determine their tension lines. Deformation of the holes into straight lines indicated the direction of maximum tension. A regular pattern was observed in adult rabbits and humans: Tension was at right angles to the long axis at the auricular base and parallel at the apex. This pattern was not present at birth, but developed at 1 to 2 weeks of age in rabbits. It is felt that these tension lines are responsible for the clinical results of auricular reconstruction. In children less than 1 week of age, tension lines are disorganized so that nonsurgical correction will be successful as long as hypoplasia is not present. In older children, correction will be successful when the deformity is parallel to the tension lines.     

The role of watercourse versus overland dispersal and niche effects on ostracod distribution in Mediterranean streams (eastern Iberian Peninsula)

The processes behind the heterogeneous distribution of species involve a combination of environmental and spatial effects. In the spatial context, stream networks constitute appropriate systems to compare the relative importance of two dispersal modes in aquatic organisms: overland and watercourse dispersal. In the present study, we analyzed the distribution of ostracod species in a river network in the eastern Iberian Peninsula, with variation partitioning between environmental and spatial factors, using Moran and Asymmetric Eigenvector Maps (MEMs, AEMs) as spatial variables. Our aims were to determine the relative importance of environmental and spatial control and to compare the importance of overland and watercourse dispersal for species distribution of passively-dispersing aquatic organisms. Our results suggest that watercourse was the most important dispersal mode, favoring mass-effects. The role of species sorting was significant and related to temperature, stream width and water quality, measured as a biotic index (IBMWP). These results stress the major importance of connectivity, besides niche-related factors, in structuring riverine communities of passively-dispersing aquatic organisms.     

Rise of CC398 Lineage of Staphylococcus aureus among Infective Endocarditis Isolates Revealed by Two Consecutive Population-Based Studies in France

Staphylococcus aureus isolates from two prospective studies on infective endocarditis (IE) conducted in 1999 and 2008 and isolated from non-IE bacteremia collected in 2006 were spa-typed and their virulence factors were analyzed with a microarray. Both populations were genetically diverse, with no virulence factors or genotypes significantly more associated with the IE isolates compared with the non-IE isolates. The population structure of the IE isolates did not change much between 1999 and 2008, with the exception of the appearance of CC398 methicillin-susceptible Staphylococcus aureus (MSSA) isolates responsible for 5.6% of all cases in 2008. In 1999, this lineage was responsible for no cases. The increasing prevalence of S. aureus in IE is apparently not the result of a major change in staphylococcal population structure over time, with the exception of the emerging CC398 MSSA lineage.     

Development and implementation of a reduced risk peach arthropod management program in New Jersey

We implemented a 2-yr program to reduce organophosphorus and carbamate insecticide use and mitigate their associated risks as they relate to peach production in New Jersey and elsewhere. The main thrust integrated mating disruption with ground cover management practices to reduce oriental fruit moth, Grapholita molesta (Busck) (Lepidoptera: Tortricidae), and tarnished plant bug, Lygus lineolaris (Palisot de Beauvois) (Heteroptera: Miridae), abundance and damage. This Reduced Risk Peach Arthropod Management Program was compared with adjacent conventionally managed peach orchards. In 1999, we found 2.3 times fewer L. lineolaris and stink bugs (Euschistus servus (Say), E. tristigmus (Say), Acrostemum hilare (Say) (Heteroptera: Pentatomidae) and 2.0 times less heteropteran damaged peaches in reduced-risk orchards when compared with conventionally managed orchards. In 2000, we observed 4.9 times fewer heteropteran insects in reduced-risk orchards but damage levels were not significantly different between the two programs. In both years, G. molesta mating disruption gave at least 4 mo of noninsecticidal control of this major pest. The reduced-risk program provided a level of pest control that was equal to or better than conventional peach pest management programs while using fewer organophosporus and carbamate insecticides.     

Jabba: hybrid error correction for long sequencing reads

Background

Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned.

Results

In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is the use of a pseudo alignment approach with a seed-and-extend methodology, using maximal exact matches (MEMs) as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of MEMs in the context of third generation reads are presented.

Conclusion

Jabba produces highly reliable corrected reads: almost all corrected reads align to the reference, and these alignments have a very high identity. Many of the aligned reads are error-free. Additionally, Jabba corrects reads using a very low amount of CPU time. From this we conclude that pseudo alignment with MEMs is a fast and reliable method to map long highly erroneous sequences on a de Bruijn graph.

     

Modified Antia-Buch repair for full-thickness upper pole auricular defects

Various reconstructive techniques have been described for repair of full-thickness upper pole auricular defects. The wedge excision commonly used for treatment of upper pole tumors allows excision and reconstruction in a single stage. However, this technique suffers from major deficiencies. We apply the concept of crescentic scaphal excision and the Antia-Buch advancement-rotation flap principle to repair various full-thickness upper pole auricular defects resulting from excision of skin lesions in eight consecutive patients. The technique achieves a natural auricular shape in three dimensions with minimal disruption of the anatomic landmarks and avoids conspicuous scars. It has several advantages over the original Antia-Buch repair and other techniques used for reconstruction of full-thickness upper pole auricular defects.     

Management of apple scab (Venturia inaequalis) in Romania based on electronic warnings

Apple scab, Venturia inaequalis (Cke) Wint., is a major problem in Romanian apple orchards and is responsible for serious economic losses. The purchase of spraying equipment and phytopharmaceutical products is very expensive in comparison to the income of local apple growers. This is one of the reasons why reduced fungicide sprayings are becoming more and more important. That's why a project was started to investigate the influence of West-European control measures and to improve interaction between local apple growers and research facilities. This experiment took place in an orchard of the university of Timisoara (USABT), where occurrence of apple scab was very high, and in a well managed commercial orchard, both in the Banat region. In July 2006, a comparative study between a traditional Romanian management program, a calendar-based program and a computerized weather-based management program was conducted. Four test plots were taken. The sprayments in plot 1 happened according to the integrated computerized model. No sprayings took place in plot 2. In plot 3 were some sprayments done with sulphur according to the traditional Romanian program. The sprayings in plot 4 were done following a calendar-based spraying program. The products that were used for the sprayments were all easy to obtain in Romania such as dodine (Sillit flow), dithianon (Delan flow), difenoconazole (Score), pyrimethanil (Scala), metiram (Polyram), kresoxim-methyl (Stroby). The occurrence of scab in plot 1 was very low in comparison to the other plots. Analysing the data, on average, the treatments done in plot 1 caused about 50% less damage than the traditional sprayings. This indicated that with a relative small amount of well timed sprayings a enormous amount of damage can be prevented. A calendar-based management program seems to be less effective (more sprayings needed and the results are worse). These results also emphasize the importance of the development of an adequate apple scab management program that should be presented to local apple growers.     

Application of the automated spatial surveillance program to birth defects surveillance data

BACKGROUND: Although many birth defects surveillance programs incorporate georeferenced records into their databases, practical methods for routine spatial surveillance are lacking. We present a macroprogram written for the software package R designed for routine exploratory spatial analysis of birth defects data, the Automated Spatial Surveillance Program (ASSP), and present an application of this program using spina bifida prevalence data for metropolitan Atlanta. METHODS: Birth defects surveillance data were collected by the Metropolitan Atlanta Congenital Defects Program. We generated ASSP maps for two groups of years that correspond roughly to the periods before (1994-1998) and after (1999-2002) folic acid fortification of flour. ASSP maps display census tract-specific spina bifida prevalence, smoothed prevalence contours, and locations of statistically elevated prevalence. We used these maps to identify areas of elevated prevalence for spina bifida. RESULTS: We identified a large area of potential concern in the years following fortification of grains and cereals with folic acid. This area overlapped census tracts containing large numbers of Hispanic residents. CONCLUSIONS: The potential utility of ASSP for spatial disease monitoring was demonstrated by the identification of areas of high prevalence of spina bifida and may warrant further study and monitoring. We intend to further develop ASSP so that it becomes practical for routine spatial monitoring of birth defects.     

Bioinformatics in the community college

Biotechnology is becoming an information-based field. In this article we describe some resources available to instructors, show how these resources are used in the biotechnology training program, and provide examples of activities used by non-science majors to increase their understanding of biology. We discuss some of the challenges we have encountered using these tools in the classroom. Journal of Industrial Microbiology & Biotechnology (2000) 24, 314–318. Received 08 April 1999/ Accepted in revised form 10 November 1999     

Assessment of physician performance in Alberta: the Physician Achievement Review

The College of Physicians and Surgeons of Alberta, in collaboration with the Universities of Calgary and Alberta, has developed a program to routinely assess the performance of physicians, intended primarily for quality improvement in medical practice. The Physician Achievement Review (PAR) provides a multidimensional view of performance through structured feedback to physicians. The program will also provide a new mechanism for identifying physicians for whom more detailed assessment of practice performance or medical competence may be needed. Questionnaires were created to assess an array of performance attributes, and then appropriate assessors were designated--the physician himself or herself (self-evaluation), patients, medical peers, consultants and referring physicians, and non-physician coworkers. A pilot study with 308 physician volunteers was used to evaluate the psychometric and statistical properties of the questionnaires and to develop operating policies. The pilot surveys showed good statistical validity and technical reliability of the PAR questionnaires. For only 28 (9.1%) of the physicians were the PAR results more than one standard deviation from the peer group means for 3 or more of the 5 major domains of assessment (self, patients, peers, consultants and coworkers). In post-survey feedback, two-thirds of the physicians indicated that they were considering or had implemented changes to their medical practice on the basis of their PAR data. The estimated operating cost of the PAR program is approximately $200 per physician. In February 1999, on the basis of the operating experience and the results of the pilot survey, the College of Physicians and Surgeons of Alberta implemented this innovative program, in which all Alberta physicians will be required to participate every 5 years.