A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP)

As metagenomic studies continue to increase in their number, sequence volume and complexity, the scalability of biological analysis frameworks has become a rate-limiting factor to meaningful data interpretation. To address this issue, we have developed JCVI Metagenomics Reports (METAREP) as an open source tool to query, browse, and compare extremely large volumes of metagenomic annotations. Here we present improvements to this software including the implementation of a dynamic weighting of taxonomic and functional annotation, support for distributed searches, advanced clustering routines, and integration of additional annotation input formats. The utility of these improvements to data interpretation are demonstrated through the application of multiple comparative analysis strategies to shotgun metagenomic data produced by the National Institutes of Health Roadmap for Biomedical Research Human Microbiome Project (HMP) (http://nihroadmap.nih.gov). Specifically, the scalability of the dynamic weighting feature is evaluated and established by its application to the analysis of over 400 million weighted gene annotations derived from 14 billion short reads as predicted by the HMP Unified Metabolic Analysis Network (HUMAnN) pipeline. Further, the capacity of METAREP to facilitate the identification and simultaneous comparison of taxonomic and functional annotations including biological pathway and individual enzyme abundances from hundreds of community samples is demonstrated by providing scenarios that describe how these data can be mined to answer biological questions related to the human microbiome. These strategies provide users with a reference of how to conduct similar large-scale metagenomic analyses using METAREP with their own sequence data, while in this study they reveal insights into the nature and extent of variation in taxonomic and functional profiles across body habitats and individuals. Over one thousand HMP WGS datasets and the latest open source code are available at http://www.jcvi.org/hmp-metarep.     

阴茎折断诊断治疗体会(附11例报道)

目的:探讨阴茎折断伤的诊断和治疗方法的经验.方法:2003年4月-2008年11月我院共诊治阴茎折断患者11例.结果:10例采用急诊手术治疗,1例患者,拒绝手术治疗,予以采取保守治疗.11例患者住院时间为4-9天,平均6天.随访3个月～2年,行手术治疗患者10例和保守治疗的患者1例,均恢复良好,没有出现勃起功能障碍、排尿困难及疼痛等并发症.结论:阴茎折断的诊断主要依据是典型痛史及临床表现,急诊行手术探查是可靠和有效的治疗方法.     

Utilization of extremely low frequency (ELF) magnetic fields in chronic disease; five years experience: three case reports

We present three examples of the use of ELF magnetic therapy, two cases of multiple sclerosis and one of chronic pulmonary disease. In each of the two MS cases the Seqex device was applied as an adjunct to antioxidant medication two times a week for six weeks. Radiological and MRI examination indicated improvement in the two MS patients and stabilization in the patient with obstructive pulmonary disease following merely five treatments.     

Five years of experience teaching pathology to dental students using the WebMicroscope

Background

We describe development and evaluation of the user-friendly web based virtual microscopy - WebMicroscope for teaching and learning dental students basic and oral pathology. Traditional students microscopes were replaced by computer workstations.

Methods

The transition of the basic and oral pathology courses from light to virtual microscopy has been completed gradually over a five-year period. A pilot study was conducted in academic year 2005/2006 to estimate the feasibility of integrating virtual microscopy into a traditional light microscopy-based pathology course. The entire training set of glass slides was subsequently converted to virtual slides and placed on the WebMicroscope server. Giving access to fully digitized slides on the web with a browser and a viewer plug-in, the computer has become a perfect companion of the student.

Results

The study material consists now of over 400 fully digitized slides which covering 15 entities in basic and systemic pathology and 15 entities in oral pathology. Digitized slides are linked with still macro- and microscopic images, organized with clinical information into virtual cases and supplemented with text files, syllabus, PowerPoint presentations and animations on the web, serving additionally as material for individual studies. After their examinations, the students rated the use of the software, quality of the images, the ease of handling the images, and the effective use of virtual slides during the laboratory practicals. Responses were evaluated on a standardized scale. Because of the positive opinions and support from the students, the satisfaction surveys had shown a progressive improvement over the past 5 years. The WebMicroscope as a didactic tool for laboratory practicals was rated over 8 on a 1-10 scale for basic and systemic pathology and 9/10 for oral pathology especially as various students’ suggestions were implemented. Overall, the quality of the images was rated as very good.

Conclusions

An overwhelming majority of our students regarded a possibility of using virtual slides at their convenience as highly desirable. Our students and faculty consider the use of the virtual microscope for the study of basic as well as oral pathology as a significant improvement over the light microscope.

     

Inherited prion disease (PrP lysine 200) in Britain: two case reports.

OBJECTIVE--To identify cases of inherited prion diseases in Britain and to assess their phenotypic features. DESIGN--Screening study of patients suspected clinically to have Creutzfeldt-Jakob disease and other neurodegenerative diseases by prion protein gene analysis. SETTING--Biochemical research department. SUBJECTS--Patients suspected to have Creutzfeldt-Jakob disease and other neurodegenerative diseases. RESULTS--Two patients with symptoms characteristic of sporadic Creutzfeldt-Jakob disease were found to have inherited prion protein disease (PrP lysine 200), with a mutation at codon 200 of the prion protein gene. Both were homozygous at codon 129 of the gene. One patient was a man aged 58 of British descent while the other was of Libyan Jewish origin. CONCLUSION--Two foci of inherited prion disease are known, among Libyan Jews and in Slovakia. A separate British focus of the disease may also exist. Heterozygosity at codon 129 may lead to reduced penetrance of the mutation.     

Prenatal detection of maternal UPD15 in a new case with i(15p) by Timing Replication Test (TRT) and methylation analysis

DNA replication kinetics of the Prader-Willi/Angelman Critical Region (PWACR) was studied with and without synchronisation in human amniotic cell cultures obtained from 20 cases with normal karyotype and 4 cases with a marker of chromosome 15, respectively. A Timing Replication Test (TRT) was performed by synchronisation of amniotic cell cultures and followed by interphase FISH to analyse and compare the early/late replication patterns in SNRPN and UBE3A genes between the homologues of chromosome 15. Asynchronous replication patterns of the analysed genes were observed in both amniotic cell cultures but the percentage of interphase nuclei presenting with asynchronous replication was significantly increased in the cultures with synchronisation (40-51%), as compared to those without synchronisation (20-23%). The evaluations, performed by means of TRT, showed asynchronous replication patterns on control values: between 39% and 46% of cells in all the cases with inv dup(15). In contrast, the percentage of cells with asynchronous replication in the case with i(15p) was significantly decreased (3-6%), as compared to the control value, and it may be indicated by uniparental disomy of chromosome 15 (UPD15). In addition, those results have been confirmed by molecular evaluation, using the methylation diagnostic test for diagnosis of the Prader-Willi Syndrome.     

A simple technique using skin implants to produce histocompatability (BoLA) typing sera*

We describe a technique to produce high-titered bovine lymphocytotoxic anti-sera using skin implants. The main advantage of this technique is that the skin does not need to be processed prior to implantation and no surgical skill is required. In addition, the skin can be stored for up to 2 weeks and can be shipped to other laboratories without special handling and without loss of immunogenicity.     

Five new species of Pythium (Peronosporomycetidae)

Five new species of Pythium are described, following ecological studies of the genus in the Reading (U.K.) area. Two of the new species were found abundantly, three were rarely isolated. Neither of the abundant species produces sporangia and both have very small oospores. Of the rarer species, two have filamentous sporangia and all three have rather large oospores.     

Adolescent female volleyballers' (aged 13-15 years) body build classification and proficiency in competitions

The present paper studies the body build and proficiency in the game of 74 female volleyballers aged 13-15 years from eight teams, who participated in Estonian championships. Fourteen anthropometric measurements were taken from the players, and these data were systematized into a 5 SD height-weight classification (small, medium, large, pyknomorphous and leptomorphous). The players participated in 28 matches, which were recorded in parallel with two computers equipped with the program Game. The girls' proficiency in the game was assessed in the same body build classes. For each class, the total number of serves, receptions, attacks and blocks, their mean values per player and percentage from elements performed during the whole tournament were calculated. In the same way, for each class the total number of points scored and separately the number of points scored in serve, attack and block were calculated. For each class the mean index of proficiency was calculated for serve, reception, attack and block. The results showed, that the most successful were the girls of class 3 with big height and weight. The small girls of class 1 were the least successful. The players belonging to the other classes formed an intermediate group. The authors recommend the use of the body build classification as it enables simultaneous assessment of body build and proficiency in competitions.     

Histoplasmosis as cause of penile ulcer in acquired immune deficiency syndrome (AIDS): three case reports

Background Histoplasma capsulatum is the causative agent of American histoplasmosis. The relationship between disseminated histoplasmosis and AIDS has been well established. Widespread hematogenous dissemination of Histoplasma capsulatum in HIV positive patients can cause a plethora of clinical manifestations; virtually any organic system can be affected. However, genital ulceration by H. capsulatum in patients with AIDS is a real challenge during investigation of the infection due to the great variety of differential diagnoses that are involved. Method The diagnosis was performed by histopathologic study; H. capsulatum was detected by silver staining (Grocott staining) and confirmed by immunocytochemistry. Results We report three cases of histoplasmosis in patients with AIDS, in which we observed genital ulcers, an unusual form of presentation of this disease. In one of these cases, the treatment resulted in total cure. Conclusion The cases reported herein are to illustrate the plurality of pathologies and clinical manifestations, which may affect immunocompromised patients. The correct diagnosis of fungal diseases in these patients following well established treatment will improve the prognosis.     

Definition of the methodology for a Sector EPD (Environmental Product Declaration): case study of the average Italian cement

Purpose  

The objective of this paper is to describe the process of development of an appropriate methodology for a type III label that can be used by a trade association, namely “Sector Environmental Product Declaration” (EPD). The study starts from the definition of required data, data collection procedures, sample selection criteria etc. With this aim, the application of the scheme on a case study has been conducted, regarding the cement production in Italy.     

Gastric antisecretory effect of 15(R)-15-menthyl PGE2, methyl ester and of 15(S)-15-methyl ester.

Gastric juice was collected from gastric pouches in dogs stimulated with histamine. 15(R)-15-methyl PGE2, methyl ester inhibited gastric secretion in dogs when given orally, but was almost inactive when given intravenously, whereas 15(S)-15-methyl PGE2 methyl ester was active by both routes. When given directly into the small intestine (intrajejunally), the 15(S) was active and the 15(R) was inactive. The 15(R), diluted in acid and administered intrajejunally, became active in inhibiting gastric secretion. When the 15(S) was diluted in acid and administered intrajejunally, it lost half of its activity. When each analog was incubated in an acid medium, each was epimerized to give approximately a 1:1 mixture of both 15(R) and 15(S). Incubation of the 15(R) in pH 3 buffer resulted in only a trace of formation of 15(S). These results explain why the 15(R) is active orally but not intrajejunally. When given orally, the low pH of gastric secretion epimerizes much of the 15(R) into the 15(S),which is active by any route. The degree of acidity of gastric contents may determine whether the 15(R) will exert an antisecretory effect.     

Prosthetic rehabilitation of a patient with mandibular resection prosthesis using mini dental implants (MDIs)--case report

Physical disfigurement and functional impairments associated with facial trauma are a challenge to a prosthodontist, because even novel sophisticated surgical reconstructive techniques fail to provide adequate support for dental resection prosthesis. Therefore, different endosseous implants are often used as prosthesis-supporting elements. Manufacturers of dental implants have recently presented mini dental implants (MDIs) with diameter of only 1.8-2.4 mm. These implants allow very suitable prosthetic solutions within the range of their indications due to good osseointegration success rates, simple surgical technique, and immediate loading possibility. In this report, a case was presented for prosthetic rehabilitation including implantation of two Sendax type (IMTEC, Ardmore, Oklahoma, USA) MDIs in mental region, to obtain better retention and stability of the mandibular resection prosthesis and to improve function, phonation and aesthetics. The use of these implants, among aforementioned preferences, is also very cost-effective, so this implantation possibility should be taken into consideration during prosthetic treatment planning.