Comparative genomics suggests primary homothallism of Pneumocystis species.

UNLABELLED: Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two different MAT loci on separate DNA molecules would have been detected, nor with secondary homothallism, because the latter involves generally more MAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identical MAT genes in P. jirovecii isolates from six patients. A strong synteny of the genomic region surrounding the putative MAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. deformans. IMPORTANCE: Sexual reproduction among fungi can involve a single partner (homothallism) or two compatible partners (heterothallism). We investigated the issue in three pathogenic fungal relatives: Pneumocystis jirovecii, which causes severe pneumonia in immunocompromised humans; Pneumocystis carinii, which infects rats; and the plant pathogen Taphrina deformans. The nature, the number, and the organization within the genome of the genes involved in sexual reproduction were determined. The three species appeared to harbor a single genomic region gathering only three genes involved in sexual differentiation, an organization which is compatible with sexual reproduction involving a single partner. These findings illuminate the strategy adopted by fungal pathogens to infect their hosts.

Novel Genome-Editing Tools to Model and Correct Primary Immunodeficiencies.

Severe combined immunodeficiency (SCID) and other severe non-SCID primary immunodeficiencies (non-SCID PID) can be treated by allogeneic hematopoietic stem cell (HSC) transplantation, but when histocompatibility leukocyte antigen-matched donors are lacking, this can be a high-risk procedure. Correcting the patient's own HSCs with gene therapy offers an attractive alternative. Gene therapies currently being used in clinical settings insert a functional copy of the entire gene by means of a viral vector. With this treatment, severe complications may result due to integration within oncogenes. A promising alternative is the use of endonucleases such as ZFNs, TALENs, and CRISPR/Cas9 to introduce a double-stranded break in the DNA and thus induce homology-directed repair. With these genome-editing tools a correct copy can be inserted in a precisely targeted "safe harbor." They can also be used to correct pathogenic mutations in situ and to develop cellular or animal models needed to study the pathogenic effects of specific genetic defects found in immunodeficient patients. This review discusses the advantages and disadvantages of these endonucleases in gene correction and modeling with an emphasis on CRISPR/Cas9, which offers the most promise due to its efficacy and versatility.

Syöttövesisäiliöiden pinnanheilahteluiden hallinta Loviisan voimalaitoksella

Tässä työssä tarkastellaan syöttövesisäiliöiden käyttäytymistä Loviisan voimalaitoksella. Työssä käydään läpi laitoksen kaikki pääjärjestelmät primääri- ja sekundääripuolelta. Lisäksi selvitetään myös säiliöiden käyttäytymiseen liittyvät apujärjestelmät niiltä osin kuin tarpeellista. Työn pääpaino laitosesittelyn jälkeen siirtyy täysin syöttövesisäiliömallin luomiseen ja simulointeihin. Työssä on tutkittu useita esille tulleita ideoita syöttövesisäiliöiden pinnanheilahdusten minimoimiseksi. Säiliömallin luominen ja simuloinnit on suoritettu APROS-voimalaitossimulaattorilla. Työssä on alustavasti tarkasteltu kaikki pinnanheilahdusten hallintaideat. Mahdolliset jatkotutkimukset ja parannustyöt aloitetaan tämän työn pohjalta. Työn aikana saatiin paljon uutta tietoa syöttövesisäiliöiden käyttäytymisestä. Tätä tietoa pystytään hyödyntämään käytössä, prosessisuunnittelussa ja koulutussimulaattoria päivitettäessä.

Evaluation of the indication for surgical extraction of third molars according to the oral surgeon and the primary care dentist. Experience in the Master of Oral Surgery and Implantology at Barcelona University Dental School

Introduction: Third molar extraction is the most frequent procedure in oral surgery. The present study evaluates the indication of third molar extraction as established by the primary care dentist (PCD) and the oral surgeon, and compares the justification for extraction with the principal reason for patient consultation. Patients and method: A descriptive study was made of 319 patients subjected to surgical removal of a third molar in the context of the Master of Oral Surgery and Implantology (Barcelona University Dental School, Barcelona, Spain) between July 2004 and March 2005. The following parameters were evaluated: sex, age, molar, type of impaction, position according to the classifications of Pell and Gregory and of Winter, and the reasons justifying extraction. Results: The lower third molars were the most commonly extracted molars (73.7%). A total of 69.6% of the teeth were covered by soft tissues only. Fifty-six percent of the lower molars corresponded to Pell and Gregory Class IIB, while 42.1% were in the vertical position. The most common reason for patient reference to our Service of Oral Surgery on the part of the PCD was prophylactic removal (51.0% versus 46.1% in the case of the oral surgeon). Discussion and conclusions. Our results show prophylaxis to be the principal indication of third molar extraction, followed by orthodontic reasons. Regarding third molars with associated clinical symptoms or signs, infectious disease-including pericoronitis- was the pathology most often observed by the oral surgeon, followed by caries. This order of frequency was seen to invert in the case of third molars referred for extraction by the PCD. A vertical position predominated among the third molars with associated pathology

Determinants of school efficiency : The case of primary schools in the State of Geneva, Switzerland

Purpose The purpose of this paper is (1) to measure school technical efficiency and (2) to identify the determinants of primary school performance. Design/methodology/approach A two-stage Data Envelopment Analysis (DEA) of school efficiency is conducted. At the first stage, DEA is employed to calculate an individual efficiency score for each school. At the second stage, efficiency is regressed on school characteristics and environmental variables. Findings The mean technical efficiency of schools in the State of Geneva is equal to 93%. By improving the operation of schools, 7% (100 - 93) of inputs could be saved, representing 17'744'656.2 Swiss francs in 2010. School efficiency is negatively influenced by (1) operations being held on multiple sites, (2) the proportion of disadvantaged pupils enrolled at the school and (3) the provision of special education, but positively influenced by school size (captured by the number of pupils). Practical implications Technically, the determinants of school efficiency are outside of the control of the headteachers. However, it is still possible to either boost the positive impact or curb the negative impact. Potential actions are discussed. Originality/value Unlike most similar studies, the model in this study is tested for multicollinearity, heteroskedasticity and endogeneity. It is therefore robust. Moreover, one explanatory variable of school efficiency (operations being held on multiple sites) is a truly original variable as it has never been tested so far.

Full-Body MRI in Patients With an Implantable Cardioverter-Defibrillator: Primary Results of a Randomized Study.

BACKGROUND: Magnetic resonance imaging (MRI) of patients with conventional implantable cardioverter-defibrillators (ICD) is contraindicated. OBJECTIVES: This multicenter, randomized trial evaluated safety and efficacy of a novel ICD system specially designed for full-body MRI without restrictions on heart rate or pacing dependency. The primary safety objective was >90% freedom from MRI-related events composite endpoint within 30 days post-MRI. The primary efficacy endpoints were ventricular pacing capture threshold and ventricular sensing amplitude. METHODS: Subjects received either a single- or dual-chamber ICD. In a 2:1 randomization, subjects either underwent MRI at 1.5-T of the chest, cervical, and head regions to maximize radiofrequency exposure up to 2 W/kg specific absorption rate and gradient field exposure to 200 T/m/s per axis (MRI group, n = 175), or they underwent a 1-h waiting period without MRI (control group, n = 88). A subset of MRI patients underwent ventricular fibrillation induction testing post-MRI to characterize defibrillation function. RESULTS: In 42 centers, 275 patients were enrolled (76% male, age 60.4 ± 13.8 years). The safety endpoint was met with 100% freedom from the composite endpoint (p < 0.0001). Both efficacy endpoints were met with minimal differences in the proportion of MRI and control patients who demonstrated a ≤0.5 V increase in ventricular pacing capture threshold (100% MRI vs. 98.8% control, noninferiority p < 0.0001) or a ≤50% decrease in R-wave amplitude (99.3% MRI vs. 98.8% control, noninferiority p = 0.0001). A total of 34 ventricular tachyarrhythmia/ventricular fibrillation episodes (20 induced; 14 spontaneous) occurred in 24 subjects post-MRI, with no observed effect on sensing, detection, or treatment. CONCLUSIONS: This is the first randomized clinical study of an ICD system designed for full-body MRI at 1.5-T. These data support that the system is safe and the MRI scan does not adversely affect electrical performance or efficacy. (Confirmatory Clinical Trial of the Evera MRI System for Conditionally-Safe MRI Access; NCT02117414).

Training primary care physicians in shared decision making for colorectal cancer screening : Insights from the first statewide colorectal cancer screening program in Switzerland

Background: The State of Vaud has launched the first population-based, organized, colorectal cancer screening program in Switzerland for the population aged 50 to 69. Each primary care physician (PCP) has been invited to participate in an interactive session preparing them to enroll patients in the screening program. We aimed at testing the impact of an interactive seminar for PCPs on their intention to discuss the options of no screening, screening with the fecal-immunological test (FIT) and colonoscopy. We measured attitude, intentions and knowledge through questionnaires filled by PCPs before and after a 2.5 hour-long interactive seminar. The main outcome was the proportion of physicians foreseeing to offer coloscopy vs FIT on an equal basis. Physicians estimated the proportion of their patients prescribed a fecal occult blood test (FOBT) vs coloscopy over the months before the seminar and after the interactive seminar. We used a clinical vignette to test for knowledge about screening indications. The interactive seminar included powerpoint presentations with quizzes and clickers, an 8-minute video presenting a shared decision making (SDM) consultation around CRC screening and distribution of educational materials such as a SDM decision aid and background epidemiological information.

USER'S GUIDE FOR ADVANCED PROCESS SIMULATION SOFTWARE APROS 5

Tässä diplomityössä tehtiin käyttäjän opas kehittyneelle prosessisimulointiohjelmistolle APROS 5. Opas on osa VTT Energialle tehtävää APROS 5 käyttäjän koulutuspakettia, joka julkaistaan myöhemmin CD-ROM -muotoisena. Prosessisimulointiohjelmistoa AAPROS 5 voidaan käyttää termohydraulisten prosessien, automaatiopiirien ja sähköjärjestelmien mallinnuksessa. Ohjelma sisältää myös neutroniikkamallin ydinreaktorin käyttäytymisen mallintamiseksi. APROS:in aikaisemmilla UNIX-ympäristössä toimivilla versioilla on toteutettu useita ydinvoimalaitosten turvallisuustutkimukseen liittyviä analyysejä ja sekä ydinvoimalaitosten että konventionaalisten voimalaitosten koulutussimulaattoreita. APROS 5 toimii Windows NT -ympäristössä ja on oleellisesti erilainen käyttää kuin aikaisemmat versiot. Tämän myötä syntyi tarve uudelle käyttäjän oppaalle. Käyttäjän oppaassa esitetään APROS 5:n tärkeimmät toiminnot, mallinnuksen periaatteet ja termohydraulisten ja neutroniikan ratkaisumallit. Lisäksi oppaassa esitetään esimerkki, jossa mallinnetaan yksinkertaistettu VVER-440 -tyyppisen ydinvoimalaitoksen primääripiiri. Yksityiskohtaisempaa tietoa ohjelmistosta on saatavilla APROS 5 -dokumentaatiosta.

Molecular Analysis of NOTCH2 in Patients with Primary Open-Angle Glaucoma.

BACKGROUND AND PURPOSE: Transgenic mice overexpressing Notch2 in the uvea exhibit a hyperplastic ciliary body leading to increased IOP and glaucoma. The aim of this study was to investigate the possible presence of NOTCH2 variants in patients with primary open-angle glaucoma (POAG). METHODS: We screened DNA samples from 130 patients with POAG for NOTCH2 variants by denaturing high-performance liquid chromatography after PCR amplification and validated our data by direct Sanger sequencing. RESULTS: No mutations were observed in the coding regions of NOTCH2 or in the splice sites. 19 known SNPs (single nucleotide polymorphisms) were detected. An SNP located in intron 24, c.[4005+45A>G], was seen in 28.5% of the patients (37/130 patients). As this SNP is reported to have a minor allele frequency of 7% in the 1000 genomes database, it could be associated with POAG. However, we evaluated its frequency in an ethnic-matched control group of 96 subjects unaffected by POAG and observed a frequency of 29%, indicating that it was not related to POAG. CONCLUSION: NOTCH2 seemed to be a good candidate for POAG as it is expressed in the anterior segment in the human eye. However, mutational analysis did not show any causative mutation. This study also shows that proper ethnic-matched control groups are essential in association studies and that values given in databases are sometimes misleading.

Multiple Myeloma with primary manifestation in the mandible: a case report

Multiple myeloma is a monoclonal malignant proliferation of plasma cells that causes osteolytic lesions in the vertebrae, ribs, pelvic bone, skull and jaw. We report on a clinical case of an 81-year-old male patient who presented with a tumefaction in the mandibular symphysis region, which had evolved over the previous seven months. In the radiographic examination, an extensive osteolytic lesion was observed in the region mentioned above. An incisional biopsy was performed and a histopathological study revealed a malignant hematopoietic neoplasm formed by plasmacytoid cells. During the bone gammagraphy a dissemination of the disease was detected in the scapula, clavicle and ribs. The diagnosis was multiple myeloma. Knowledge about the maxillofacial manifestations of multiple myeloma is important for the early diagnosis of the disease, since its primary form can manifest itself in the jaw. In the clinical case presented here, we highlight the interdisciplinarity needed to obtain a diagnosis and treatment of multiple myeloma

Effectiveness of a primary care-based intervention to reduce sitting time in overweight and obese patients (SEDESTACTIV): a randomized controlled trial; rationale and study design

Background: There is growing evidence suggesting that prolonged sitting has negative effects on people's weight, chronic diseases and mortality. Interventions to reduce sedentary time can be an effective strategy to increase daily energy expenditure. The purpose of this study is to evaluate the effectiveness of a six-month primary care intervention to reduce daily of sitting time in overweight and mild obese sedentary patients. Method/Design: The study is a randomized controlled trial (RCT). Professionals from thirteen primary health care centers (PHC) will randomly invite to participate mild obese or overweight patients of both gender, aged between 25 and 65 years old, who spend 6 hours at least daily sitting. A total of 232 subjects will be randomly allocated to an intervention (IG) and control group (CG) (116 individuals each group). In addition, 50 subjects with fibromyalgia will be included. Primary outcome is: (1) sitting time using the activPAL device and the Marshall questionnaire. The following parameters will be also assessed: (2) sitting time in work place (Occupational Sitting and Physical Activity Questionnaire), (3) health-related quality of life (EQ-5D), (4) evolution of stage of change (Prochaska and DiClemente's Stages of Change Model), (5) physical inactivity (catalan version of Brief Physical Activity Assessment Tool), (6) number of steps walked (pedometer and activPAL), (7) control based on analysis (triglycerides, total cholesterol, HDL, LDL, glycemia and, glycated haemoglobin in diabetic patients) and (8) blood pressure and anthropometric variables. All parameters will be assessed pre and post intervention and there will be a follow up three, six and twelve months after the intervention. A descriptive analysis of all variables and a multivariate analysis to assess differences among groups will be undertaken. Multivariate analysis will be carried out to assess time changes of dependent variables. All the analysis will be done under the intention to treat principle. Discussion: If the SEDESTACTIV intervention shows its effectiveness in reducing sitting time, health professionals would have a low-cost intervention tool for sedentary overweight and obese patients management.

Risk Prediction Scores for Recurrence and Progression of Non-Muscle Invasive Bladder Cancer: An International Validation in Primary Tumours

Abstract Objective: We aimed to determine the validity of two risk scores for patients with non-muscle invasive bladder cancer in different European settings, in patients with primary tumours. Methods: We included 1,892 patients with primary stage Ta or T1 non-muscle invasive bladder cancer who underwent a transurethral resection in Spain (n = 973), the Netherlands (n = 639), or Denmark (n = 280). We evaluated recurrence-free survival and progression-free survival according to the European Organisation for Research and Treatment of Cancer (EORTC) and the Spanish Urological Club for Oncological Treatment (CUETO) risk scores for each patient and used the concordance index (c-index) to indicate discriminative ability. Results: The 3 cohorts were comparable according to age and sex, but patients from Denmark had a larger proportion of patients with the high stage and grade at diagnosis (p,0.01). At least one recurrence occurred in 839 (44%) patients and 258 (14%) patients had a progression during a median follow-up of 74 months. Patients from Denmark had the highest 10- year recurrence and progression rates (75% and 24%, respectively), whereas patients from Spain had the lowest rates (34% and 10%, respectively). The EORTC and CUETO risk scores both predicted progression better than recurrence with c-indices ranging from 0.72 to 0.82 while for recurrence, those ranged from 0.55 to 0.61. Conclusion: The EORTC and CUETO risk scores can reasonably predict progression, while prediction of recurrence is more difficult. New prognostic markers are needed to better predict recurrence of tumours in primary non-muscle invasive bladder cancer patients.

Quality of Disease Management and Risk of Mortality in English Primary Care Practices

OBJECTIVE: To investigate whether better management of chronic conditions by family practices reduces mortality risk. DATA: Two random samples of 5 million patients registered with over 8,000 English family practices followed up for 4 years (2004/5-2007/8). Measures of the quality of disease management for 10 conditions were constructed for each family practice for each year. The outcome measure was an indicator taking the value 1 if the patient died during a specified year, 0 otherwise. STUDY DESIGN: Cross-section and multilevel panel data multiple logistic regressions were estimated. Covariates included age, gender, morbidity, hospitalizations, attributed socio-economic characteristics, and local health care supply measures. PRINCIPAL FINDINGS: Although a composite measure of the quality of disease management for all 10 conditions was significantly associated with lower mortality, only the quality of stroke care was significant when all 10 quality measures were entered in the regression. CONCLUSIONS: The panel data results suggest that a 1 percent improvement in the quality of stroke care could reduce the annual number of deaths in England by 782 [95 percent CI: 423, 1140]. A longer study period may be necessary to detect any mortality impact of better management of other conditions.

Neural Circuits: Male Mating Motifs.

Characterizing microcircuit motifs in intact nervous systems is essential to relate neural computations to behavior. In this issue of Neuron, Clowney et al. (2015) identify recurring, parallel feedforward excitatory and inhibitory pathways in male Drosophila's courtship circuitry, which might explain decisive mate choice.