MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.

UNLABELLED: As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n-dimensional setting. AVAILABILITY AND IMPLEMENTATION: The R package MultiMeta can be downloaded from CRAN. CONTACT: dragana.vuckovic@burlo.trieste.it; vi1@sanger.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hereditary hearing loss: a 96 gene targeted sequencing protocol reveals novel alleles in a series of Italian and Qatari patients.

Deafness is a really common disorder in humans. It can begin at any age with any degree of severity. Hereditary hearing loss is characterized by a vast genetic heterogeneity with more than 140 loci described in humans but only 65 genes so far identified. Families affected by hearing impairment would have real advantages from an early molecular diagnosis that is of primary relevance in genetic counseling. In this perspective, here we report a family-based approach employing Ion Torrent DNA sequencing technology to analyze coding and UTR regions of 96 genes related to hearing function and loss in a first series of 12 families coming from Italy and Qatar. Using this approach we were able to find the causative gene in 4 out of these 12 families (33%). In particular 5 novel alleles were identified in the following genes LOXHD1, TMPRSS3, TECTA and MYO15A already associated with hearing impairment. Our study confirms the usefulness of a targeted sequencing approach despite larger numbers are required for further validation and for defining a molecular epidemiology picture of hearing loss in these two countries.

Salmonella enterica arthritis in a patient with rheumatoid arthritis receiving antitumour necrosis factor therapy / Artritis por Salmonella enterica en un paciente con artritis reumatoide que recibe terapia con factor de necrosis antitumoral

Antitumour necrosis factor (TNF) monoclonal antibodies have become an invaluable treatment against chronic inflammatory diseases such as rheumatoid arthritis (RA). However, due to increased risk of opportunistic infections, patients receiving antiTNF therapy should be closely monitored for serious infections. Here, we describe a case of acute Salmonella enteritidis infection of a joint arthroplasty that previously was functioning well, in a patient receiving infliximab treatment for RA. After prolonged antimicrobial chemotherapy and interrupted infliximab treatment, reimplantation of a new prosthesis was successfully performed two years after Salmonella septic arthritis. Therefore, because of the possibility of extraintestinal salmonellosis, screening for fecal colonization could be advisable in patients undergoing antiTNF treatment. Moreover, we emphasize the importance of appropriate counselling of these patients concerning food hygiene.

Los anticuerpos monoclonales del factor de necrosis antitumoral (FNT) se han convertido en un valioso tratamiento contra las enfermedades inflamatorias crónicas como la artritis reumatoide (AR). Sin embargo, debido al mayor riesgo de infecciones oportunistas, los pacientes que reciben terapia antiFNT se deben se monitoreados muy de cerca con respecto a la posibilidad de infecciones serias. Aquí describimos un caso de infección aguda por Salmonella enteritidis de una artroplastia de articulación que anteriormente funcionaba bien, en un paciente que recibía tratamiento con infliximab por RA. Después de prolongadas quimioterapias antimicrobianas y tratamiento interrumpido con infliximab, se realizó exitosamente la reimplantación de una nueva prótesis, dos años después de la artritis séptica por Salmonella. Por lo tanto, debido a la posibilidad de una salmonelosis extraintestinal, podría ser aconsejable el tamizaje de la colonización fecal en pacientes sometidos a tratamiento antiFNT. Por otra parte, hacemos hincapié en la importancia de aconsejar apropiadamente a estos pacientes con respecto a la higiene de los alimentos.

Salmonella enterica arthritis in a patient with rheumatoid arthritis receiving anti-tumour necrosis factor therapy.

Anti-tumour necrosis factor (TNF) monoclonal antibodies have become an invaluable treatment against chronic inflammatory diseases such as rheumatoid arthritis (RA). However, due to increased risk of opportunistic infections, patients receiving anti-TNF therapy should be closely monitored for serious infections. Here, we describe a case of acute Salmonella_enteritidis infection of a joint arthroplasty that previously was functioning well, in a patient receiving infliximab treatment for RA. After prolonged antimicrobial chemotherapy and interrupted infliximab treatment, reimplantation of a new prosthesis was successfully performed two years after Salmonella septic arthritis. Therefore, because of the possibility of extraintestinal salmonellosis, screening for fecal colonization could be advisable in patients undergoing anti-TNF treatment. Moreover we emphasize the importance of appropriate counselling of these patients concerning food hygiene.

Automated high-throughput method using solid-phase microextraction-liquid chromatography-tandem mass spectrometry for the determination of ochratoxin A in human urine.

A new automated, high-throughput method for the determination of ochratoxin A (OTA) in human urine samples has been optimized and validated using solid-phase microextraction coupled to liquid chromatography-tandem mass spectrometry (SPME-LC-MS/MS). High-throughput was achieved by simultaneous preparation of up to 96 samples using multi-fiber SPME device and multi-well plates. A carbon-tape coating was chosen for the first time as the best extracting phase for this contaminant. The proposed method required only minimal sample pre-treatment to adjust sample pH to 3.0 using a dilution (1:1) with 0.5M phosphate-buffered saline. A simple gradient guaranteed a good chromatographic separation from matrix interferences in only 8min. Relative recovery (%), precision and linearity validation results met Food and Drug Administration acceptance criteria at three concentration levels (1, 10, and 50ng/mL), indicating excellent performance of the proposed method. Limits of detection and quantitation were 0.3 and 0.7ng/mL in urine, respectively. OTA determination in urine is a good marker for human exposure to this mycotoxin. It is also less invasive than blood analysis. This method is fully automated and the SPME technique is simpler, less time-consuming and cheaper compared with most widely adopted clean-up procedures for OTA extraction from urine.

Level of left ventricular dysfunction in endomyocardial biopsy-proven myocarditis.

The level of myocardial functional impairment in the course of myocarditis still remains associated with controversial data. However, many investigators agree that there is a significant heart failure during myocarditis and a large number of studies suggest development of global chronic or acute heart failure. The objective of this study was to establish haemodynamic parameters as descriptors of the level of myocardial systolic and diastolic impairment. From 131 investigated patients, 95 were assigned to the study group and 36 to the control group. All patients underwent right and left heart catheterization. A group of patients underwent EMB (endomyocardial biopsy) of the right ventricle. According to the Dallas Criteria, patients were divided into three groups: active myocarditis with fibrosis, active myocarditis without fibrosis and borderline myocarditis. The following haemodynamic parameters were evaluated: left ventricle EF (ejection fraction), cardiac index and end diastolic pressure of the left ventricle. EF, which reflects left ventricular systolic impairment, showed a difference related to the control group, while there was no difference in cardiac index between the groups. Diastolic dysfunction (end diastolic pressure of the left ventricle) was noted in the group with active myocarditis, but not in the group with borderline myocarditis.

Primary Campylobacter jejuni infection in different mice strains.

Campylobacter jejuni is one of the most frequent causes of diarrhoea in man. Extra-intestinal manifestations may also occur, particularly in immunocompromised individuals. However, because of the lack of appropriate animal models the pathophysiology and immunological response of the host to C. jejuni infection are still poorly understood. In our laboratory an experimental infection of adult BALB/c, C57BL/6 and DBA/2 mice has been established. After intraperitoneal injection of 0.5-1x10(9) cfu of C. jejuni none of the infected mice showed clinical symptoms of illness, but bacterial spreading and tissue invasion were achieved. We have concentrated our studies on the duration of primary infection, recovery of bacteria from livers and spleens of infected animals and pathohistological changes of these organs. Our results showed differences in the course of systemic infection among the tested mice strains. BALB/c mice were most sensitive, resulting in the most pronounced pathohistological changes in the examined organs. The duration of the primary liver infection was the longest in BALB/c mice while the duration of the splenic infection also differed among the tested mice strains. Nevertheless, the experimental model used in this study can be efficiently used in further analysis of the pathogenesis of this bacterial infection. However, the strain differences should be taken into account depending on the parameters to be followed.

Changes in macrophage function during chemotherapy.

Antibiotics, in addition to killing or inhibiting the growth of microorganisms, may also affect the mechanism of host defence in many ways. Such effects may be clinically relevant especially in the case where an impairment of immunological function can be seen. We, therefore, decided to study the influence of penicillin G, cefotaxim, ceftazidime, streptomycin, and lincomycin on the function of phagocytes by using the macrophage adherence assay and the macrophage spreading assay. We also followed the concentrations of neopterin and interferon gamma (IFN gamma) in the plasma of mice treated with the above mentioned antibiotics. Changes in adherence of peritoneal macrophages were seen in mice treated with therapeutic doses of penicillin G and cefotaxim, after 2 h of incubation. Cefotaxim and streptomycin in the usual therapeutic dose and ceftazidime in a fourfold higher dose influenced the capacity of peritoneal macrophages to spread on a glass surface. The same was seen with lincomycin when administered in the therapeutic dose and in a fourfold higher dose. In all the mice treated with antibiotics the concentration of IFN gamma was higher than in the control mice, while the reverse was seen concerning neopterin release, with an exception in mice treated with streptomycin.

[Atherosclerotic plaque hemorrhage as one form of a complicated atherosclerotic lesion]. / Krvarenje u ateroskleroznom plaku kao jedan od oblika komplikovane aterosklerozne lezije.

Atherosclerotic plaque hemorrhage is a form of a complicated atherosclerotic lesion. It is a finding of extravasation of erythrocytes (fresh hemorrhage) or siderophages (old hemorrhage) in the defined atherosclerotic changes. 510 segments of the main epicardial coronary arteries (right coronary artery, anterior interventricular branch of the left coronary artery, circumflex branch of the left coronary artery) were microscopically examined in 50 obduction cases of patients with ischemic heart diseases. Fresh hemorrhage in the atherosclerotic plaque was established in 25 cases, that is in 40 microscopically examined coronary artery segments. It was established in all cases where there was a atherosclerotic plaque rupture, in some segments where process of thrombotic organization occurred, as well as in some segments of arteries which supply the region of early myocardial infarction. All hemorrhages occur inside lipidic and fibrolipidic atherosclerotic changes of intima. The average length of fresh hemorrhage was 0.8 cm. 92.50% of segments with fresh hemorrhages occur in the first 4 cm of the examined arteries. 88% of plaque hemorrhages occur in segments with 76-100% lumen obstruction. Signs of old hemorrhages most often occur in segments with 51-75% and 76-100% lumen obstruction. Siderophages mostly occur in complicated atherosclerotic changes and thrombotic organization.

[Calcification in atherosclerotic plaque as one of the types of complicated atherosclerotic lesions]. / Kalcifikacije u ateroskleroznom plaku kao jedan od oblika komplikovane aterosklerozne lezije.

Calcifications of the atherosclerotic plaque is the form of a complicated atherosclerotic lesion. It is characterized by granular or massive deposits of calcium chloride inside the atherosclerotic plaque. It was found in at least one of the three main coronary arteries in 43 (86.00%) out of 50 autopsy cases. In all three, coronary arteries calcifications were found in 8 (18.60%) cases, in two coronary arteries in 19 (44.19%), and one coronary artery in 16 (37.21%) cases. Calcifications of atherosclerotic changes which contain fats were statistically significantly more frequently established than those which did not contain fats. In three fourths of cases calcifications were present in segments with significant narrowing of the arterial lumen (group 3 and 4). In 59.61% of calcificated atherosclerotic changes the residual lumen was of eccentric shape, in 20.51% of concentric shape, in 7.69% it was semilunar, and in 12.18% a few lumens were detected (channeled and organized thrombi). Granular deposits of calcium were established 63.46%, while massive in 36.54% of segments of atherosclerotic lesions, but no statistically significant difference in distribution of these two types of calcifications was established in regard to the type of atherosclerotic change.

Ultrastructural aspect of myocarditis: its relevance for the diagnosis.

The Dallas consensus was used to reveal active or borderline inflammatory loci by light microscopy (LM). When lymphocyte-cardiocyte interaction was observed by electron microscopy (EM), the deleterious or dormant pattern of inflammatory process was recognized. The first was determined by lymphocytes that adhered to cardiocytes, next to necrotic cardiocytes or admixed with debris. The second was marked by scattered lymphocytes between preserved cardiocytes and the absence of lymphocytes adhered to cardiocytes and necrotic cardiocytes. The deleterious pattern of the inflammatory process (EM) commonly supplemented the active appearance of inflammatory loci (LM). In contrast, the borderline outlook of the LM completed either the deleterious or dormant pattern of the EM. This discrepancy was related to the restricted resolution of LM, which might hide the actual stage of the disease. The diagnosis of myocarditis was founded on mutual LM and EM observations. The active or borderline appearance of LM of the deleterious pattern (EM) was considered indicative for the active stage of myocarditis. The borderline outlook of the LM of the dormant pattern of the EM was admitted to indicate either the healing phase of the disease with lymphocytes still lagging behind, or a latent phase of the ongoing myocarditis, according to the patient's hemodynamic status.

[Pathohistologic changes in aortocoronary venous grafts]. / Patohistoloske promene u aortokoronarnim venskim graftovima.

This paper analyses histological changes of venous grafts in 52 obduction cases who had undergone aortocoronary bypass grafting and in whom death occurred after more than 30 days from surgery. The group consisted of 46 males and 6 females. The mean age at the moment of surgery was 51.5, while on the average the patients lived 4.83 years after the surgery. 144 venous grafts were implanted, that is 2.77 per patient. In 49 (34.03%) venous grafts fibrosis intima was established. As in 43 (29.86%) grafts it did not cause occlusion of the lumen greater than 25%, these kinds of grafts were marked as unchanged, normal. In 43 (29.00%) grafts atherosclerosis was established, in 14 (9.72%) fibrointimal proliferation, and in 38 (26.39) lumen obliteration. A year after the surgery the most important pathohistologic change was fibrointimal proliferation, and two years after the surgery and on-atherosclerosis. The percentage of certain pathohistologic types of graft changes, no matter how long patients survived after the surgery was the same in both patients with implants of the coronary artery and those with anterior interventricular branch of the left coronary artery. Grafts implanted into branches of the circumflex artery were statistically significantly more often obliterated. The locality of anastomosis of the venous graft and artery was not occluded in 67.31% of all obduction cases, whereas it was occluded in 32.69% of cases or 32 (22.22%) implanted grafts. Occlusions were caused by atherosclerotic change of the anastomosis in 84.37% of grafts, and by simultaneous occurrence of atherosclerotic change and thromb in 15.63% of grafts.

[Correlation of postmortem coronarography and the macroscopic and microscopic determination of luminal narrowing of coronary arteries in ischemic heart disease]. / Korelacija postmortalne koronarografije i makroskopski i mikroskopski odredenih stepena suzenja lumena koronarnih arterija kod ishemijske bolesti srca.

In our work we used 30 consecutive abduction cases of individuals suffering from ischemic heart disease. Postmortal coronarography was performed in all and we examined the narrowness of artery lumen, its degree, existence and locality of the obturatory thrombus, artery domination, state of aortocoronary grafts and the existence of anastomoses. Coronary arteries were macroscopically examined by cuts on every 0.5 cm of the established aims, and then segments were examined microscopically. The gathered results were compared and the degree of agreement of the two methods was calculated. An agreement of 100% was established when determining artery domination and presence of obturatory thrombus, although the number of found thrombi was bigger when macroscopic/microscopic examination was done. The defined degree of artery lumen narrowness was identical in 75% of cases.

[Analysis of the cause of death in patients with aortocoronary bypass implants]. / Analiza uzroka smrti bolesnika sa implantiranim aortokoronarnim bajpasom.

This paper analyzes causes of death in 91 autopsied patients in whom aortocoronary bypass surgery was performed as a therapy of ischemic heart disease. Patients who died within 30 days after surgery made up the group of so-called "early deaths", while those who died 30 or more days after the surgery made up the group of so-called "late deaths". The leading cause of death in the group of "early deaths" was myocardial infarction (51%) and then causes of death connected to other systems of organs (38%). Hematopericardium and consequential cardiac tamponade was the cause of death in 8% of cases, while in 3% of cases it was cardiac decompensation. In the group of "late deaths" the most important cause of death was myocardial infarction (56%), and then cardiac decompensation (27%), as well as causes of death connected to other systems of organs (17%).

Why do our patients die of active tuberculosis in the era of effective therapy?

SETTING: All patients with tuberculosis as a primary or underlying cause of death who were autopsied at the Institute for Lung Diseases and Tuberculosis, Sremska Kamenica, in the former Yugoslavia, between 1981 and 1990 were investigated. OBJECTIVE: To study why people die of active tuberculosis in the era of effective chemotherapy and to identify factors contributing to death. DESIGN: In a retrospective investigation, this index group was compared with a control group consisting of patients who suffered from tuberculosis over the same period but who improved and were discharged from hospital. RESULTS: A significant difference in age (P < 0.05) was found between those patients who died with an antemortem-established diagnosis and those who died with unrecognised tuberculosis (median 49 and 60 years respectively). When it came to the index group, 28 patients (56%) had one or more risk factors and the frequency of alcohol abuse was significantly higher (P < 0.001). Antituberculosis treatment had been introduced in 27 cases (54%). The median duration of hospitalization before therapy was 2 days and the median duration of antituberculosis therapy was 7 days. Of the 23 untreated tuberculosis patients, 74% died within the first 4 days. CONCLUSION: Delay in the detection of tuberculosis was the main factor contributing to death in our patients.

[Distribution of macroscopic determination of narrowing of the lumen of coronary arteries in ischemic heart disease]. / Distribucija makroskopski odredenih suzenja lumena koronarnih arterija kod ishemijske bolesti srca.

The paper presents macroscopically analyzed 2600 segments 0.5 cm of length of all three main coronary arteries in 50 consecutive autopsy cases suffering from ischemic (coronary) heart disease. A quarter of segments had had a "critical" lumen narrowness (75% of more). The greatest concentration of "critical" lumen narrowness is within the first 6 cm of length. Similar distribution of "critical" lumen narrownesses was found in the first 4 cm of length of circumflex branch of left coronary artery with a remark that concentration of examined segments was higher between the second and fourth cm. The greatest concentration of "critical" lumen narrownesses was not established, because these segments are evenly arranged along the first 10 cm, when examined according to the assumed thirds. Single coronary disease was found in 10% of cases, double coronary disease in 44%, triple coronary in 44% and stenosis of the left coronary arteries in 2%. On the average 2.3 coronary arteries with "critical" lumen narrownesses were found in each case.

[Dissecting aortic aneurysms]. / Disekantne aneurizme aorte.

33 autopsy cases of dissecting aneurysms of aorta were analyzed to find out the frequency, localization, macroscopic appearance, histological changes and causes of death. On the basis of disturbed appearance and orientation of elastic muscular elements of tunica media aortae, existing cystic spaces, areas of fibrosis and increase of mucoid basic substance in media as well as the severity of atherosclerotic changes, we classified our cases into familiar morentities which are connected with the origin of dissecting aneurysms of aorta (cystic medionecrosis, "noninflammatory aortopathy", atherosclerosis hypoplasia). In the third part of all cases media aortae contains areas similar to those of infarct, which could, considering the absence of cellular reaction, be corresponding with ischemic phenomena which directly preceded the genesis of dissection of aorta.

[Types of atherosclerotic changes in relation to the type of residual lumen and degree of narrowing in coronary arteries in ischemic heart disease]. / Vrsta aterosklerozne promene u odnosu na tip rezidualnog lumena i stepen suzenja koronarnih arterija kod ishemijske bolesti srca.

510 segments of all three coronary arteries in 50 obduction cases of individuals suffering from ischemic (coronary) heart disease were microscopically examined. We examined the type of atherosclerotic change, the degree of narrowness of lumen artery and the type of residual lumen. In the group one of the narrowness of artery lumen 44 segments with fibrotic plaque were found, where concentric shape of lumen dominates. In the group two of the narrowness 176 segments were found. Most of them were with fibrotic plaque, but complicated atherosclerotic lesions were also present. According to the shape of residual lumen the concentric narrow shape dominates. In the group three of the narrowness of the lumen 191 segments were found; considering the type of atherosclerotic change complicated lesions were most common, while lipidic plaque was also present. An eccentric shape of residual lumen dominates this group. In the group four of the narrowness of lumen artery 99 segments were found; in this group we found fibrotic plaque and complicated atherosclerotic lesions. The most common finding of the residual lumen is the type of multiple lumen (channelled thrombi).

[Cystic teratoma of the neck]. / Cisticni teratom vrata.

Teratomas of the neck are very rare, and up to now only a small number of cases has been described (10 in adults), while in children it is a more frequent finding (132 described cases). It is judged that up to 4% of all teratomas in children are located in the cervicothyroid region. The paper presents a case of a cystic teratoma of the neck in a male child of 1.5 years of age, which gradually increased in it's size during the course of 12 months prior to operation. The tumor had the dimensions 3.7 x 3.2 x 2.7 cm, it was multicystic, and clinically it gave the impression of a bronchial cyst. Histologically the tumor contained elements of all three primary embryonic germ layers.