Time course based artifact identification for independent components of resting-state FMRI

In functional magnetic resonance imaging (fMRI) coherent oscillations of the blood oxygen level-dependent (BOLD) signal can be detected. These arise when brain regions respond to external stimuli or are activated by tasks. The same networks have been characterized during wakeful rest when functional connectivity of the human brain is organized in generic resting-state networks (RSN). Alterations of RSN emerge as neurobiological markers of pathological conditions such as altered mental state. In single-subject fMRI data the coherent components can be identified by blind source separation of the pre-processed BOLD data using spatial independent component analysis (ICA) and related approaches. The resulting maps may represent physiological RSNs or may be due to various artifacts. In this methodological study, we propose a conceptually simple and fully automatic time course based filtering procedure to detect obvious artifacts in the ICA output for resting-state fMRI. The filter is trained on six and tested on 29 healthy subjects, yielding mean filter accuracy, sensitivity and specificity of 0.80, 0.82, and 0.75 in out-of-sample tests. To estimate the impact of clearly artifactual single-subject components on group resting-state studies we analyze unfiltered and filtered output with a second level ICA procedure. Although the automated filter does not reach performance values of visual analysis by human raters, we propose that resting-state compatible analysis of ICA time courses could be very useful to complement the existing map or task/event oriented artifact classification algorithms.

Graphical Model-Based Vertebra Identification from X-Ray Image(s)

Automated identification of vertebrae from X-ray image(s) is an important step for various medical image computing tasks such as 2D/3D rigid and non-rigid registration. In this chapter we present a graphical model-based solution for automated vertebra identification from X-ray image(s). Our solution does not ask for a training process using training data and has the capability to automatically determine the number of vertebrae visible in the image(s). This is achieved by combining a graphical model-based maximum a posterior probability (MAP) estimate with a mean-shift based clustering. Experiments conducted on simulated X-ray images as well as on a low-dose low quality X-ray spinal image of a scoliotic patient verified its performance.

Rapid qualitative urinary tract infection pathogen identification by SeptiFast real-time PCR

Background Urinary tract infections (UTI) are frequent in outpatients. Fast pathogen identification is mandatory for shortening the time of discomfort and preventing serious complications. Urine culture needs up to 48 hours until pathogen identification. Consequently, the initial antibiotic regimen is empirical. Aim To evaluate the feasibility of qualitative urine pathogen identification by a commercially available real-time PCR blood pathogen test (SeptiFast®) and to compare the results with dipslide and microbiological culture. Design of study Pilot study with prospectively collected urine samples. Setting University hospital. Methods 82 prospectively collected urine samples from 81 patients with suspected UTI were included. Dipslide urine culture was followed by microbiological pathogen identification in dipslide positive samples. In parallel, qualitative DNA based pathogen identification (SeptiFast®) was performed in all samples. Results 61 samples were SeptiFast® positive, whereas 67 samples were dipslide culture positive. The inter-methodological concordance of positive and negative findings in the gram+, gram- and fungi sector was 371/410 (90%), 477/492 (97%) and 238/246 (97%), respectively. Sensitivity and specificity of the SeptiFast® test for the detection of an infection was 0.82 and 0.60, respectively. SeptiFast® pathogen identifications were available at least 43 hours prior to culture results. Conclusion The SeptiFast® platform identified bacterial DNA in urine specimens considerably faster compared to conventional culture. For UTI diagnosis sensitivity and specificity is limited by its present qualitative setup which does not allow pathogen quantification. Future quantitative assays may hold promise for PCR based UTI pathogen identification as a supplementation of conventional culture methods.

Phylogenetic analysis of Prevotella nigrescens, Prevotella intermedia and Porphyromonas gingivalis clinical strains reveals a clear species clustering

Prevotella nigrescens, Prevotella intermedia and Porphyromonas gingivalis are oral pathogens from the family Bacteroidaceae, regularly isolated from cases of gingivitis and periodontitis. In this study, the phylogenetic variability of these three bacterial species was investigated by means of 16S rRNA (rrs) gene sequence comparisons of a set of epidemiologically and geographically diverse isolates. For each of the three species, the rrs gene sequences of 11 clinical isolates as well as the corresponding type strains was determined. Comparison of all rrs sequences obtained with those of closely related species revealed a clear clustering of species, with only a little intraspecies variability but a clear difference in the rrs gene with respect to the next related taxon. The results indicate that the three species form stable, homogeneous genetic groups, which favours an rrs-based species identification of these oral pathogens. This is especially useful given the 7% sequence divergence between Prevotella intermedia and Prevotella nigrescens, since phenotypic distinction between the two Prevotella species is inconsistent or involves techniques not applicable in routine identification.

Somatostatin receptors as targets for nuclear medicine imaging and radionuclide treatment

Radiolabeled peptides have been an important class of compounds in radiopharmaceutical sciences and nuclear medicine for more than 20 years. Despite strong research efforts, only somatostatin-based radiopeptides have a real impact on patient care, diagnostically and therapeutically. [(111)In-diethylenetriaminepentaacetic acid(0)]octreotide is commercially available for imaging. Imaging was highly improved by the introduction of PET radionuclides such as (68)Ga, (64)Cu, and (18)F. Two peptides are successfully used in targeted radionuclide therapy when bound to DOTA and labeled with (90)Y and (177)Lu.

In situ cardiac performance of Atlantic cod (Gadus morhua) at cold temperatures: long-term acclimation, acute thermal challenge and the role of adrenaline

The resting and maximum in situ cardiac performance of Newfoundland Atlantic cod (Gadus morhua) acclimated to 10, 4 and 0°C were measured at their respective acclimation temperatures, and when acutely exposed to temperature changes: i.e. hearts from 10°C fish cooled to 4°C, and hearts from 4°C fish measured at 10 and 0°C. Intrinsic heart rate (f(H)) decreased from 41 beats min(-1) at 10°C to 33 beats min(-1) at 4°C and 25 beats min(-1) at 0°C. However, this degree of thermal dependency was not reflected in maximal cardiac output (Q(max) values were ~44, ~37 and ~34 ml min(-1) kg(-1) at 10, 4 and 0°C, respectively). Further, cardiac scope showed a slight positive compensation between 4 and 0°C (Q(10)=1.7), and full, if not a slight over compensation between 10 and 4°C (Q(10)=0.9). The maximal performance of hearts exposed to an acute decrease in temperature (i.e. from 10 to 4°C and 4 to 0°C) was comparable to that measured for hearts from 4°C- and 0°C-acclimated fish, respectively. In contrast, 4°C-acclimated hearts significantly out-performed 10°C-acclimated hearts when tested at a common temperature of 10°C (in terms of both Q(max) and power output). Only minimal differences in cardiac function were seen between hearts stimulated with basal (5 nmol l(-1)) versus maximal (200 nmol l(-1)) levels of adrenaline, the effects of which were not temperature dependent. These results: (1) show that maximum performance of the isolated cod heart is not compromised by exposure to cold temperatures; and (2) support data from other studies, which show that, in contrast to salmonids, cod cardiac performance/myocardial contractility is not dependent upon humoral adrenergic stimulation.

Quality in emergency departments: a study on 3,285,440 admissions

INTRODUCTION: A multi-centre study has been conducted, during 2005, by means of a questionnaire posted on the Italian Society of Emergency Medicine (SIMEU) web page. Our intention was to carry out an organisational and functional analysis of Italian Emergency Departments (ED) in order to pick out some macro-indicators of the activities performed. Participation was good, in that 69 ED (3,285,440 admissions to emergency services) responded to the questionnaire. METHODS: The study was based on 18 questions: 3 regarding the personnel of the ED, 2 regarding organisational and functional aspects, 5 on the activity of the ED, 7 on triage and 1 on the assessment of the quality perceived by the users of the ED. RESULTS AND CONCLUSION: The replies revealed that 91.30% of the ED were equipped with data-processing software, which, in 96.83% of cases, tracked the entire itinerary of the patient. About 48,000 patients/year used the ED: 76.72% were discharged and 18.31% were hospitalised. Observation Units were active in 81.16% of the ED examined. Triage programmes were in place in 92.75% of ED: in 75.81% of these, triage was performed throughout the entire itinerary of the patient; in 16.13% it was performed only symptom-based, and in 8.06% only on-call. Of the patients arriving at the ED, 24.19% were assigned a non-urgent triage code, 60.01% a urgent code, 14.30% a emergent code and 1.49% a life-threatening code. Waiting times were: 52.39 min for non-urgent patients, 40.26 min for urgent, 12.08 for emergent, and 1.19 for life-threatening patients.

Photodynamic therapy for cholangiocarcinoma: overview and new developments

PURPOSE OF REVIEW: Photodynamic therapy (PDT) with hematoporphyrins has emerged as promising treatment for nonresectable cholangiocarcinoma in several prospective observational studies and two randomized studies. This review describes the mechanism of action of PDT, gives an overview of clinical experience in cholangiocarcinoma and summarizes the results published in 2007 and 2008. RECENT FINDINGS: The mechanism of action of PDT has been further elucidated. PDT induces an apoptotic, antiangiogenic as well as an immunomodulatory response. Interleukin-6, a bile duct epithelium growth factor correlating with tumor burden, decreases after PDT. The efficacy of PDT was confirmed in a comparative study in the United States. Patients with no visible mass on imaging studies, high serum albumin levels and treatment immediately after diagnosis seem to benefit most from PDT. Although it is recommended to perform PDT in bile ducts without stents in place, illumination through metal stents is possible if the light dose is adjusted. Meso-tetrahydroxyphenyl chlorine is a new potent photosensitizer for PDT of cholangiocarcinoma. SUMMARY: In advanced nonresectable cholangiocarcinoma, PDT is the only evidence-based treatment that improves survival when compared with stenting. Therefore, PDT should be offered to those who are unsuitable for surgery.

Bevezető: utak és úton lévők

A kvalitatív módszerekkel nyert kutatási eredményeink értelmezése során a transznacionális tér, a transznacionális és az etnikai migráció elméleti és szemléleti kereteit egyaránt figyelembe vettük. Az általunk vizsgált migrációs folyamatok transznacionális térben zajlanak, és a transznacionális irodalomban leírt migráns élethelyzetek, gyakorlatok – különböző nemzetállamokban elhelyezkedő lokalitásokhoz való egyidejű, bár eltérő intenzitású kötődés, kapcsolatok – több példájával is találkoztunk. Ludger Pries nyomán a transznacionális migrációt és a transznacionális migráns alakját olyan ideáltípusnak tekintettük, amelyhez az egyes migráns utak és helyzetek csupán közelítenek, és empirikus eredményeink alapján azt mondhatjuk, hogy a valóban plurilokális, vagyis a két helyhez való egyidejű, intenzív és tartós kötődés s az ehhez kapcsolódó gyakorlatok csupán a migránsok kisebbségét, illetve a migrációs életpályák egy-egy szakaszát jellemzik. A vizsgált migrációs folyamatokban az etnicitás strukturális tényezőként és a migráns tapasztalatok értelmezési kereteként egyaránt perdöntő szerepet játszik. Az etnikai migráció szakirodalomban tárgyalt mindhárom magyarázó modellje – az anyaországba való hazatérés, a gazdasági okokból való, illetve a kisebbségi létben elszenvedett sérelmek által ösztönzött migráció – alkalmas a migrációt kiváltó és mozgató okok elemzésére, a migráns narratívák értelmezésére, azt azonban nem állíthatjuk, hogy bármelyikük kizárólagos érvényre tehet szert. Más kutatókhoz hasonlóan Rogers Brubaker meghatározását tartjuk a leginkább gyümölcsözőnek, aki az etnikai migráció tág értelmezését használva minden olyan vándorlási folyamatot etnikai migrációnak tekint, amelyben az etnicitás kulturális és szimbolikus tőkeként szabályozó szerepet játszik. This special issue of Tér és Társadalom presents some results of an international research project carried out by researchers from Switzerland, Hungary and Serbia between 2010 and 2012. The topic of the research was “Integrating (Trans-)national Migrants in Transition States” (TRANSMIG) and was financed by the Swiss National Science Foundation (SNSF). The research aimed to explore and interpret migration flows from the Vojvodina (Serbia) to Hungary and from ex-Yugoslav republics to the Vojvodina. In the first period of the last twenty years, wars which contributed to the disintegration of Yugoslavia and the formation of new national states have caused migration flows. After the change of the millennium, educational migration of Vojvodina Hungarian youth can be considered the most important migratory movement from the Vojvodina to Hungary. Labour (economic) migration also occurs, but this cannot be understood as a one-way movement, since in the Hungarian–Serbian border zone migrants from the Vojvodina who already resettled to Hungary commute to the Vojvodina. While interpreting the qualitative research data the theoretical frameworks and approaches of transnational space, transnationalism and ethnic migration were taken into consideration. The migration movement in question occurs in a transnational social space where migrants are in constant motion. By their movements and actions that space is continually recreated. With Ludger Pries we see a transnational migrant as an ideal type to whom individual migratory movements and positions only approximate. Based on our empirical results we can conclude that real pluri-local, intensive and long-lasting bonding to two places at the same time and the relating practices only characterise a minority of migrants and certain sections of migratory careers. In the migration processes studied, ethnicity as a term is needed as a “structural factor” and frame of interpretation to approach migrant experiences. All three explanatory models for ethnic migration – return migration, economic migration, migration motivated by grievances suffered in a minority situation – are suitable to analyse the reasons that initiated migration and kept it in motion. They are helpful in interpreting migrant narratives. However, none of the reasons can claim exclusive validity. Agreeing with other researchers, we find Roger Brubaker’s definition the most useful: Ethnic migration should be comprehended in a broad sense. In addition, every migration can be considered as “ethnically” motivated where ethnicity plays a dominant role as a cultural and symbolic capital.

A global historical ozone data set and prominent features of stratospheric variability prior to 1979

We present a vertically resolved zonal mean monthly mean global ozone data set spanning the period 1901 to 2007, called HISTOZ.1.0. It is based on a new approach that combines information from an ensemble of chemistry climate model (CCM) simulations with historical total column ozone information. The CCM simulations incorporate important external drivers of stratospheric chemistry and dynamics (in particular solar and volcanic effects, greenhouse gases and ozone depleting substances, sea surface temperatures, and the quasi-biennial oscillation). The historical total column ozone observations include ground-based measurements from the 1920s onward and satellite observations from 1970 to 1976. An off-line data assimilation approach is used to combine model simulations, observations, and information on the observation error. The period starting in 1979 was used for validation with existing ozone data sets and therefore only ground-based measurements were assimilated. Results demonstrate considerable skill from the CCM simulations alone. Assimilating observations provides additional skill for total column ozone. With respect to the vertical ozone distribution, assimilating observations increases on average the correlation with a reference data set, but does not decrease the mean squared error. Analyses of HISTOZ.1.0 with respect to the effects of El Niño–Southern Oscillation (ENSO) and of the 11 yr solar cycle on stratospheric ozone from 1934 to 1979 qualitatively confirm previous studies that focussed on the post-1979 period. The ENSO signature exhibits a much clearer imprint of a change in strength of the Brewer–Dobson circulation compared to the post-1979 period. The imprint of the 11 yr solar cycle is slightly weaker in the earlier period. Furthermore, the total column ozone increase from the 1950s to around 1970 at northern mid-latitudes is briefly discussed. Indications for contributions of a tropospheric ozone increase, greenhouse gases, and changes in atmospheric circulation are found. Finally, the paper points at several possible future improvements of HISTOZ.1.0.

Caspase-3 mediates hippocampal apoptosis in pneumococcal meningitis

Bacterial meningitis causes neuronal apoptosis in the hippocampal dentate gyrus, which is associated with learning and memory impairments after cured disease. The execution of the apoptotic program involves pathways that converge on activation of caspase-3, which is required for morphological changes associated with apoptosis. Here, the time course and the role of caspase-3 in neuronal apoptosis was assessed in an infant rat model of pneumococcal meningitis. During clinically asymptotic meningitis (0-12 h after infection), only minor apoptotic damage to the dentate gyrus was observed, while the acute phase (18-24 h) was characterized by a massive increase of apoptotic cells, which peaked at 36 h. In the subacute phase of the disease (36-72 h), the number of apoptotic cells decreased to control levels. Enzymatic caspase-3 activity was significantly increased in hippocampal tissue of infected animals compared to controls at 22 h. The activated enzyme was localized to immature cells of the dentate gyrus, and in vivo activity was evidenced by cleavage of the amyloid-beta precursor protein. Intracisternal administration of the caspase-3-specific inhibitor Ac-DEVD-CHO significantly reduced apoptosis in the hippocampal dentate gyrus. In contrast to a study where the decrease of hippocampal apoptosis after administration of a pan-caspase inhibitor was due to downmodulation of the inflammatory response, our data demonstrate that specific inhibition of caspase-3 did not affect inflammation assessed by TNF-alpha and IL-1beta concentrations in the cerebrospinal fluid space. Taken together, the present results identify caspase-3 as a key effector of neuronal apoptosis in pneumococcal meningitis.

Jatropha mahafalensis for rural energy supply in south-western Madagascar?

In many parts of the eastern African region wood-based fuels will remain dominant sources of energy in coming decades. Pressure on forests, especially in semi-arid areas will therefore continue increasing. In this context, the role of liquid biofuels as substitutes for firewood and charcoal, to help reducing pressure on woody biomass and contributing to a better energy security of rural communities, has remained controversial among researchers and practitioners. At household level, the economic and technical feasibility of straight vegetable oil (SVO) was assessed mainly on Jatropha curcas, with unpersuasive results. So far nothing is known about the suitability as an energy carrier of Jatropha mahafalensis Jum. & H. Perrier, the only endemic representative of the Jatropha genus in Madagascar. This paper explores the potential of this plant as a biofuel feedstock in the agro-pastoral area of Soalara, in the semi-arid south-western part of Madagascar. Only hedge-based production was considered to rule out competition over land with food crops. Yield data, the length of currently existing hedges and energy consumption patterns of households were used to assess the quantitative potential and economic viability of J. mahafalensis SVO for lighting and cooking. Tests were conducted with cooking and lighting devices to assess their technical suitability at household level. The paper concludes that J. mahafalensis hedges have some potential to replace paraffin for lighting (though without much economic benefit for the concerned households), but not to replace charcoal or firewood for cooking. The paper recommends that rural energy strategies in similar contexts do not focus only on substituting current fuels with SVO, but should also take into consideration other alternatives. In the case of cooking, there seems to be substantially more potential in increasing the efficiency of current fuel production and consumption technologies (kilns and stoves); and in the case of lighting, solutions based on SVO need to be compared against other options such as portable solar devices.

Dexmedetomidine versus standard care sedation with propofol or midazolam in intensive care: an economic evaluation.

INTRODUCTION Dexmedetomidine was shown in two European randomized double-blind double-dummy trials (PRODEX and MIDEX) to be non-inferior to propofol and midazolam in maintaining target sedation levels in mechanically ventilated intensive care unit (ICU) patients. Additionally, dexmedetomidine shortened the time to extubation versus both standard sedatives, suggesting that it may reduce ICU resource needs and thus lower ICU costs. Considering resource utilization data from these two trials, we performed a secondary, cost-minimization analysis assessing the economics of dexmedetomidine versus standard care sedation. METHODS The total ICU costs associated with each study sedative were calculated on the basis of total study sedative consumption and the number of days patients remained intubated, required non-invasive ventilation, or required ICU care without mechanical ventilation. The daily unit costs for these three consecutive ICU periods were set to decline toward discharge, reflecting the observed reduction in mean daily Therapeutic Intervention Scoring System (TISS) points between the periods. A number of additional sensitivity analyses were performed, including one in which the total ICU costs were based on the cumulative sum of daily TISS points over the ICU period, and two further scenarios, with declining direct variable daily costs only. RESULTS Based on pooled data from both trials, sedation with dexmedetomidine resulted in lower total ICU costs than using the standard sedatives, with a difference of €2,656 in the median (interquartile range) total ICU costs-€11,864 (€7,070 to €23,457) versus €14,520 (€7,871 to €26,254)-and €1,649 in the mean total ICU costs. The median (mean) total ICU costs with dexmedetomidine compared with those of propofol or midazolam were €1,292 (€747) and €3,573 (€2,536) lower, respectively. The result was robust, indicating lower costs with dexmedetomidine in all sensitivity analyses, including those in which only direct variable ICU costs were considered. The likelihood of dexmedetomidine resulting in lower total ICU costs compared with pooled standard care was 91.0% (72.4% versus propofol and 98.0% versus midazolam). CONCLUSIONS From an economic point of view, dexmedetomidine appears to be a preferable option compared with standard sedatives for providing light to moderate ICU sedation exceeding 24 hours. The savings potential results primarily from shorter time to extubation. TRIAL REGISTRATION ClinicalTrials.gov NCT00479661 (PRODEX), NCT00481312 (MIDEX).

The European Registry for Patients with Mechanical Circulatory Support (EUROMACS): first annual report

The European Registry for Patients with Mechanical Circulatory Support (EUROMACS) was founded on 10 December 2009 with the initiative of Roland Hetzer (Deutsches Herzzentrum Berlin, Berlin, Germany) and Jan Gummert (Herz- und Diabeteszentrum Nordrhein-Westfalen, Bad Oeynhausen, Germany) with 15 other founding international members. It aims to promote scientific research to improve care of end-stage heart failure patients with ventricular assist device or a total artificial heart as long-term mechanical circulatory support. Likewise, the organization aims to provide and maintain a registry of device implantation data and long-term follow-up of patients with mechanical circulatory support. Hence, EUROMACS affiliated itself with Dendrite Clinical Systems Ltd to offer its members a software tool that allows input and analysis of patient clinical data on a daily basis. EUROMACS facilitates further scientific studies by offering research groups access to any available data wherein patients and centres are anonymized. Furthermore, EUROMACS aims to stimulate cooperation with clinical and research institutions and with peer associations involved to further its aims. EUROMACS is the only European-based Registry for Patients with Mechanical Circulatory Support with rapid increase in institutional and individual membership. Because of the expeditious data input, the European Association for Cardiothoracic Surgeons saw the need to optimize the data availability and the significance of the registry to improve care of patients with mechanical circulatory support and its potential contribution to scientific intents; hence, the beginning of their alliance in 2012. This first annual report is designed to provide an overview of EUROMACS' structure, its activities, a first data collection and an insight to its scientific contributions.

DNA-based identification of novel bovine casein gene variants

In cattle, at least 39 variants of the 4 casein proteins (α(S1)-, β-, α(S2)- and κ-casein) have been described to date. Many of these variants are known to affect milk-production traits, cheese-processing properties, and the nutritive value of milk. They also provide valuable information for phylogenetic studies. So far, the majority of studies exploring the genetic variability of bovine caseins considered European taurine cattle breeds and were carried out at the protein level by electrophoretic techniques. This only allows the identification of variants that, due to amino acid exchanges, differ in their electric charge, molecular weight, or isoelectric point. In this study, the open reading frames of the casein genes CSN1S1, CSN2, CSN1S2, and CSN3 of 356 animals belonging to 14 taurine and 3 indicine cattle breeds were sequenced. With this approach, we identified 23 alleles, including 5 new DNA sequence variants, with a predicted effect on the protein sequence. The new variants were only found in indicine breeds and in one local Iranian breed, which has been phenotypically classified as a taurine breed. A multidimensional scaling approach based on available SNP chip data, however, revealed an admixture of taurine and indicine populations in this breed as well as in the local Iranian breed Golpayegani. Specific indicine casein alleles were also identified in a few European taurine breeds, indicating the introgression of indicine breeds into these populations. This study shows the existence of substantial undiscovered genetic variability of bovine casein loci, especially in indicine cattle breeds. The identification of new variants is a valuable tool for phylogenetic studies and investigations into the evolution of the milk protein genes.