Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization

Quantitative reverse transcriptase real-time PCR (QRT-PCR) is a robust method to quantitate RNA abundance. The procedure is highly sensitive and reproducible as long as the initial RNA is intact. However, breaks in the RNA due to chemical or enzymatic cleavage may reduce the number of RNA molecules that contain intact amplicons. As a consequence, the number of molecules available for amplification decreases. We determined the relation between RNA fragmentation and threshold values (Ct values) in subsequent QRT-PCR for four genes in an experimental model of intact and partially hydrolyzed RNA derived from a cell line and we describe the relation between RNA integrity, amplicon size and Ct values in this biologically homogenous system. We demonstrate that degradation-related shifts of Ct values can be compensated by calculating delta Ct values between test genes and the mean values of several control genes. These delta Ct values are less sensitive to fragmentation of the RNA and are unaffected by varying amounts of input RNA. The feasibility of the procedure was demonstrated by comparing Ct values from a larger panel of genes in intact and in partially degraded RNA. We compared Ct values from intact RNA derived from well-preserved tumor material and from fragmented RNA derived from formalin-fixed, paraffin-embedded (FFPE) samples of the same tumors. We demonstrate that the relative abundance of gene expression can be based on FFPE material even when the amount of RNA in the sample and the extent of fragmentation are not known.

Prospective population-based study of RSV-related intermediate care and intensive care unit admissions in Switzerland over a 4-year period (2001-2005)

OBJECTIVES: Respiratory syncytial virus (RSV) infections are a leading cause of hospital admissions in small children. A substantial proportion of these patients require medical and nursing care, which can only be provided in intermediate (IMC) or intensive care units (ICU). This article reports on all children aged < 3 years who required admission to IMC and/or ICU between October 1, 2001 and September 30, 2005 in Switzerland. PATIENTS AND METHODS: We prospectively collected data on all children aged < 3 years who were admitted to an IMC or ICU for an RSV-related illness. Using a detailed questionnaire, we collected information on risk factors, therapy requirements, length of stay in the IMC/ICU and hospital, and outcome. RESULTS: Of the 577 cases reported during the study period, 90 were excluded because the patients did not fulfill the inclusion criteria; data were incomplete in another 25 cases (5%). Therefore, a total of 462 verified cases were eligible for analysis. At the time of hospital admission, only 31 patients (11%) were older than 12 months. Since RSV infection was not the main reason for IMC/ICU admission in 52% of these patients, we chose to exclude this subgroup from further analyses. Among the 431 infants aged < 12 months, the majority (77%) were former near term or full term (NT/FT) infants with a gestational age > or = 35 weeks without additional risk factors who were hospitalized at a median age of 1.5 months. Gestational age (GA) < 32 weeks, moderate to severe bronchopulmonary dysplasia (BPD), and congenital heart disease (CHD) were all associated with a significant risk increase for IMC/ICU admission (relative risk 14, 56, and 10, for GA < or = 32 weeks, BPD, and CHD, respectively). Compared with NT/FT infants, high-risk infants were hospitalized at an older age (except for infants with CHD), required more invasive and longer respiratory support, and had longer stays in the IMC/ICU and hospital. CONCLUSIONS: In Switzerland, RSV infections lead to the IMC/ICU admission of approximately 1%-2% of each annual birth cohort. Although prematurity, BPD, and CHD are significant risk factors, non-pharmacological preventive strategies should not be restricted to these high-risk patients but also target young NT/FT infants since they constitute 77% of infants requiring IMC/ICU admission.

Japanese-US common-arm analysis of paclitaxel plus carboplatin in advanced non-small-cell lung cancer: a model for assessing population-related pharmacogenomics

PURPOSE To explore whether population-related pharmacogenomics contribute to differences in patient outcomes between clinical trials performed in Japan and the United States, given similar study designs, eligibility criteria, staging, and treatment regimens. METHODS We prospectively designed and conducted three phase III trials (Four-Arm Cooperative Study, LC00-03, and S0003) in advanced-stage, non-small-cell lung cancer, each with a common arm of paclitaxel plus carboplatin. Genomic DNA was collected from patients in LC00-03 and S0003 who received paclitaxel (225 mg/m(2)) and carboplatin (area under the concentration-time curve, 6). Genotypic variants of CYP3A4, CYP3A5, CYP2C8, NR1I2-206, ABCB1, ERCC1, and ERCC2 were analyzed by pyrosequencing or by PCR restriction fragment length polymorphism. Results were assessed by Cox model for survival and by logistic regression for response and toxicity. Results Clinical results were similar in the two Japanese trials, and were significantly different from the US trial, for survival, neutropenia, febrile neutropenia, and anemia. There was a significant difference between Japanese and US patients in genotypic distribution for CYP3A4*1B (P = .01), CYP3A5*3C (P = .03), ERCC1 118 (P < .0001), ERCC2 K751Q (P < .001), and CYP2C8 R139K (P = .01). Genotypic associations were observed between CYP3A4*1B for progression-free survival (hazard ratio [HR], 0.36; 95% CI, 0.14 to 0.94; P = .04) and ERCC2 K751Q for response (HR, 0.33; 95% CI, 0.13 to 0.83; P = .02). For grade 4 neutropenia, the HR for ABCB1 3425C-->T was 1.84 (95% CI, 0.77 to 4.48; P = .19). CONCLUSION Differences in allelic distribution for genes involved in paclitaxel disposition or DNA repair were observed between Japanese and US patients. In an exploratory analysis, genotype-related associations with patient outcomes were observed for CYP3A4*1B and ERCC2 K751Q. This common-arm approach facilitates the prospective study of population-related pharmacogenomics in which ethnic differences in antineoplastic drug disposition are anticipated.

Left parietal activation related to planning, executing and suppressing praxis hand movements

OBJECTIVE: We sought to investigate the activity of bilateral parietal and premotor areas during a Go/No Go paradigm involving praxis movements of the dominant hand. METHODS: A sentence was presented which instructed subjects on what movement to make (S1; for example, "Show me how to use a hammer."). After an 8-s delay, "Go" or "No Go" (S2) was presented. If Go, they were instructed to make the movement described in the S1 instruction sentence as quickly as possible, and continuously until the "Rest" cue was presented 3 s later. If No Go, subjects were to simply relax until the next instruction sentence. Event-related potentials (ERP) and event-related desynchronization (ERD) in the beta band (18-22 Hz) were evaluated for three time bins: after S1, after S2, and from -2.5 to -1.5 s before the S2 period. RESULTS: Bilateral premotor ERP was greater than bilateral parietal ERP after the S2 Go compared with the No Go. Additionally, left premotor ERP was greater than that from the right premotor area. There was predominant left parietal ERD immediately after S1 for both Go and No Go, which was sustained for the duration of the interval between S1 and S2. For both S2 stimuli, predominant left parietal ERD was again seen when compared to that from the left premotor or right parietal area. However, the left parietal ERD was greater for Go than No Go. CONCLUSION: The results suggest a dominant role in the left parietal cortex for planning, executing, and suppressing praxis movements. The ERP and ERD show different patterns of activation and may reflect distinct neural movement-related activities. SIGNIFICANCE: The data can guide further studies to determine the neurophysiological changes occurring in apraxia patients and help explain the unique error profiles seen in patients with left parietal damage.

Infection prevention strategies in a stem cell transplant unit: impact of change of care in isolation practice and routine use of high dose intravenous immunoglobulins on infectious complications and transplant related mortality

OBJECTIVE: Nursing in 'live islands' and routine high dose intravenous immunoglobulins after allogeneic hematopoietic stem cell transplantation were abandoned by many teams in view of limited evidence and high costs. METHODS: This retrospective single-center study examines the impact of change from nursing in 'live islands' to care in single rooms (SR) and from high dose to targeted intravenous immunoglobulins (IVIG) on mortality and infection rate of adult patients receiving an allogeneic stem cell or bone marrow transplantation in two steps and three time cohorts (1993-1997, 1997-2000, 2000-2003). RESULTS: Two hundred forty-eight allogeneic hematopoetic stem cell transplantations were performed in 227 patients. Patient characteristics were comparable in the three cohorts for gender, median age, underlying disease, and disease stage, prophylaxis for graft versus host disease (GvHD) and cytomegalovirus constellation. The incidence of infections (78.4%) and infection rates remained stable (rates/1000 days of neutropenia for sepsis 17.61, for pneumonia 6.76). Cumulative incidence of GvHD and transplant-related mortality did not change over time. CONCLUSIONS: Change from nursing in 'live islands' to SR and reduction of high dose to targeted IVIG did not result in increased infection rates or mortality despite an increase in patient age. These results support the current practice.

Health related quality of life: a changing construct?

In 186 patients with early colon cancer, we investigated the assumption that the meaning of 'quality of life' (QL) remains constant over time. Within a phase-III trial (SAKK 40/93), patients estimated both their overall QL and a range of disease- and treatment-related domains at five timepoints, comprising three concurrent and 2 retrospective estimates: their pre-surgery QL both before surgery and retrospectively thereafter, and their pre-adjuvant QL both at the beginning of adjuvant treatment and retrospectively about 2 months later, and their current QL 2 weeks thereafter. Multilevel models were developed to determine whether the selected domains made stable contributions to overall QL at the concurrent estimates. The weights of the domains changed over time. They did not differ significantly according to whether patients were considering their concurrent state or reflecting on this state at a later timepoint. In the process of adaptation, patients with early colon cancer substantially change the relative importance of QL domains to overall QL. This finding argues for QL as a changing construct and against the assumption that domain-specific weights are stable across distinct clinical phases.

Diagnostic approach to hypercalcemia: relevance of parathyroid hormone and parathyroid hormone-related protein measurements

Background: Parathyroid hormone (PTH) and parathyroid hormone-related protein (PTH-rP) are two potent hypercalcemic hormones that act on the same targets. Autonomous secretion of the former is involved in primary hyperparathyroidism (PHPT), whereas the latter is responsible for humoral hypercalcemia of malignancy (HHM). Methods: From 250 consecutive, hypercalcemic serum samples sent to our laboratory for assessment of intact PTH, we were able to obtain clinical information, as well as an additional plasma sample for PTH-rP measurement, in 134 patients. At the time of sampling, patients could be classified into seven groups: cancer without known bone metastases (CaNoMeta, n=36), cancer with bone metastases (CaMeta, n=9), no evidence of cancer (noEvCa, n=71), sarcoidosis (Sarc, n=3), end-stage renal disease (ESRD, n=12), vitamin D overdose (VIT-D, n=2), and hyperthyroidism (Thyr, n=1). Results: In the CaNoMeta group, 29/36 patients had elevated PTH-rP levels, 9/36 patients had inappropriately elevated PTH levels, and 5/36 had elevated levels of both hormones. In the CaMeta group, three of the nine patients had inappropriately elevated PTH levels, two of them with concomitantly elevated PTH-rP levels. In the NoEvCa group, 63/71 patients had an inappropriate elevation of PTH levels and were diagnosed as having PHPT. Four of the 71 patients had elevated levels of both PTH and PTH-rP; three of them were in poor health and died within a short period of time. All of the ESRD patients had very high PTH and normal PTH-rP levels, except for one woman with high PTH-rP and undetectable PTH levels; she died from what later turned out to be a recurrent bladder carcinoma. In the Sarc, Vit-D, and Thyr groups, both PTH and PTH-rP levels were normal. Conclusions: (1) Elevated PTH-rP levels are a common finding in cancer patients without bone metastases. Intact PTH, however, should always be measured in hypercalcemic patients with malignancy because concurrent primary hyperparathyroidism is not rare. (2) Primary hyperparathyroidism accounts for hypercalcemia in 90% of patients without evidence of cancer whose PTH-rP levels may also be found to be elevated in a few cases, even some with surgically demonstrated parathyroid adenoma.

The Implementation of Full-time Schools: The Situation in the Federal State of Sao Paulo (Brazil)

During the past years, Brazil has been mentioned internationally as a one of the so-called BRICs (Brazil, Russia, India and China). These countries have been taking increasing space in the economical and political global scenarios in the XXI century. The facts that they possess a vast territory and stand among the highest populated countries increase their relevance within the United Nations. Besides, three of them constitute nuclear powers and two of them belong to the United Nations Security Council. Brazil has significantly participated in forums such as WTO and UNO, representing central political articulation and stability to Latin America and in the structuring and growth of MERCOSUL (Brazil, Argentina, Uruguay, Paraguay and Venezuela). Once again among the ten greatest economies of the world, the country has launched ambitious poverty-fighting programs helping more than 20 million people in the last years, such as the “Bolsa Família” (Familienstipendium) Program or and its complements). Nevertheless, Latin American countries are far from generating structural funds as the “European Social Fund” to assist specific demands of big cities as Sao Paulo and Buenos Aires. The commitments are restricted to commercial areas and bring nothing but slow and scarce advances to education or infra-structure and to the integration of systems related to these areas.

Monitoring the Time Course of Perception without Awareness: A Comparison of Mirror Masked Words and Nonwords

Mirror masked words are embedded into a context that makes them appear as senseless patterns or as strings of unfamiliar letters. Thus, mirror masked words can be shown for several hundreds of milliseconds without being recognised as words. We sought to further investigate effects of nonsconscious reading by monitoring event-related brain potentials (ERPs) while participants observed mirror masked letter strings. ERPs were recorded while participants observed mirror masked words and nonwords. Data of 15 participants was segmented into periods of quasi-stable field topography (microstates). Microstates for masked words and nonwords were compared using randomization tests, statistical parametric scalp maps and Low Resolution Electromagnetic Tomography (LORETA). ERPs to masked words and nonwords showed significant topographic differences between 136 and 256 ms, indicating that stimuli were nonconsciously discriminated. A LORETA model localised sources of activation discriminating between masked words and nonwords in left operculum, the right superior parietal lobe and right superior temporal gyrus indicating higher current density for nonwords than for words in these areas. ERPs of mirror masked stimuli can indicate unconscious discrimination even in cases where behavioural priming is unreliable. This approach might be useful for investigating differences in early, nonconscious stages of word perception.

Linking brain connectivity across different time scales with electroencephalogram, functional magnetic resonance imaging, and diffusion tensor imaging

Structural and functional connectivity are intrinsic properties of the human brain and represent the amount of cognitive capacities of individual subjects. These connections are modulated due to development, learning, and disease. Momentary adaptations in functional connectivity alter the structural connections, which in turn affect the functional connectivity. Thus, structural and functional connectivity interact on a broad timescale. In this study, we aimed to explore distinct measures of connectivity assessed by functional magnetic resonance imaging and diffusion tensor imaging and their association to the dominant electroencephalogram oscillatory property at rest: the individual alpha frequency (IAF). We found that in 21 healthy young subjects, small intraindividual temporal IAF fluctuations were correlated to increased blood oxygenation level-dependent signal in brain areas associated to working memory functions and to the modulation of attention. These areas colocalized with functionally connected networks supporting the respective functions. Furthermore, subjects with higher IAF show increased fractional anisotropy values in fascicles connecting the above-mentioned areas and networks. Hence, due to a multimodal approach a consistent functionally and structurally connected network related to IAF was observed.

Event-related potential P300 microstate topography during visual one- and two-dimensional tasks in chronic schizophrenics

Reports on left-lateralized abnormalities of component P300 of event-related brain potentials (ERP) in schizophrenics typically did not vary task difficulties. We collected 16-channel ERP in 13 chronic, medicated schizophrenics (25±4.9 years) and 13 matched controls in a visual P300 paradigm with targets defined by one or two stimulus dimensions (C1: color; C2: color and tilt); subjects key-pressed to targets. The mean target-ERP map landscapes were assessed numerically by the locations of the positive and negative map-area centroids. The centroids' time-space trajectories were searched for the P300 microstate landscape defined by the positive centroid posterior of the negative centroid. At P300 microstate centre latencies in C1, patients' maps tended to a right shift of the positive centroid (p<0.10); in C2 the anterior centroid was more posterior (p<0.07) and the posterior (positive) centroid more anterior (p<0.03), but without leftright difference. Duration of P300 microstate in C2 was shorter in patients (232 vs 347 ms;p<0.03) and the latency of maximal strength of P300 microstate increased significantly in patients (C1: 459 vs 376 ms; C2: 585 vs 525 ms). In summary only the one-dimensional task C1 supported left-sided abnormalities; the two-dimensional task C2 produced abnormal P300 microstate map landscapes in schizophrenics, but no abnormal lateralization. Thus, information processing involved clearly aberrant neural populations in schizophrenics, different when processing one and two stimulus dimensions. The lack of lateralization in the two-dimensional task supported the view that left-temporal abnormality in schizophrenics is only one of several task-dependent aberrations.

Event-related electric microstates of the brain differ between words with visual and abstract meaning

The present study shows that different neural activity during mental imagery and abstract mentation can be assigned to well-defined steps of the brain's information-processing. During randomized visual presentation of single, imagery-type and abstract-type words, 27 channel event-related potential (ERP) field maps were obtained from 25 subjects (sequence-divided into a first and second group for statistics). The brain field map series showed a sequence of typical map configurations that were quasi-stable for brief time periods (microstates). The microstates were concatenated by rapid map changes. As different map configurations must result from different spatial patterns of neural activity, each microstate represents different active neural networks. Accordingly, microstates are assumed to correspond to discrete steps of information-processing. Comparing microstate topographies (using centroids) between imagery- and abstract-type words, significantly different microstates were found in both subject groups at 286–354 ms where imagery-type words were more right-lateralized than abstract-type words, and at 550–606 ms and 606–666 ms where anterior-posterior differences occurred. We conclude that language-processing consists of several, well-defined steps and that the brain-states incorporating those steps are altered by the stimuli's capacities to generate mental imagery or abstract mentation in a state-dependent manner.

Ragu: a free tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics

We present a program (Ragu; Randomization Graphical User interface) for statistical analyses of multichannel event-related EEG and MEG experiments. Based on measures of scalp field differences including all sensors, and using powerful, assumption-free randomization statistics, the program yields robust, physiologically meaningful conclusions based on the entire, untransformed, and unbiased set of measurements. Ragu accommodates up to two within-subject factors and one between-subject factor with multiple levels each. Significance is computed as function of time and can be controlled for type II errors with overall analyses. Results are displayed in an intuitive visual interface that allows further exploration of the findings. A sample analysis of an ERP experiment illustrates the different possibilities offered by Ragu. The aim of Ragu is to maximize statistical power while minimizing the need for a-priori choices of models and parameters (like inverse models or sensors of interest) that interact with and bias statistics.

Microstates in language-related brain potential maps show noun-verb differences

Brain processing of grammatical word class was studied analyzing event-related potential (ERP) brain fields. Normal subjects observed a randomized sequence of single German nouns and verbs on a computer screen, while 20-channel ERP field map series were recorded separately for both word classes. Spatial microstate analysis was applied, based on the observation that series of ERP maps consist of epochs of quasi-stable map landscapes and based on the rationale that different map landscapes must have been generated by different neural generators and thus suggest different brain functions. Space-oriented segmentation of the mean map series identified nine successive, different functional microstates, i.e., steps of brain information processing characterized by quasi-stable map landscapes. In the microstate from 116 to 172 msec, noun-related maps differed significantly from verb-related maps along the left–right axis. The results indicate that different neural populations represent different grammatical word classes in language processing, in agreement with clinical observations. This word class differentiation as revealed by the spatial–temporal organization of neural activity occurred at a time after word input compatible with speed of reading.

Gender-related mortality trends among diabetic patients with ST-segment elevation myocardial infarction: insights from a nationwide registry 1997-2010

BACKGROUND Data on temporal trends in outcomes, gender differences, and adherence to evidence-based therapy (EBT) of diabetic patients with ST-segment elevation myocardial infarction (STEMI) are sparse. METHODS We performed a retrospective analysis of prospectively acquired data on 3565 diabetic (2412 males and 1153 females) STEMI patients enrolled in the Swiss AMIS Plus registry between 1997 and 2010 and compared in-hospital outcomes and adherence to EBT with the nondiabetic population (n=15,531). RESULTS In-hospital mortality dramatically decreased in diabetic patients, from 19.9% in 1997 to 9.0% in 2010 (p trend<0.001) with an age-adjusted decrease of 6% per year of admission. Similar trends were observed for age-adjusted reinfarction (OR 0.86, p<0.001), cardiogenic shock (OR 0.88, p<0.001), as well as death, reinfarction, or stroke (OR 0.92, p<0.001). However, the mortality benefit over time was observed in diabetic males (p trend=0.006) but not females (p trend=0.082). In addition, mortality remained twice as high in diabetic patients compared with nondiabetic ones (12.1 vs. 6.1%, p<0.001) and diabetes was identified as independent predictor of mortality (OR 1.23, p=0.022). Within the diabetic cohort, females had higher mortality than males (16.1 vs. 10.2%, p<0.001) and female gender independently predicted in-hospital mortality (OR 1.45, p=0.015). Adherence to EBT significantly improved over time in diabetic patients (p trend<0.001) but remained inferior - especially in women - to the one of nondiabetic individuals. CONCLUSIONS In-hospital mortality and morbidity of diabetic STEMI patients in Switzerland improved dramatically over time but, compared with nondiabetic counterparts, gaps in outcomes as well as EBT use persisted, especially in women.