DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling

Motivation

Patient and sample diversity is one of the main challenges when dealing with clinical cohorts in biomedical genomics studies. During last decade, several methods have been developed to identify biomarkers assigned to specific individuals or subtypes of samples. However, current methods still fail to discover markers in complex scenarios where heterogeneity or hidden phenotypical factors are present. Here, we propose a method to analyze and understand heterogeneous data avoiding classical normalization approaches of reducing or removing variation.

Results

DEcomposing heterogeneous Cohorts using Omic data profiling (DECO) is a method to find significant association among biological features (biomarkers) and samples (individuals) analyzing large-scale omic data. The method identifies and categorizes biomarkers of specific phenotypic conditions based on a recurrent differential analysis integrated with a non-symmetrical correspondence analysis. DECO integrates both omic data dispersion and predictor–response relationship from non-symmetrical correspondence analysis in a unique statistic (called h-statistic), allowing the identification of closely related sample categories within complex cohorts. The performance is demonstrated using simulated data and five experimental transcriptomic datasets, and comparing to seven other methods. We show DECO greatly enhances the discovery and subtle identification of biomarkers, making it especially suited for deep and accurate patient stratification.

Availability and implementation

DECO is freely available as an R package (including a practical vignette) at Bioconductor repository (http://bioconductor.org/packages/deco/).

Supplementary information

Supplementary data are available at Bioinformatics online.

First Measurement of the g Factor in the Chiral Band: The Case of the ^{128}Cs Isomeric State

The g factor of the 56 ns half-life isomeric state in ^{128}Cs has been measured using the time-differential perturbed angular distribution method. This state is the bandhead of the positive-parity chiral rotational band, which emerges when an unpaired proton, an unpaired neutron hole, and an even-even core are coupled such that their angular momentum vectors are aplanar (chiral configuration). g-factor measurements can give important information on the relative orientation of the three angular momentum vectors. The measured g factor g=+0.59(1) shows that there is an important contribution of the core rotation in the total angular momentum of the isomeric state. Moreover, a quantitative theoretical analysis supports the conclusion that the three angular momentum vectors lie almost in one plane, which suggests that the chiral configuration in ^{128}Cs demonstrated in previous works by characteristic patterns of electromagnetic transitions appears only above some value of the total nuclear spin.

University of Lodz an electron spectrometer--a new conversion-electron spectrometer for "in-beam" measurements

The designed and constructed at the University of Lodz an electron spectrometer is devoted to "in-beam" measurements. The apparatus is characterized by high efficiency up to 9%, good energy resolution (FWHM = 5 keV at 482 keV) and, what is very important good suppression of delta electrons, positrons, and photons emitted by the targets. This achievement was obtained using a combination of magnetic field in two different layouts: perpendicular and parallel to the axis of the spectrometer being orthogonal to the beamline. The conversion-electron spectrometer coupled to the EAGLE array was successfully tested in an "in-beam" measurement.

128Cs as the best example revealing chiral symmetry breaking

The results of the Doppler-shift attenuation method lifetime measurements in partner bands of 128Cs and 132La are presented. Experimental reduced transition probabilities in 128Cs are compared with theoretical calculations done in the frame of the core-quasiparticle coupling model. The electromagnetic properties, energy and spin of levels belonging to the partner bands show that 128Cs is the best known example revealing the chiral symmetry breaking phenomenon.

Symptomatic myocardial ischemia and everyday life: implications for clinical use of interactive monitoring

In coronary heart disease (CHD), pathological myocardial ischemic changes do not always occur with the symptom of heart pain. Methodological problems make it difficult to examine the factors that influence silent and symptomatic myocardial ischemia in everyday life. This study uses a computer-assisted monitoring system with an interactive Holter ECG, an actometer, and an electronic diary. Self-report measurements indicate that symptomatic patients tend toward increased neuroticism, whereas asymptomatic patients engage in beneficial and active coping skills more frequently. The results of the monitoring study demonstrate the same degree of ischemia in silent and symptomatic episodes. However, these episodes show differences in certain psychological context variables. Symptomatic episodes are linked to high subjective strain and severe tension. Because angina pectoris is not a reliable warning signal of myocardial ischemia, the use of the interactive monitoring system is recommended for educating CHD patients on how to cope with excessive strain in everyday life.

Verbal memory after three months of intranasal vasopressin in healthy old humans

In animals, evidence has been accumulated that vasopressin (VP) improves learning and memory. In humans, this effect was not consistently demonstrated, and attempts to restore age-related memory deficits by VP also remained inconsistent. Assuming that in old subjects a beneficial effect on memory occurs only after prolonged treatment with VP, we conducted a study in 26 healthy elderly persons receiving 40 IU of VP for three months through the intranasal route. The trial was randomized, placebo-controlled and held double-blind. Memory was assessed by the Auditory Verbal Learning Test (AVLT) requiring the subject to learn repeatedly presented lists of 15 words. Results demonstrated no general effect of long-term treatment with VP on memory in aged humans. However, recall of an interfering word list was improved, indicating a diminished proactive interference by the peptide. Additionally, VP influenced recall depending on the serial position of an item: it improved the primacy effect (i.e. recall of the first words of a list) and impaired the recency effect. This result may indicate an improved semantic encoding (i.e. a primary effect on processes of attention) after long-term administration of VP.

Sensory effects of baroreceptor activation and perceived stress together predict long-term blood pressure elevations

Activating the arterial baroreceptors in animals has been shown to blunt pain sensation and provide other forms of central nervous system inhibition. This study tested the hypothesis that, among human subjects, a tonic increase in blood pressure (BP) could be a learned response to environmental stressors among subjects in whom the baroreceptor inhibitory mechanism is active. In a sample of 96 healthy, normotensive men and women, amount of pain-reduction produced by baroreceptor stimulation predicted an increase in resting BP 20 months later: the increase was proportional to self-assessed daily life stress. Among the subjects reporting the greatest amount of stress, the pain inhibition effect accounted for more than 80% of the BP variance. These results support the hypothesis that the reduction in perceived stress produced by baroreceptor stimulation may reward learned increases in BP.

Central effects of baroreceptor activation in humans: attenuation of skeletal reflexes and pain perception

Activating the arterial baroreceptors blunts pain sensation and produces other forms of central nervous system inhibition in animals. These effects may be important to blood pressure regulation but have not been rigorously verified in humans. We describe (i) a noninvasive behaviorally unbiased method for baroreceptor stimulation and (ii) the application of this method to measurement of baroreceptor-mediated attenuation of pain perception and of the Achilles tendon reflex. The findings are relevant to basic mechanisms of blood pressure stabilization and cardiovascular reactivity and may also have implications for noncompliance with antihypertensive medications and for the pathophysiology of essential hypertension.

Reduced pain during baroreceptor stimulation in patients with symptomatic and silent myocardial ischaemia

OBJECTIVE

Baroreceptor activation has been shown to reduce pain, and the accumulation of such pain reduction has been implicated in the operant learning (under certain circumstances) of hypertension. The current study is an examination of differences in the pain dampening effects of baroreceptor activity in patients with symptomatic and asymptomatic myocardial ischaemia. The objective was to determine whether there are differences between patients with symptomatic and silent myocardial ischaemia with respect to their antinociceptive response to baroreceptor stimulation, and, if so, whether these differences could be related to the absence of angina pectoris pain in patients with silent myocardial ischaemia.

METHODS

Sensory detection and electrical pain thresholds were compared in nine symptomatic and 10 asymptomatic patients with replicable myocardial ischaemia during PRES (phase related external suction) carotid baroreceptor manipulation in which the pressure inside a neck cuff was phase locked in time to the R wave of the ECG and negative pressure was applied during either systole or diastole. Tourniquet pain thresholds were also determined.

RESULTS

It was found that (1) external baroreceptor manipulation had no effect on detection thresholds; (2) painful stimuli were judged by both symptomatic and asymptomatic patients as less intense when delivered during maximum baroreceptor activity; (3) symptomatic and asymptomatic patients did not differ in their sensory detection thresholds; and (4) asymptomatic patients had significantly higher ischaemic (tourniquet) pain thresholds than symptomatic patients.

CONCLUSIONS

The results indicate that baroreceptor activity can modify the intensity of painful stimuli. The degree to which baroreceptor manipulation affects pain does not appear to differ between patients with painful and silent myocardial ischaemia. Thus the baroreceptor dependent pain inhibition effects seems not to be responsible for the higher ischaemic pain threshold found in the silent myocardial ischaemia group.

Baroreceptor stimulation: pain perception and sensory thresholds

Baroreceptor activity has been implicated in the modulation of pain. Sensory detection thresholds and pain ratings were measured in a group of 28 men during carotid baroreceptor manipulation with the PRES (phase-related external suction) neck suction technique. Brief, cardiac phase-related electrical impulses were delivered intracutaneously to the finger. The results indicate that minimum baroreceptor activity was associated with more severe pain, but had no effect on sensory detection threshold. The results are discussed in terms of the learned model of hypertension.

Development of angina pectoris pain and cardiac events in asymptomatic patients with myocardial ischemia

A total of 389 patients with angiographically determined coronary artery disease, who exhibited a complete absence of angina pectoris in the presence of reproducible myocardial ischemia, were studied in a follow-up investigation. After an initial coronary angiogram, anti-ischemic medication was prescribed as treatment. After a mean follow-up time of 4.9 years (maximum 13.4 years) patients were sent a questionnaire that assessed any new development of angina pectoris pain and cardiac events. In 48 of these patients a second angiogram was recorded after a mean period of 4.2 years. Asymptomatic patients had a worse prognosis than an age-adjusted normal population. After 5 and 10 years, 9 and 26% of the patients, respectively, had died, nonfatal cardiac events (myocardial infarction, bypass surgery or percutaneous transluminal coronary angioplasty) occurred after 5 and 10 years in 19 and 46%, respectively. A large number of initially asymptomatic patients developed angina pectoris pain over the follow-up period (34% after 5 years, 58% after 10 years). Novel angina pectoris pain often preceded cardiac events by months to years. Multivariate analysis indicated that vessel disease (p = 0.0001) and degree of ischemia (defined by ST-segment depression free exercise tolerance, p = 0.04) proved to have independent predictive value with respect to mortality rate. Newly developed angina pectoris was associated with an increase in objective signs of myocardial ischemia and a progression in coronary stenosis. The results indicate that patients who originally had myocardial ischemia with a marked absence of pain can develop angina pectoris over the course of years and that newly developed pain often precedes cardiac events.

Blood pressure changes validate phase related external suction, a controlled method for stimulation of human baroreceptors

Phase related external suction (PRES), a new controlled method for manipulating activity in human baroreceptors, applies precisely timed bursts of suction and pressure within the cardiac cycle through an external neck cuff. Seven healthy adult men participated in 32 pseudo-random trials of baroreceptor stimulation and inhibition. Blood pressure was assessed both intra-arterially and with a noninvasive device. In the present study, PRES baroreceptor stimulation elicited invasively measured blood pressure decreases of about 2.5 mmHg (0.33 kPa) and heart rate decreases of about 5 beats,min-1, while baroreceptor inhibition increased invasively measured blood pressure by about 1.5 mmHg (0.20 kPa) and heart rate about 2.5 beats.min-1. It was concluded that PRES is an effective method for baroreceptor manipulation with weaker size effect but better control of nonspecific factors in human subjects than other baroreceptor manipulation techniques. The noninvasive blood pressure measurement device was less sensitive to experimental variation than was the invasive device.

Ambulatory electrocardiography evaluation of the post-coronary artery bypass graft and post-percutaneous transluminal coronary angioplasty patient. Diagnostic and prognostic value

Investigations carried out in recent years have shown that patients with coronary heart disease display partial to considerable extent transient ST-segment changes that can be determined with ambulatory ECG. An interesting question is how often transient ST-segment changes are present in patients in whom the indication for an aortocoronary bypass operation or percutaneous transluminal coronary angioplasty (PTCA) has already been determined. In the patients who are waiting for a bypass operation or PTCA, the proof of myocardial ischemia has been determined, and which subgroups of patients display ST changes in the ambulatory ECG must be tested. It is interesting to ask what happens to such transient ischemic episodes as a result of surgical or catheter intervention, how often such episodes are present even after these interventions, and whether the latter has a clinical significance in view of the success of the intervention (graft patency in coronary artery bypass graft patients or reocclusion in PTCA patients). Furthermore, it is to be tested whether transient ST-segment changes take on a prognostic significance in the long-term follow-up after bypass operation or PTCA.

Transient hypoalgesia under physical exercise--relation to silent ischaemia and implications for cardiac rehabilitation

A series of studies with humans as well as experiments carried out on animals could show that physical exercise leads to temporary hypoalgesia. Reduced sensitivity to pain is not only demonstrable after long-distance exercise (such as marathon run) but also after intensive physical exercise on a laboratory ergometer. Pain threshold elevation is most pronounced during maximal exertion, but hypoalgesia remains present also after exercise is stopped demonstrating that a systemic analgetic effect is induced by the exercise process. Pre-exercise pain threshold level is returned to approximately 60 minutes after the exercise. The cause of the exercise-induced hypoalgesia is probably an activation of central pain inhibitory mechanisms by the "stimulus" of physical exercise (stimulation- or stress-induced analgesia). Central pain inhibitory systems are thereby triggered by the stimulation of afferent nerve endings (group III and IV) in the skeletal muscle. The same trigger mechanism also plays a role as a release stimulus for hormones such for beta-endorphin which is increased under physical exercise. Plasma-beta-endorphin is probably not directly involved in the exercise-induced hypoalgesia but is rather a "marker" for the activating of central analgesia mechanisms. Stress-induced hypoalgesia plays also a role in the coronary heart disease. The activation of endogenous analgetic mechanisms leads to a part of the myocardial ischaemia provoked by exercise being silent under exercise. Completely asymptomatic myocardial ischaemia patients display a generalized hypoalgesia which is demonstrable independent of an exertion stimulus and which indicates a central set-point change in the antinociceptive system.

A molecular defect causing fish eye disease: an amino acid exchange in lecithin-cholesterol acyltransferase (LCAT) leads to the selective loss of alpha-LCAT activity

Epidemiological as well as biochemical evidence of recent years has established that a low plasma level of high density lipoprotein-cholesterol is a predictor for the risk of coronary artery disease. However, there is a heterogeneous group of rare familial disorders, characterized by severe high density lipoprotein deficiency, in which the predicted increased risk is not clearly apparent. One such disorder has been called fish eye disease to reflect the massive corneal opacification seen in these patients. In this report, we describe the biochemical and genetic presentation of two German fish eye disease homozygotes and their family members. Vertical transmission of a decrease in the specific activity of lecithin-cholesterol acyltransferase (EC 2.3.1.43) indicated that this enzyme was a candidate gene for harboring the defect responsible for this disorder. Direct sequencing of DNA segments amplified by the polymerase chain reaction (PCR) that encode the exons of the lecithin-cholesterol acyltransferase gene led to the identification of a homozygous mutation resulting in the substitution of threonine at codon 123 for an isoleucine residue in both individuals. Family analysis in an extended pedigree was used to establish a causal relationship between this mutation and the biochemical phenotype for fish eye disease. The homozygous presence of this mutation in two phenotypically homozygous members of an unrelated Dutch family with fish eye disease further supports this finding.

Experimental pain thresholds and plasma beta-endorphin levels during exercise

Experimental pain thresholds (electrical intracutaneous finger and dental pulp stimulation) and plasma hormone levels (beta-endorphin, cortisol, and catecholamines) were measured in ten healthy sportive men before, during, and after progressively more strenuous physical exercise. In a double-blind study conducted on two different days, 20 mg of the opioid-antagonist naloxone or placebo was administered prior to exercise. A significant pain threshold elevation was found during exercise for finger (ANOVA, P less than 0.004) and dental pulp stimulation (P less than 0.01). Pain threshold elevation was most pronounced during maximal exertion, at which time the subjects reported the greatest subjective fatigue. Thresholds remained elevated 10-15 min after the end of exercise, and, 60 min after exercise, thresholds returned to baseline values. The subjective magnitude estimation of suprathreshold stimuli was significantly reduced (P less than 0.0001) 5-10 min after exercise. Plasma beta-endorphin, cortisol, and catecholamines increased significantly (P less than 0.0005, all values) during exercise. Plasma beta-endorphin levels did not correlate significantly with pain thresholds (r = -0.37, NS). Naloxone failed to affect pain thresholds, although beta-endorphin and cortisol increased significantly more (P less than 0.02) during exercise after naloxone. It is concluded that short-term, exhaustive physical exercise can evoke a transient elevation in pain thresholds. This exercise-induced elevation in pain threshold does not, however, appear to be directly related to plasma endorphin levels.

Effect of physical exercise on pain thresholds and plasma beta-endorphins in patients with silent and symptomatic myocardial ischaemia

In a double-blind study, eight patients with symptomatic myocardial ischaemia and nine with asymptomatic myocardial ischaemia were compared during physical exercise under naloxone (6 mg i.v.) or placebo. Plasma beta-endorphin, cortisol and catecholamines were measured before exercise, during maximal exercise, and 10, 20 and 60 min after exercise. A tourniquet pain test (on the forearm, under control of transcutaneous PO2), and an electrical pain test (intracutaneous electrode placed in the finger with the electrical stimulus under computer control and two-interval forced-choice psychophysical technique) were performed before exercise as well as immediately after, and 60 min after exercise. Plasma beta-endorphin levels increased significantly (P less than 0.01) during exercise in symptomatic and asymptomatic patient groups; every patient showed an increase on beta-endorphins during and after exercise. However, the increase found in beta-endorphins during and after exercise was significantly larger (P less than 0.01) in asymptomatic than in symptomatic patients. After naloxone, this difference was no longer evident. Angina pectoris during exercise was reported with less latency in symptomatic patients (P less than 0.05) and occurred in two of nine asymptomatic patients following naloxone. The time course of plasma cortisol levels exhibited the same pattern as beta-endorphins with the same significant differences between symptomatic and asymptomatic groups. Electrical pain thresholds, though on average higher in asymptomatic patients (2.21 mA vs. 0.79 mA), were not affected by exercise or naloxone. Asymptomatic patients required more time to reach pain thresholds in the tourniquet pain test (P less than 0.02). After exercise, tourniquet pain thresholds were significantly lower (P less than 0.01) under naloxone compared with placebo.(ABSTRACT TRUNCATED AT 250 WORDS)

ST segment monitoring before, three weeks and six months after aortocoronary bypass surgery

ST segment monitoring by Holter ECG was conducted in 80 consecutive patients 2-4 weeks before aortocoronary bypass surgery and three weeks and six months after surgery. Preoperatively, all patients were under maximal medical therapy. In 31 out of 80 patients medical therapy could be stopped and thus 24-h ST monitoring could also be conducted without medication. Preoperative and early postoperative (three weeks) examinations were performed under hospital conditions. At 6 months after surgery the patients were monitored at home during their everyday activities. Twenty-eight per cent of patients waiting for aortocoronary bypass surgery under full medication showed transient ischaemic episodes in 24-h Holter ECG. Seventy-eight per cent of these episodes were asymptomatic. Without medication, 55% of patients had transient ischaemia. The exercise ECG data partly predicted the Holter ECG data. Patients with ST segment depression greater than 0.1 mV during exercise ECG had on Holter monitoring more and longer lasting ischaemic episodes than those with ST segment depression less than or equal to 0.1 mV. In patients with asymptomatic ST segment depression during exercise ECG the relation of silent episodes to symptomatic episodes on Holter monitoring was 5.3:1 while in patients with symptomatic ST segment depression during exercise ECG this relation was 2.3:1. Three weeks after operation the informative value of the Holter ECG was very restricted due to changes in the resting ECG caused by the operation and because patients do not exert themselves much at this time. Six months after surgery, Holter ECG is more informative, especially when conducted at home.(ABSTRACT TRUNCATED AT 250 WORDS)

[Pathophysiology of painful and silent myocardial ischemia]

Regardless of the factor assumed responsible for precipitation of myocardial ischemia - varying from coronary occlusion in acute myocardial infarction to increased oxygen demand in exertional angina pectoris and reduced myocardial oxygen supply due to plaque rupture or changes in vasomotor tone in unstable angina - its incurrence may or may not be associated with pain. In the vast majority of cases, silent myocardial ischemia is observed in patients with established symptomatic coronary artery disease. Interindividual comparisons have not enabled reliable differentiation between those with painful and those with silent ischemia based on the anatomic extent of coronary artery disease, left ventricular function or previous myocardial infarction. Similarly, functional parameters such as exercise capacity, exercise duration, time to onset of ST-segment depression during exercise as well as heart rate and blood pressure both at rest and during exercise have failed to reveal differences between the symptomatic and the asymptomatic patients. Intraindividual differences have also been noted, but not consistently corroborated, and postulated as responsible for the fact that ischemia in a given patient alternates in its presence with and without pain. Since most patients with silent ischemia either have, or at some time in the past have experienced, painful ischemia, the integrity of the appropriate nervous system function can be assumed to be intact and neurocardiologic factors seem most likely to account for apparent discrepancies in pain perception. Prior to precipitation of pain, myocardial ischemia must elicit an adequate stimulus. According to some investigators, the adequate stimulus is that associated with a duration of the ischemic episode of at least three minutes and with increase in left ventricular filling pressure of more than 7 mm Hg. This threshold, consequently, represents a prerequisite but not invariably sufficient criteria for the occurrence of pain. The next step in the sequence of pain is generation of an action potential, that is, transduction by means of chemical or mechanical stimuli. During this process, a latency of 20 to 40 seconds is incurred such that the appearance of pain usually has its onset after derangement of relaxation and contraction, increased filling pressure and the observation of ECG changes. Through conduction, the information is forwarded to the central nervous system after coding of the details with regard to intensity. The intensity, in turn, is determined by the number of receptors (free nerve endings) in the field activated by the ischemic event.(ABSTRACT TRUNCATED AT 400 WORDS)

Psychophysiological mechanisms in silent myocardial ischaemia

Six levels of coronary pain are defined and for each of them explanations for absence of pain in asymptomatic myocardial ischaemia are given: Level I: Myocardial ischaemia which can be less pronounced in amount during asymptomatic episodes. Level II: Adequate stimulus (chemical, mechanical) where biosynthesis of algogesic substances, degree of local mechanical involvement and spatial distribution may be different. Level III: For neuronal encoding the intensity theory is mainly for coronary pain, presupposing a central pain threshold which is higher in asymptomatic patients. Level IV: Conduction of painful information may be interrupted by destruction of afferent nerve ways. Level V: Spinal transmission: resting tone and ability to activate neural and humoral (endorphinergic) pain inhibition systems are stronger in asymptomatic patients. Level VI: Central processing: cognitive mechanisms (coping style) affect perception of coronary pain with differences in symptomatic and silent myocardial ischaemia.

Experimental pain measurement in patients with asymptomatic myocardial ischemia

Men with substantial coronary heart disease determined angiographically and with reproducible myocardial ischemia were studied. During exercise electrocardiography, 22 patients exhibited significant ST segment depression with concomitant angina pectoris (that is, symptomatic myocardial ischemia) and 20 patients demonstrated significant ST segment depression without any symptoms (that is, asymptomatic myocardial ischemia). No significant differences were found between the patient groups in functional variables, coronary angiographic data or coronary risk factors. In contrast, various experimental pain measures (for example, electrical pain threshold, according to Notermans' method, cold pressor test and tourniquet pain test) yielded significant differences between groups. Results indicate that patients with asymptomatic myocardial ischemia demonstrated significantly higher electrical pain thresholds and ischemic pain thresholds, as well as more tolerance to cold and ischemia, so that individual differences in sensibility to pain may partly explain lack of pain in patients with asymptomatic myocardial ischemia.

Results of exercise tests and prognosis in postinfarction patients below age 40

In a follow-up study (mean = 3.6 years) of 555 men under 40 years of age (mean = 35.7 years) who had recently suffered transmural myocardial infarction, 44 patients (7.9%) suffered cardiac death with an annual rate of 2.2%. In a bivariate analysis a significant correlation was found between cardiac death and work capacity (p less than 0.02), vessel involvement (greater than 50% stenosis), left ventricular impairment as evaluated by ventriculography (p less than 0.001) and heart volume enlargement (p less than 0.01). There was no significant correlation between the degree of ST-segment depression and ventricular premature depolarisation (during exercise test). Complex results from non-invasive approaches can identify groups with good and bad prognosis as effectively as invasive techniques.