Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases

Background

Targeted Next Generation Sequencing is a common and powerful approach used in both clinical and research settings. However, at present, a large fraction of the acquired genetic information is not used since pathogenicity cannot be assessed for most variants. Further complicating this scenario is the increasingly frequent description of a poli/oligogenic pattern of inheritance showing the contribution of multiple variants in increasing disease risk. We present an approach in which the entire genetic information provided by target sequencing is transformed into binary data on which we performed statistical, machine learning, and network analyses to extract all valuable information from the entire genetic profile. To test this approach and unbiasedly explore the presence of recurrent genetic patterns, we studied a cohort of 112 patients affected either by genetic Creutzfeldt–Jakob (CJD) disease caused by two mutations in the PRNP gene (p.E200K and p.V210I) with different penetrance or by sporadic Alzheimer disease (sAD).

Results

Unsupervised methods can identify functionally relevant sources of variation in the data, like haplogroups and polymorphisms that do not follow Hardy–Weinberg equilibrium, such as the NOTCH3 rs11670823 (c.3837 + 21 T > A). Supervised classifiers can recognize clinical phenotypes with high accuracy based on the mutational profile of patients. In addition, we found a similar alteration of allele frequencies compared the European population in sporadic patients and in V210I-CJD, a poorly penetrant PRNP mutation, and sAD, suggesting shared oligogenic patterns in different types of dementia. Pathway enrichment and protein–protein interaction network revealed different altered pathways between the two PRNP mutations.

Conclusions

We propose this workflow as a possible approach to gain deeper insights into the genetic information derived from target sequencing, to identify recurrent genetic patterns and improve the understanding of complex diseases. This work could also represent a possible starting point of a predictive tool for personalized medicine and advanced diagnostic applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01173-4.

Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results

In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and alignment statistics; number of single nucleotide polymorphisms (SNPs), detected applying assembly- and alignment-based strategies; antimicrobial resistance genes (ARGs), identified on de novo assemblies of all sequenced genomes. The investigated nucleic acid extraction procedures, library preparation kits and sequencing platforms do not significantly affect de novo assembly statistics and number of SNPs and ARGs. The only exception was observed for two duplicates, which were associated to one PCR-based library preparation kit. Results from this comparative study can support researchers in the choice toward the available pre-sequencing and sequencing options, and might suggest further comparisons to be performed.

Early effects comparison of X-rays delivered at high-dose-rate pulses by a plasma focus device and at low dose rate on human tumour cells

A comparative study has been performed on the effects of high-dose-rate (DR) X-ray beams produced by a plasma focus device (PFMA-3), to exploit its potential medical applications (e.g. radiotherapy), and low-DR X-ray beams produced by a conventional source (XRT). Experiments have been performed at 0.5 and 2 Gy doses on a human glioblastoma cell line (T98G). Cell proliferation rate and potassium outward currents (IK) have been investigated by time lapse imaging and patch clamp recordings. The results showed that PFMA-3 irradiation has a greater capability to reduce the proliferation rate activity with respect to XRT, while it does not affect IK of T98G cells at any of the dose levels tested. XRT irradiation significantly reduces the mean IK amplitude of T98G cells only at 0.5 Gy. This work confirms that the DR, and therefore the source of radiation, is crucial for the planning and optimisation of radiotherapy applications.

A simple stochastic model for the feedback circuit between p16INK4a and p53 mediated by p38MAPK: implications for senescence and apoptosis

The mechanisms leading to the cell fate decision between apoptosis and senescence upon DNA damage are still unclear and have stochastic features. Cellular oxidative stress can generate DNA damage and activate the important mitogen-activated protein kinase 14 (p38MAPK) that is involved in pathologies like Alzheimer's disease. Based on experimental evidence we propose a simple network that might operate at the core of the cell control machinery for the choice between apoptosis and senescence involving the cross-talk between p38MAPK, the tumor suppressor protein p53 and the cyclin-dependent kinase inhibitor (p16INK4a). We have performed two types of analyses, deterministic and stochastic, exploring the system's parameter space, in the first, we calculated the fixed points of the deterministic model and, in the second, we numerically integrated the master equation for the stochastic version. The model shows a variety of behaviors dependent on the parameters including states of high expression levels of p53 or p16INK4a that can be associated with an apoptotic or senescent phenotype, respectively, in agreement with experimental data. In addition, we observe both monostable and bistable behavior (where bistability is a phenomenon in which two stable steady states coexist for a fixed set of control parameter values) which here we suggest to be involved in the cell fate decision problem.

Immune parameters identify Italian centenarians with a longer five-year survival independent of their health and functional status

Centenarians are rare and exceptional individuals characterized by a peculiar phenotype. They are the best example of healthy aging in humans as most of them have escaped or substantially delayed the onset of major age-related diseases. Within this scenario, the purpose of the present work was to understand if immune status is associated with survival and health status in centenarians. To this aim, 116 centenarians were concomitantly characterized for their immunological, health and functional status, and followed-up for five-year survival. On the basis of previous knowledge we focused on a core of fundamental and basic immune parameters (number of leukocytes, monocytes, total lymphocytes, CD3(+) T lymphocytes, CD4(+) helper T lymphocytes, CD8(+) cytotoxic T lymphocytes, CD19(+) B lymphocytes and plasma levels of IgM), and the most important findings can be summarized as follows: i. a hierarchical cluster analysis was able to define Cluster1 (88 centenarians) and Cluster2 (28 centenarians) characterized by low and high values of all these immune parameters, respectively; ii. centenarians of Cluster2 showed a statistically longer five-year survival and more favorable values of other important immune (naïve, activated/memory and effector/memory T cells) and metabolic (glycemia, insulin and HOMA-IR) parameters, in accord with previous observations that centenarians have a peculiar immune profile, a preserved insulin pathway and a lower incidence of type 2 diabetes; and iii. unexpectedly, parameters related to frailty, as well as functional and cognitive status, did not show any significant correlation with the immune clustering, despite being capable per se of predicting survival. In conclusion, high values of basic immunological parameters and important T cell subsets correlate with five-year survival in centenarians, independent of other phenotypic characteristics. This unexpected biological scenario is compatible with the general hypothesis that in centenarians a progressive disconnection and loss of biological coherence among the different functions of the body occur, where survival/mortality result from the failure of any of these domains which apparently follow an independent age-related trajectory.

Pulsatile intracranial pressure and cerebral autoregulation after traumatic brain injury

BACKGROUND

Strong correlation between mean intracranial pressure (ICP) and its pulse wave amplitude (AMP) has been demonstrated in different clinical scenarios. We investigated the relationship between invasive mean arterial blood pressure (ABP) and AMP to explore its potential role as a descriptor of cerebrovascular pressure reactivity after traumatic brain injury (TBI).

METHODS

We retrospectively analyzed data of patients suffering from TBI with brain monitoring. Transcranial Doppler blood flow velocity, ABP, ICP were recorded digitally. Cerebral perfusion pressure (CPP) and AMP were derived. A new index-pressure-amplitude index (PAx)-was calculated as the Pearson correlation between (averaged over 10 s intervals) ABP and AMP with a 5 min long moving average window. The previously introduced transcranial Doppler-based autoregulation index Mx was evaluated in a similar way, as the moving correlation between blood flow velocity and CPP. The clinical outcome was assessed after 6 months using the Glasgow outcome score.

RESULTS

293 patients were studied. The mean PAx was -0.09 (standard deviation 0.21). This negative value indicates that, on average, an increase in ABP causes a decrease in AMP and vice versa. PAx correlated strong with Mx (R (2) = 0.46, P < 0.0002). PAx also correlated with age (R (2) = 0.18, P < 0.05). PAx was found to have as good predictive outcome value (area under curve 0.71, P < 0.001) as Mx (area under curve 0.69, P < 0.001).

CONCLUSIONS

We demonstrated significant correlation between the known cerebral autoregulation index Mx and PAx. This new index of cerebrovascular pressure reactivity using ICP pulse wave information showed to have a strong association with outcome in TBI patients.

Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies

Human aging and longevity are complex and multi-factorial traits that result from a combination of environmental, genetic, epigenetic and stochastic factors, each contributing to the overall phenotype. The multi-factorial process of aging acts at different levels of complexity, from molecule to cell, from organ to organ systems and finally to organism, giving rise to the dynamic "aging mosaic". At present, an increasing amount of experimental data on genetics, genomics, proteomics and other -omics are available thanks to new high-throughput technologies but a comprehensive model for the study of human aging and longevity is still lacking. Systems biology represents a strategy to integrate and quantify the existing knowledge from different sources into predictive models, to be later tested and then implemented with new experimental data for validation and refinement in a recursive process. The ultimate goal is to compact the new acquired knowledge into a single picture, ideally able to characterize the phenotype at systemic/organism level. In this review we will briefly discuss the aging phenotype in a systems biology perspective, showing four specific examples at different levels of complexity, from a systemic process (inflammation) to a cascade-process pathways (coagulation) and from cellular organelle (proteasome) to single gene-network (PON-1), which could also represent targets for anti-aging strategies.

Human models of aging and longevity

BACKGROUND

The aging phenotype in humans is very heterogeneous and can be described as a complex mosaic resulting from the interaction of a variety of environmental, stochastic and genetic-epigenetic variables. Therefore, each old person must be considered as a singleton, and consequently the definition of 'aging phenotype' is very difficult.

OBJECTIVE

We discuss the phenotype of centenarians, the best example of successful aging, as well as other models exploited to study human aging and longevity, such as families enriched in long-living subjects, twins and cohorts of unrelated subjects.

METHODS

A critical review of literature available until March 2008.

CONCLUSIONS

No single model can be considered the gold standard for the study of aging and longevity, instead the combination of results obtained from different models must be considered in order to better understand these complex phenomena. We propose that a systems biology concept such as that of 'bow-tie' architecture, useful for managing information flow, could help in this demanding task.

Leptin concentrations in plasma and follicular fluid from prepubertal gilts as influenced by fasting, refeeding and insulin

This study's aim was to examine whether fasting and refeeding would influence leptin levels in both plasma and follicular fluid from prepubertal gilts, and whether insulin affects leptin levels in fasting gilts. In experiment 1, four gilts were fasted for 72 h and then refed. Blood samples were withdrawn during normoalimentation, at the end of fasting, and for 4 h after refeeding. All samples were assayed for leptin; alternate samples were assayed for insulin, glucose and non-esterified fatty acids (NEFA). Fasting caused a decrease in leptin, glucose and insulin levels in plasma, while NEFA concentrations increased. In experiment 2, four gilts were given insulin as a bolus (0.2 IU/kg body weight) after 68 h of fasting. Blood samples were collected every 15 min around insulin administration and were assayed for leptin, insulin and glucose. This experiment shows that insulin administration increases leptin levels during fasting. In experiment 3, gilts were ovariectomized during normal alimentation (n=4), after 48 h of fasting (n=4), and after 48 h of realimentation following 48 h of fasting (n=4). Leptin levels in both plasma and follicular fluid collected after 48 h of fasting were significantly lower than those observed during normoalimentation or refeeding. In conclusion, a transient increase in insulin during fasting is effective in restoring leptin concentrations; in addition, leptin levels in follicular fluid parallel those in plasma.

Cadmium, chromium and lead contamination of Athene noctua, the little owl, of Bologna and Parma, Italy

A study was conducted to determine cadmium, chromium and lead concentrations in liver and brain of 52 little owls (Athene noctua) from two provinces of Emilia Romagna region, with the aim of furnishing indirect information concerning contamination of their habitat, also considering possible environmental dispersion of the metals. Metal analysis was performed by atomic absorption spectrophotometry with graphite furnace. Variance analysis with sampling area, gender and age shows that no statistical difference was found for gender, while a significant difference (P<0.05) was found for cadmium and lead, but not for chromium, when sampling areas and age were of concern. For all metals highest mean concentrations were found in liver (170 ppb for cadmium, 297 ppb for chromium and 312 ppb for lead). These levels can be considered as indicative of chronic exposure to low and "background" amounts of pollutants and they are of no toxicological concern, as they are always well below the toxic thresholds defined for each metal. The present study can be considered as a starting point for further analyses, aimed to the definition of any possible subtle effect (e.g. effects on enzymes activity) and of any possible correlation between levels of pollutants and appearance of possible adverse effects. It also furnished useful data for diagnostic cases and potentially for monitoring local contamination.

Follicle activation involves vascular endothelial growth factor production and increased blood vessel extension

The authors evaluated the relationship between vascular endothelial growth factor (VEGF) production, blood vessel extension, and steroidogenesis in small (<4 mm), medium (4-5 mm), and large (>5 mm) follicles isolated from gilts treated with eCG. VEGF and estradiol levels were measured in follicular fluid by an enzyme immunoassay and radioimmunoassay, respectively, and then each follicle wall was used to evaluate VEGF mRNA content and for the immunohistochemical analysis of blood vessels. VEGF production was low in small follicles (<3 ng/ml), high in large follicles (>10 ng/ml), and markedly differentiated in medium follicles; 44% exhibited values up to 15 ng/ml, whereas the levels never exceeded 3 ng/ml in the remaining aliquot. Medium follicles were then used as a model to investigate angiogenesis. Reverse transcription-polymerase chain reaction for VEGF mRNA demonstrated that granulosa cells represent the main component involved in the production of VEGF. The follicle wall, which presents two distinct concentric vessel networks, showed a vascular area (positive stained area/percent of field area) that was significantly wider in high VEGF follicles than in low VEGF follicles (2.54% +/- 0.58% vs. 1.29% +/- 0.58%, respectively). Medium follicles with high VEGF levels and extensive vascularization accumulated high estradiol levels (150-300 ng/ml), whereas follicles with low VEGF levels had basal estradiol levels that never exceeded 30 ng/ml. Early atretic medium-size follicles had undetectable levels of VEGF and estradiol paralleled by a marked reduction in blood vessel. The data presented propose an improved model for follicle dynamics in which the production of VEGF, stimulated by gonadotropin, creates the vascular conditions required for follicle growth and activity.

Phenotypic characteristics and tendency to apoptosis of peripheral blood mononuclear cells from HIV+ long term non progressors

The aim of this study was to analyze (i) phenotype, (ii) in vitro spontaneous and induced apoptosis, (iii) glutathione (GSH) intracellular content and (iv) inhibitors of apoptosis of potential therapeutical use in peripheral blood mononuclear cells (PBMC) from HIV+ long term non progressors (LTNP), in comparison with progressors (HIV+P) and seronegative controls (HIV-). Three groups of subjects were studied: 15 HIV+P (patients losing >150 CD4+/year), 9 LTNP (subjects infected by HIV for at least 7 years without clinical and immunological signs of progression, with a mean of 898 CD4+/microL) and 18 HIV-. All subjects were living in a large community for former drug addicts, and were matched for age and sex. We used flow cytometry for analyzing PBMC phenotype and apoptosis; high performance liquid chromatography for measuring intracellular GSH content. PBMC phenotype of LTNP shared characteristics with those of both HIV- and HIV+P. Indeed, LTNP showed a normal number CD4+ cells (an inclusion criteria), but significantly increased numbers of CD8+ lymphocytes, activated T cells, CD19+, CD5+ B lymphocytes and CD57+ cells, as well as a decrease in CD19+, CD5- B lymphocytes and CD16+ cells. In LTNP, spontaneous apoptosis was similar to that of HIV- and significantly lower than that of HIV+P. Adding interleukin-2 (IL-2) or nicotinamide (NAM) significantly decreased spontaneous apoptosis in LTNP and HIV+P. Pokeweed mitogen-induced apoptosis was also similar in LTNP and HIV-, but significantly lower than that of HIV+P. In HIV+P, but also in LTNP, spontaneous apoptosis was inversely correlated to the absolute number and percentage of CD4+ cells and directly correlated to the number and percentage of activated T cells present in peripheral blood. GSH intracellular content was greatly decreased in PBMC from HIV+P and slightly, but significantly, reduced in LTNP. Adding 2-deoxy-D-ribose, an agent provoking apoptosis through GSH depletion, to quiescent PBMC resulted in similar levels of massive cell death in the three groups. This phenomenon was equally prevented in the three groups by N-acetyl-cysteine but not by IL-2. A complex immunological situation seems to occur in LTNP. Indeed, PBMC from LTNP are characterized by a normal in vitro tendency to undergo apoptosis despite the presence of a strong activation of their immune system, unexpectedly similar to that of HIV+P. Our data suggest that NAM and IL-2 are possible candidates for reducing spontaneous apoptosis in HIV infection.

Absorption kinetics and bioavailability of cephalexin in the dog after oral and intramuscular administration

The pharmacokinetics of cephalexin, a first generation cephalosporin, were investigated in dogs using two formulations marketed for humans, but also often employed by practitioners for pet therapy. Cephalexin was administered to five dogs intravenously and intramuscularly as a sodium salt and by the oral route as a monohydrate. The dosage was always 20 mg/kg of active ingredient. A microbiological assay with Sarcina lutea as the test organism was adopted to measure cephalexin concentrations in serum. The mean residence time (MRT) median values after intravenous (i.v.), intramuscular (i.m.) and oral administration (p.o.) were 86 min, 200 min, and 279 min, respectively. After i.m. and oral dosing the peak serum concentrations (24.2 +/- 1.8 micrograms/mL and 20.3 +/- 1.7 micrograms/mL, respectively) were attained at 90 min in all dogs and bioavailabilities were 63 +/- 10% and 57 +/- 5%, respectively. The time course of the cephalexin serum concentrations after oral administration was best described by a model incorporating saturable absorption kinetics of the Michaelis-Menten type: thus in the gastrointestinal tract of dogs a carrier mediated transport for cephalexin similar to that reported in humans, may exist. The predicted average serum concentrations of cephalexin after repeated i.m. and oral administration indicated that, in order to maintain the therapeutic concentrations, the 20 mg/kg b.w. dosage should be administered every 6-8 h.

Gastric emptying and dyspeptic symptoms in patients with gastroesophageal reflux

OBJECTIVES

To clarify 1) whether gastric emptying of a mixed meal is delayed in patients with gastroesophageal reflux and 2) the relationship between dyspeptic symptoms and delayed gastric emptying in refluxers.

METHODS

Gastric emptying of a solid meal was studied by ultrasound in 25 patients with pathological esophageal acid exposure. Gastric emptying was then assessed in relation to upper digestive endoscopy, esophageal manometry, 24-h pH monitoring and quantification of symptoms of reflux- and dysmotility-like dyspepsia.

RESULTS

Fifteen of 25 refluxers had esophagitis, and 15 were "dyspeptic". Refluxers exhibited a significant delay in gastric emptying compared with controls [307.6 (21.0) vs. 209 (10.4) min, p < 0.001). Patients with delayed emptying had low LES pressure [11.9 (2.1) vs. 18.6 (2.1) mm Hg, p < 0.05]. There was no correlation between delayed emptying and either pH monitoring or presence of esophagitis. There were no differences in any of the pH monitoring parameters between refluxers with and without coexisting dysmotility-like symptoms.

CONCLUSIONS

Gastric emptying of a solid meal is markedly delayed in patients with gastroesophageal reflux. However, no direct causal link was found between delayed emptying and reflux. Our data suggest the presence of a motility disorder in gastroesophageal reflux which is not confined to the esophagogastric junction.

Community-acquired pneumonia in a cohort of former injection drug users with and without human immunodeficiency virus infection: incidence, etiologies, and clinical aspects

Although the association among bacterial pneumonia, human immunodeficiency virus (HIV) infection, and injection-drug use seems to have been well established, accurate estimates of the risk of community-acquired pneumonia among HIV-positive and HIV-negative injection-drug users (IDUs) are still needed. To estimate the incidence of pneumonia in a community of former IDUs, we followed 4,236 persons between 1991 and 1994; 1,114 (26.3%) were HIV-positive and 3,122 (73.7%) were HIV-negative. All patients were evaluated for pneumonia by standard criteria, a serum sample was obtained from each participant at least once a year, and laboratory values were monitored. Overall, 149 episodes of pneumonia occurred among HIV-positive patients and 61 among HIV-negative patients; incidence rates were 90.5 and 14.2 (per 1,000 person-years), respectively. The most common etiologic agents were Streptococcus pneumoniae, Chlamydia pneumoniae, and Haemophilus influenzae. Among the HIV-positive former IDUs, there was a 1.37-fold increase in the relative risk of pneumonia for every decrease of 100/mm3 in the CD4 cell count (95% confidence interval, 1.16-1.61). The incidence of community-acquired pneumonia was markedly higher among HIV-positive participants than among HIV-negative ones, a finding similar to that concerning the general population.

CD45 isoforms expression on CD4+ and CD8+ T cells throughout life, from newborns to centenarians: implications for T cell memory

CD4+ and CD8+ peripheral blood T lymphocytes show mutually exclusive expression of CD45RA or CD45R0, two isoforms of the common leukocyte antigen that seem to recognize so-called virgin/unprimed and memory/activated T cells. The expression of these isoforms has been studied by three colour cytofluorimetric analysis on CD4+ or CD8+ peripheral blood CD3+ cells from 22 healthy centenarians, analyzed in a context of 202 healthy donors 0-110 years old. An age-related unbalance of virgin and memory cells was found between CD4+ and CD8+ subsets. As expected, at birgh 95-99% of the CD3+ lymphocytes expressed the CD45RA isoform. A rapid increase of CD45R0+ cells was observed in the first 2-3 decades of life, this phenomenon being much more pronounced on CD4+ cells. Subsequently, the increase of the 'memory' compartment was much less rapid, so that in centenarians a consistent reservoire of CD45RA+ among CD4+ cells was still present (about 20%). In these exceptional individuals the percentage of CD45RA+ cells among CD8+ T lymphocytes was even higher (about 50%), and only slightly lower than that of young donors (about 55-60%). Thus, the main changes occurred at a different rate in CD4+ (about 20%). In these exceptional individuals the percentage of CD45RA+ cells among CD8+ T lymphocytes was even higher (about 50%), and only slightly lower than that of young donors (about 55-60%). Thus, the main changes occurred at a different rate in CD4+ and in CD8+ T cells, at an age of between 0 and 30 years, when the thymus is still functionally active. Interestingly, no difference in the usage of CD45 isoforms was observed within T cells bearing four different V beta-T cell receptor (TCR). The significance of this age-related unbalance is unknown. However, the presence of a great number of CD45RA+ T lymphocytes within the CD4+ and the CD8+ T cell subsets even in the peripheral blood of centenarians poses the problem of their origin (thymus? extrathymic sites?), of their functional role and of their lifespan. Moreover, the data on centenarians suggest that they may represent a very selected population where a slowing of immunosenescence occurs.

Omeprazole causes delay in gastric emptying of digestible meals

We have studied gastric emptying of a solid, realistic meal (800 cal, 15% protein, 45% fat, 40% carbohydrate) in 21 healthy subjects twice, with and without a four-day pretreatment with 40 mg omeprazole. The last dose of the drug was taken 24 hr before the test, to avoid hypothetical nonsecretory side effects of the drug . Gastric emptying was measured by ultrasound of antral diameters. The results show that basal and maximal postprandial antral cross-sectional areas were the same during the two tests. A greater residual distention of the antrum was present throughout the study after the omeprazole treatment, the difference being significant at time 120 and 240. Omeprazole induced a highly significant delay in gastric emptying [control 199.6 (12.6) vs omeprazole 230.9 (12.7) min, mean (1 SEM); P<0.003]. The delay was not due to a prolonged lag phase, but rather to an effect on the slope of the emptying curve. This study shows that in normal subjects omeprazole delays gastric emptying of a digestible solid meal.

Pathological esophageal acidification and pneumatic dilitation in achalasic patients. Too much or not enough?

Endoscopy, esophageal manometry and pH monitoring, gastric emptying test, and heartburn quantification on a visual analog scale were performed in 22 achalasic patients in order to clarify which events are associated with pathological esophageal acidification after successful LES dilatation. Five patients presented pathological acidification. Dilatation reduced LES tone from 38.3 +/- 4.2 to 14.6 +/- 1.1 mm Hg (mean +/- SEM); there was, however, no difference between nonrefluxers and refluxers (14.8 +/- 1.2 vs 13.8 +/- 2.5 mm Hg). The emptying time in achalasic patients was delayed compared to controls (315.9 +/- 20.9 min vs 209 +/- 10.4) due to prolonged lag-phase and reduced slope of the antral section-time curve, but, again, there was no difference between refluxers and nonrefluxers. The acid clearance was delayed in refluxers compared to nonrefluxers (15.9 +/- 4.5 vs 2.5 +/- 1.8 min, P<0.05). Two refluxers presented grade 1 esophagitis; one of them developed an esophageal ulcer. The heartburn score was the same in refluxers and nonrefluxers. Pathological acidification after pneumatic dilatation is associated with persistent problems in esophageal emptying rather than with excessive sphincter divulsion.

Suicide attempted by burning: a 10-year study of self-immolation deaths

In a 10-year retrospective survey of 699 admissions to the Burns Centre of Verona, 31 patients (4.4 per cent) had self-inflicted burns. No sex difference was found, the mean age was 38 years, with 58 per cent of the patients in the 20-39-year age group. The mean burned surface area (BSA) was 41 per cent, and 12 patients (38.7 per cent) died: seven within the first 24 h. The other five patients died within 40 days (mean survival: 18 days). A large number of patients had a history of previous psychiatric treatment, six patients had previously attempted suicide. Four patients were drug addicts, three of whom were affected by AIDS and one had been HIV-positive for a long time. The patients had continuous psychiatric treatment during the long hospital stay. After discharge the patients were assigned to territorial staff for psychiatric treatment. Our experience shows that these patients have a higher mortality rate and they need constant psychiatric support, which can be useful in preventing further suicide attempts.

Gastric emptying of a solid meal is accelerated by the removal of dietary fibre naturally present in food

Exogenous fibre added to liquid meals delays gastric emptying. Its effect on solid meals is uncertain, and nothing is known of the effect on gastric emptying of fibre naturally present in food. This study therefore looked at gastric emptying of two different solid meals in eight healthy subjects and their blood glucose responses. The meals were exactly equivalent except for the total dietary fibre content (high fibre 20 g, low fibre 4 g of dietary fibre per 1000 kcal) and supplied 870 kcal (700 kcal women), 47% of which was from carbohydrates, 36% from fats, and 17% from proteins. Ultrasonography was used to measure antral diameters before the meal (basal), immediately after it (time 0), and at 30, 60, 120, 180, 240, and 300 minutes. In addition, subjects filled in a questionnaire on their feelings of hunger, epigastric fullness, and satiety before the meal and at hourly intervals after it. Basal and maximal postprandial antral sections were similar for the two meals (basal section: 283.9 (29.5) v 340.9 (44.7) mm2 for the low and the high fibre meal, NS; maximal postprandial section: 1726 (101.9) v 1593 (120.4) mm2, NS). Total gastric emptying time was significantly reduced by fibre removal (186.0 (15.6) v 231.7 (17.3) minutes after the low and the high fibre meal, p < 0.05). Blood glucose was higher after the low fibre meal, and the area under the glycaemic curve significantly greater (226 (23.1) v 160 (20.0) mmol/min/dl-1, p < 0.05). No difference was found in satiety or fullness feelings, but hunger returned more rapidly after the low fibre meal. In conclusion, fibre naturally present in food delays gastric emptying of a solid meal, reduces the glycaemic response, and delays the return of hunger.

Effect of neutralized and native vinegar on blood glucose and acetate responses to a mixed meal in healthy subjects

OBJECTIVE

To investigate the influence of sodium acetate and acetic acid from vinegar on blood glucose and acetate response to a mixed meal in healthy subjects.

DESIGN

Five healthy subjects consumed in random order six test meals consisting of 100 g of sliced lettuce dressed with olive oil (Blank), olive oil plus 1 g acetic acid in the form of vinegar (AcOH), or olive oil plus sodium acetate in the form of vinegar neutralized to pH 6.0 with sodium bicarbonate (AcNa). On three occasions test meals were followed by a challenge consisting of 50 g carbohydrate portions of white bread (Bread). Glucose and acetate concentrations were measured in arterialized capillary blood before and until 95 min after the meals. Ultrasonography was performed in four other subjects to measure gastric emptying times after AcOH + Bread and AcNa + Bread.

RESULTS

Blood acetate response over 95 min was markedly reduced after AcOH and AcOH+Bread meals compared to AcNa and AcNa + Bread. Similarly, the glucose response was depressed by 31.4% (P = 0.0228) after AcOH+Bread with respect to AcNa + Bread and Blank + Bread. No difference was observed between gastric emptying times after AcOH + Bread and AcNa + Bread.

CONCLUSIONS

The results suggest that oral acetic acid and acetate might have a different effect on acetataemia and that a limited dose of vinegar, in the form of salad dressing, is sufficient to influence significantly the glycaemic response to a mixed meal in normal subjects by a mechanism related to acidity but not to gastric emptying.

Gastric emptying of solids is markedly delayed when meals are fried

We studied the effect of heat-treated fats on gastric emptying. Eight healthy asymptomatic volunteers (five males; age 28-41 years) ate on different days and in random order two meals identical in contents (pasta, tomato, beef, olive oil, carrots, orange, water; 870 kcal males, 700 kcal females; 47% of calories from carbohydrate, 36% from fat, 17% from protein), but cooked differently (fats fried or not). Ultrasound measurement of antral diameters was used to calculate basal antral section, its maximal dilation after the meal, the time necessary for total emptying, and the percent retention at hourly intervals. No difference was found in basal and maximal antral diameters after the two meals. On the contrary, total gastric emptying was significantly delayed after the fried meal [317.1 (24.12) vs 226.7 (18.4) min, mean (1 SEM); P < 0.002]. A significantly greater percentage of maximal antral distension was still present between 120 and 240 min after the fried meal. The glycemic response and hunger feeling were the same after the two meals, whereas there was a longer persistence of satiety and epigastric fullness after the fried meal. In conclusion, gastric emptying can be influenced not only by the meal content, but also by the way it is cooked.

Gastric emptying of solid meals in achalasic patients after successful pneumatic dilatation of the cardia

Gastric emptying of a solid meal was measured by ultrasound scanning in 16 achalasic patients following successful pneumatic dilatation of the lower esophageal sphincter. The data were compared with those of a control group of 15 healthy subjects. Fasting and maximal postcibal antral sections were very similar in the two groups. On the contrary, the time interval before maximal antral dilatation, and the time necessary for the emptying of half or of the whole meal were significantly longer in the achalasic patients than in the controls. Half of the achalasic patients had longer emptying times than the upper normal limit. The percentage of the meal retained in the antrum at each hourly interval was significantly higher in the achalasic group. The finding of a high prevalence of gastric emptying disturbances suggests that the functional derangement in achalasia is not limited to the esophagus.

[In vitro study of a new pancreatic enzyme with high lipase content in enteric coated microtablets]

In vitro behaviour of the enteric-coating of a new pancreatic enzyme containing preparation in enteric-coated microtablets was evaluated, by incubating at 37 degrees C, under gentle agitation, the preparation under study in buffered gastric (pH 2, 3, 4, 5, 6) and in buffered duodenal juice (pH 3, 4, 5, 6, 7, 8) for 30, 60, 90, 120 minutes. Lipase and chymotripsin activities were measured at each time and pH in the solution and in the undissolved microtablets. The drug under study showed a good enteric-coating, preserving about 100% of the enzyme content, when incubated in buffered gastric juice, up to pH 6, and releasing in the solution, during incubation in buffered duodenal juice, 75% of its enzyme content at pH 7 and 8. Therefore, the pancreatic enzymes contained in this new enteric-coated microtablet preparation are well protected against inactivation from acid and are bioavailable for digestion of alimentary substrates at optimal or near optimal pH in duodenal juice.

Osteoid osteoma of the carpal scaphoid in the adult: a clinical case

The authors present one case of osteoid osteoma of the carpal scaphoid, emphasizing the clinical rareness of the disease. Methods of diagnosis used and surgical treatment performed are described.

Near infrared reflectance measurement of nitrogen faecal losses

Chemical methods of measuring nitrogen in stools are complex, unpleasant, and therefore rarely performed. Recently, near infrared reflectance (NIRA) has been suggested for stool analysis. The aim of this study was to evaluate the possible application of this method in routine faecal nitrogen measurement. Nitrogen concentration and daily output were measured in the stools of 83 patients using NIRA and, for comparison, the Kjeldahl method. Nitrogen concentration and output ranged between 0.4-2.72 g% and 0.45-8.96 g/day respectively. Correlation coefficients (r), of 0.89 and 0.97 were found between the two methods for concentration and output respectively, and similar values were found in patients on enteral nutrition. Repeated measurements from the same stool collection, requiring only a few minutes, allowed homogenisation to be avoided. NIRA seems to be an easy, fast, and reliable alternative to chemical assays of nitrogen measurement in the management of patients with digestive disorders.

Fecal fat concentration in the screening of steatorrhea

We studied if the fecal fat concentration as measured by the near infrared reflectance analysis in a spot sample is an acceptable screening test for malabsorption. This measurement was compared with the more complex fat balance in 120 patients with a suspected malabsorption [53 with chronic pancreatic disorders (CP), 67 with other digestive disorders (nCP)]. The fecal fat concentration proved to be well correlated with steatorrhea in CP (r = 0.86) but not in nCP (r = 0.35). A fat concentration of 9 g% had a sensitivity and a specificity for steatorrhea of 88.8% and of 97.1% in CP, but only of 53.8% and of 94.4% respectively in nCP. The fecal fat concentration was significantly higher in CP than in nCP, even considering patients with steatorrhea only; however, the overlap between the two groups was too high to suggest a clinical usefulness of this test in the differential diagnosis of steatorrheas. It is concluded that the fat concentration in a small sample, easily obtained also in outpatients, is useful in the selection of patients with chronic pancreatitis to submit to a proper fat balance study.

[Learning disorders in school children. An integrative approach, importance of the biological component and relational dimension]

This paper concerns the development of a diagnostic procedure for learning disorders, in line with a multifactorial approach in which the contributions of the organic and psychogenetic points of view are integrated to form a common interpretative model. The aim is to identify strategies for intervening at different levels. We examined 10 patients with learning disorders which came consecutively to our Division of Child Neuropsychiatry and an equal number of control subjects which were as old as the patients and begin school at the correct age. We used an integrative approach: we interviewed parents to know history, the relational, familial and sociocultural features and moreover, organic problems, if any, neurological examination and, if necessary, skull x-ray, EEG, skull CT; psychodynamic interview, drawing of human figure and family drawing; WISC; Bender test, Stambak test, Rorschach test, Blacky Pictures test. All the variables that could be quantified from the diagnostic protocols were compared statistically. Assessment of our case histories gives weight to the hypothesis of a multifactorial pathogenesis. We did find psychodynamic problems in all cases, and were able to identify aspects of generalised, and in particular, epistemophilic inhibition.

[Neuropsychiatric approach to a child with spinal muscular atrophy. A study of relational problems]

Various years' experience of an extensive series of children suffering from progressive chronic spinal muscular atrophy have made it possible to elaborate a neuropsychiatric approach model conducted on the basis of a viewpoint capable of integrating the clinico-medical aspect and aptitude to empathic listening aimed at establishing a therapeutic alliance with the patient. With advancing age and the course of the disease, in most cases very different difficulties and problems are encountered. These change continuously in relation to the stage reached in emotional development. Entry to school and socialisation mark a particular moment in the confrontation with peers and present the ill child with his diversity. With the emergence of adolescent problems, there is also a dramatic new impact between the body image of a wounded, deteriorated self and the evolutionary effort aimed at identifying with the peer group, the autonomisation of parental figures, the integration of a sexed image of the self. Room can be found in this framework for the child neuropsychiatrist who is able to offer himself as a point of reference and set himself up as a model for elaborating disease anxieties. From personal experience it also emerges that in children suffering from a chronic, often fatal disease there is often the need for a physician to coordinate and integrate needs of both a clinical and sociorelational nature for the purpose of allowing the family to get closer to the needs of their child and prevent him from falling prey to destructive type anxieties.

Variations in time of serum pancreatic enzyme levels in chronic pancreatitis and clinical course of the disease

Thirty-four patients with chronic calcified pancreatitis were evaluated clinically and biochemically (at a time when painful relapses were not present) every 9 mo for 3 yr; 25 of them were also studied at 4 and 9 yr. Serum elastase-1, trypsin, lipase, and amylase in the same sera were measured at each visit; levels on entry and variations during the study were compared with the clinical and functional data of the patients. On entry, low levels of elastase-1 were found in 11.7% of the patients, high levels in 41.1%; in contrast, high levels of trypsin and lipase were found in only a small number of patients (5.8 and 11.7%, respectively), whereas low levels were present in a substantial number (47.8 and 32.3% for trypsin and lipase, respectively). Over time, we found a significant (p = 0.000002) reduction in elastase-1 levels. Such reduction was not found for trypsin, lipase, or amylase. The reduction of serum elastase-1 was significantly (p less than 0.003) more frequent in patients presenting a reduction in painful relapses than in patients with a stable or increased attach rate; this association was weaker (p less than 0.05) for lipase and trypsin, and absent for amylase. No correlation was found between circulating enzymes and either alcohol consumption or age of patients. In patients with severe exocrine impairment, low levels of elastase were found in only 20% of the cases, whereas trypsin and lipase were reduced in 73.3 and 53.3% of the cases, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Spontaneous and mitomycin-C-induced micronuclei in human lymphocytes exposed to extremely low frequency pulsed magnetic fields

The cytokinesis block micronucleus method, a very sensitive cytogenetic assay, was used to ascertain the possible genotoxic effects of extremely low frequency pulsed magnetic fields in phytohemagglutinin-stimulated human lymphocytes cultures from 16 healthy donors. Four conditions were studied: i) lymphocytes not exposed to the field (control cultures); ii) lymphocytes exposed to the field; iii) lymphocytes treated with mitomycin-C and not exposed to the field; iv) lymphocytes treated with mitomycin-C and exposed to the field. Mitomycin-C-treated cultures were used as control for the micronucleus method, because it is known that mitomycin-C is a potent genotoxic agent, capable of inducing micronuclei. The frequency of micronuclei in field-exposed cultures was similar to the spontaneous frequency observed in control unexposed-cultures. Moreover, the exposure to pulsed magnetic fields did not affect the frequency of micronuclei induced by mitomycin-C, suggesting that, in the experimental conditions used, this kind of field neither affected the integrity of chromosomes nor interfered with the genotoxic activity of mitomycin-C.

[Learning disturbances in developmental ages. Consideration of some clinical cases studied with a neuropsychiatric approach]

The psychoanalytic and neuropsychiatric literature on learning disturbances has been reviewed. Relations between learning disturbances, psycho-affective, cognitive and neurological development are examined. Particular attention is paid to Klein's theory of intellectual inhibition and the integrative approach described by Rothstein. Four clinical cases, which seem to exemplify the infantile neuropsychiatric integrative approach are then presented. Finally, stress is laid on the pathogenetic interrelations between psychopathological and organic aspects of the children considered and the similarities between learning disturbances and pseudo mental deficiency.