Current databases on biological variation: pros, cons and progress

A database with reliable information to derive definitive analytical quality specifications for a large number of clinical laboratory tests was prepared in this work. This was achieved by comparing and correlating descriptive data and relevant observations with the biological variation information, an approach that had not been used in the previous efforts of this type. The material compiled in the database was obtained from published articles referenced in BIOS, CURRENT CONTENTS, EMBASE and MEDLINE using "biological variation & laboratory medicine" as key words, as well as books and doctoral theses provided by their authors. The database covers 316 quantities and reviews 191 articles, fewer than 10 of which had to be rejected. The within- and between-subject coefficients of variation and the subsequent desirable quality specifications for precision, bias and total error for all the quantities accepted are presented. Sex-related stratification of results was justified for only four quantities and, in these cases, quality specifications were derived from the group with lower within-subject variation. For certain quantities, biological variation in pathological states was higher than in the healthy state. In these cases, quality specifications were derived only from the healthy population (most stringent). Several quantities (particularly hormones) have been treated in very few articles and the results found are highly discrepant. Therefore, professionals in laboratory medicine should be strongly encouraged to study the quantities for which results are discrepant, the 90 quantities described in only one paper and the numerous quantities that have not been the subject of study.

Neuronal correlates of parametric working memory in the prefrontal cortex

Humans and monkeys have similar abilities to discriminate the difference in frequency between two mechanical vibrations applied sequentially to the fingertips. A key component of this sensory task is that the second stimulus is compared with the trace left by the first (base) stimulus, which must involve working memory. Where and how is this trace held in the brain? This question was investigated by recording from single neurons in the prefrontal cortex of monkeys while they performed the somatosensory discrimination task. Here we describe neurons in the inferior convexity of the prefrontal cortex whose discharge rates varied, during the delay period between the two stimuli, as a monotonic function of the base stimulus frequency. We describe this as 'monotonic stimulus encoding', and we suggest that the result may generalize: monotonic stimulus encoding may be the basic representation of one-dimensional sensory stimulus quantities in working memory. Thus we predict that other behavioural tasks that require ordinal comparisons between scalar analogue stimuli would give rise to monotonic responses similar to those reported here.

Pervasive density-dependent recruitment enhances seedling diversity in a tropical forest

Negative density-dependent recruitment of seedlings, that is, seeds of a given species are less likely to become established seedlings if the density of that species is high, has been proposed to be an important mechanism contributing to the extraordinary diversity of tropical tree communities because it can potentially prevent any particular species from usurping all available space, either in close proximity to seed sources or at relatively larger spatial scales. However, density-dependent recruitment does not necessarily enhance community diversity. Furthermore, although density-dependent effects have been found at some life stages in some species, no study has shown that density-dependent recruitment affects community diversity. Here we report the results of observations in a lowland, moist forest in the Republic of Panamá in which the species identities of 386,027 seeds that arrived at 200 seed traps were compared with the species identities of 13,068 seedlings that recruited into adjacent plots over a 4-year period. Across the 200 sites, recruit seedling diversity was significantly higher than seed diversity. Part of this difference was explained by interspecies differences in average recruitment success. Even after accounting for these differences, however, negative density-dependent recruitment contributes significantly to the increase in diversity from seeds to seedling recruits.

Somatosensory discrimination based on cortical microstimulation

The sensation of flutter is produced when mechanical vibrations in the range of 5-50Hz are applied to the skin. A flutter stimulus activates neurons in the primary somatosensory cortex (S1) that somatotopically map to the site of stimulation. A subset of these neurons-those with quickly adapting properties, associated with Meissner's corpuscles-are strongly entrained by periodic flutter vibrations, firing with a probability that oscillates at the input frequency. Hence, quickly adapting neurons provide a dynamic representation of such flutter stimuli. However, are these neurons directly involved in the perception of flutter? Here we investigate this in monkeys trained to discriminate the difference in frequency between two flutter stimuli delivered sequentially on the fingertips. Microelectrodes were inserted into area 3b of S1 and the second stimulus was substituted with a train of injected current pulses. Animals reliably indicated whether the frequency of the second (electrical) signal was higher or lower than that of the first (mechanical) signal, even though both frequencies changed from trial to trial. Almost identical results were obtained with periodic and aperiodic stimuli of equal average frequencies. Thus, the quickly adapting neurons in area 3b activate the circuit leading to the perception of flutter. Furthermore, as far as can be psychophysically quantified during discrimination, the neural code underlying the sensation of flutter can be finely manipulated, to the extent that the behavioural responses produced by natural and artificial stimuli are indistinguishable.

Bone disease in predialysis, hemodialysis, and CAPD patients: evidence of a better bone response to PTH

The spectrum of bone disease in predialysis and dialysis patients has changed during the last decade. The incidence of aplastic bone disease has increased and this can not be attributed to bone aluminum deposition; moreover, low bone cellular activity is present despite a moderate elevation in PTH levels. This study compares PTH levels and types of bone disease in both predialysis and dialysis patients from the same geographical area. We prospectively studied 119 unselected end-stage renal disease patients: 38 were immediately predialysis (PreD), 49 on hemodialysis (HD), and 32 on CAPD. A bone biopsy was performed in all patients. Aplastic bone disease with < 5% bone surface aluminum was a common finding (48%, 32%, and 48%, in PreD, HD, and CAPD, respectively). In all groups, an intact PTH level below 120 pg/ml was highly predictive of low bone turnover. Conversely, a PTH level above 450 pg/ml was always associated with histologic features of hyperparathyroid bone disease. Among the bone histomorphometric parameters, osteoblast surface showed the best correlation with intact PTH in each group, and the slope of the regression line for this correlation was significantly steeper in HD and CAPD than PreD patients. Thus, the range of PTH (95% confidence limit bands) needed to obtain a normal osteoblast surface of 1.5% was greater in preD than in HD and CAPD patients (300 to 500 vs. 75 to 260 pg/ml, respectively). In all groups some degree of marrow fibrosis was observed when PTH levels were greater than 250 pg/ml.(ABSTRACT TRUNCATED AT 250 WORDS)

The voltage sensitive Lc-type Ca2+ channel is functionally coupled to the exocytotic machinery

Although N- and P-type Ca2+ channels predominant in fast-secreting systems, Lc-type Ca2+ channels (C-class) can play a similar role in certain secretory cells and synapses. For example, in retinal bipolar cells, Ca2+ entry through the Lc channels triggers ultrafast exocytosis, and in pancreatic beta-cells, evoked secretion is highly sensitive to Ca2+. These findings suggest that a rapidly release pool of vesicles colocalizes with the Ca2+ channels to allow high Ca2+ concentration and a tight coupling of the Lc channels at the release site. In binding studies, we show that the Lc channel is physically associated with synaptotagmin (p65) and the soluble N-ethylmaleimide-sensitive attachment proteins receptors: syntaxin and synaptosomal-associated protein of 25 kDa. Soluble N-ethylmaleimide-sensitive attachent proteins receptors coexpressed in Xenopus oocytes along with the Lc channel modify the kinetic properties of the channel. The modulatory action of syntaxin can be overcome by coexpressing p65, where at a certain ratio of p65/syntaxin, the channel regains its unaltered kinetic parameters. The cytosolic region of the channel, Lc753-893, separating repeats II-III of its alpha1C subunit, interacts with p65 and "pulls" down native p65 from rat brain membranes. Lc753-893 injected into single insulin-secreting beta-cell, inhibits secretion in response to channel opening, but not in response to photolysis of caged Ca2+, nor does it affect Ca2+ current. These results suggest that Lc753-893 competes with the endogenous channel for the synaptic proteins and disrupts the spatial coupling with the secretory apparatus. The molecular organization of the Lc channel and the secretory machinery into a multiprotein complex (named excitosome) appears to be essential for an effective depolarization evoked exocytosis.

Sensing without touching: psychophysical performance based on cortical microstimulation

Unequivocal proof that the activity of a localized cortical neuronal population provides sufficient basis for a specific cognitive function has rarely been obtained. We looked for such proof in monkeys trained to discriminate between two mechanical flutter stimuli applied sequentially to the fingertips. Microelectrodes were inserted into clusters of quickly adapting (QA) neurons of the primary somatosensory cortex (S1), and the first or both stimuli were then substituted with trains of current pulses during the discrimination task. Psychophysical performance with artificial stimulus frequencies was almost identical to that measured with the natural stimulus frequencies. Our results indicate that microstimulation can be used to elicit a memorizable and discriminable analog range of percepts, and shows that activation of the QA circuit of S1 is sufficient to initiate all subsequent neural processes associated with flutter discrimination.

Neuronal correlates of sensory discrimination in the somatosensory cortex

Monkeys are able to discriminate the difference in frequency between two periodic mechanical vibrations applied sequentially to the fingertips. It has been proposed that this ability is mediated by the periodicity of the responses in the quickly adapting (QA) neurons of the primary somatosensory cortex (S1), instead of the average firing rates. We recorded from QA neurons of S1 while monkeys performed the vibrotactile discrimination task. We found that the periodic mechanical vibrations can be represented both in the periodicity and in the firing rate responses to varying degrees across the QA neuronal population. We then computed neurometric functions by using both the periodicity and the firing rate and sought to determine which of these two measures is associated with the psychophysical performance. We found that neurometric thresholds based on the firing rate are very similar to the animal's psychometric thresholds whereas neurometric thresholds based on periodicity are far lower than those thresholds. These results indicate that an observer could solve this task with a precision similar to that of the monkey, based only on the firing rate produced during the stimulus periods.

The reference change value: a proposal to interpret laboratory reports in serial testing based on biological variation

BACKGROUND

A proposal to calculate and use the reference change value (RCV) as an objective guide for interpreting the numerical results obtained in clinical laboratory serial testing is introduced in this study.

METHODS

A database showing the results of a compilation of 191 publications on biological variation and including information on a number of analytes provided the standardized criterion based on biology for calculating the RCVs.

RESULTS

For each of the 261 analytes included in the study, the RCV was determined using Harris's formula, replacing analytical imprecision with the desirable specification of analytical quality based on half the within-subject biological variation at 95% probability levels. The result is a guide for a common criterion to identify clinically significant changes in serial results.

CONCLUSIONS

The RCV concept is an approach that can be offered by laboratories to assess changes in serial results. The RCV data in this study are presented as a point of departure for a widely applicable objective guide to interpret changes in serial results.

NADPH oxidases differentially regulate ROS metabolism and nutrient uptake under cadmium toxicity

The role of NADPH oxidases under cadmium (Cd) toxicity was studied using Arabidopsis thaliana mutants AtrbohC, AtrbohD and AtrbohF, which were grown under hydroponic conditions with 25 and 100 μM Cd for 1 and 5 days. Cadmium reduced the growth of leaves in WT, AtrbohC and D, but not in AtrbohF. A time-dependent increase in H₂ O₂ and lipid peroxidation was observed in all genotypes, with AtrbohC showing the smallest increase. An opposite behaviour was observed with NO accumulation. Cadmium increased catalase activity in WT plants and decreased it in Atrboh mutants, while glutathione reductase and glycolate oxidase activities increased in Atrboh mutants, and superoxide dismutases were down-regulated in AtrbohC. The GSH/GSSG and ASA/DHA couples were also affected by the treatment, principally in AtrbohC and AtrbohF, respectively. Cadmium translocation to the leaves was severely reduced in Atrboh mutants after 1 day of treatment and even after 5 days in AtrbohF. Similar results were observed for S, P, Ca, Zn and Fe accumulation, while an opposite trend was observed for K accumulation, except in AtrbohF. Thus, under Cd stress, RBOHs differentially regulate ROS metabolism, redox homeostasis and nutrient balance and could be of potential interest in biotechnology for the phytoremediation of polluted soils.

Risk factors for nosocomial pneumonia in critically ill trauma patients

OBJECTIVE

To determine risk factors for nosocomial pneumonia in critically ill trauma patients.

DESIGN

Prospective cohort study.

SETTING

The trauma intensive care unit (ICU) of a 1500-bed tertiary-care hospital.

PATIENTS

All critically ill trauma patients (n = 103) admitted consecutively between November 1995 and October 1996.

INTERVENTIONS

A comparison of data recorded at the time of ICU admission and during the clinical evolution in patients with (n = 23) and without (n = 80) nosocomial pneumonia was made. Data referred mainly to possible risk factors were recorded; they also included factors related to pneumonia etiology and evolutive factors. Predictors of nosocomial pneumonia were assessed by logistic regression analysis.

MEASUREMENTS AND MAIN RESULTS

The presence of significant growth on quantitative cultures of the protected specimen brush (> or = 103 colony forming units/mL) was required to accept pneumonia as microbiologically proven, as well as the concurrence of a cohort of clinical and radiologic signs. Twenty-three (22.3%) patients developed nosocomial pneumonia. The mean age of these patients was 41.7 yrs; 18 of them (78.3%) were men. The microorganisms isolated in significant concentrations were Acinetobacter baumanii (ten cases), Staphylococcus aureus (11 cases), Pseudomonas aeruginosa (five cases), Haemophilus influenzae (two cases), and Klebsiella pneumoniae, Citrobacter freundii, Serratia marcescens, Enterococcus spp., Enterobacter spp., coagulase-negative Staphylococcus, and Streptococcus intermedius (one case each one). Risk factors for pneumonia by univariate analysis included nasogastric tube; continuous enteral feeding; prolonged mechanical ventilation (>1 day); use of H2-receptor antagonist, sucralfate, muscle relaxants, corticosteroids, barbiturates, and inotropic agents; positive end-expiratory pressure; intense sedation; re-intubation; tracheotomy; urgent brain computed tomography (CT) scan; craniotomy; iatrogenic event; and hyperventilation. The mortality rate was 43.5% (10 of 23) in the nosocomial pneumonia group and 18.8% in patients without nosocomial pneumonia (p =.02). Also, the mean stay in the ICU, the therapeutic charge (measured with total and mean punctuation of the Therapeutic Intervention Scoring System) and the complications, infectious and noninfectious, of the clinical evolution were significantly more frequent in patients with nosocomial pneumonia than in those without pneumonia (p <.05). In the multivariate analysis, continuous enteral feeding, craniotomy, prolonged mechanical ventilation (>24 hrs), use of positive end-expiratory pressure, and corticotherapy were independent predictors of nosocomial pneumonia.

CONCLUSIONS

It seems that factors related to the patient's clinical course, rather than variables registered on the first days of ICU admission, are those that would exert an influence on the development of nosocomial pneumonia in critically ill trauma patients. In this way, from our point of view, in our study the main risk factors are the use of prolonged mechanical ventilation (>4 hrs) and positive end-expiratory pressure. At the same time, we can conclude that the reduction of this infection incidence could decrease the mean stay in the ICU, the therapeutic charge, and the prognosis in terms of mortality and morbidity.

MHC class II sequences of susceptibility and protection in Mexicans with autoimmune hepatitis

BACKGROUND/AIMS

Autoimmune hepatitis has a genetic background associated with different HLA DRB1 alleles depending on the ethnic group. The aim of this study was to analyse the immunogenetics of type I autoimmune hepatitis in Mexicans.

METHODS

Thirty Mexican Mestizo patients and 175 healthy controls were HLA typed as follows: class I antigens were determined by microlymphocytotoxicity and class II typing was done on DNA samples using PCR-SSO and PCR-SSP for DRB1, DQA1 and DQB1 loci.

RESULTS

A significant association of autoimmune hepatitis with DRB1*0404 was found, (chi2Y=19.95, pc=0.002, RR=7.71), suggesting the presence of a susceptibility gene located at the DRB1 locus. Resistance was at least partially due to a DQB1 gene, since a significant decrease in DQB1*0301 was also detected (chi2Y=8.21, pc=0.04). Analysis of subgroups according to age at onset showed an association with DRB1*0404 (chi2Y=4.31, p=0.04) in patients with late onset (after 30 years), while DQA1*0501 (chi2Y=5.12, p=0.02) was increased in the early onset group.

CONCLUSIONS

The possible mechanism of HLA association is due to "shared epitopes", since DRB1*0404, and those found in other populations namely, DRB1*0401, *0405 and *0301 share almost the same sequence at position 67-72 (LLEQRR, R or K at 71). Valine-86 is also relevant to the age at onset because DRB1*0404 is increased in the patients with an average age at onset of 32. These findings are relevant in determining which peptides in the liver are targets for T cells.

A set of recombinant antigens from Echinococcus granulosus with potential for use in the immunodiagnosis of human cystic hydatid disease

Several recombinant clones expressing antigens from Echinococcus granulosus were isolated previously from a parasite cDNA library using cystic hydatid disease (CHD) patients' sera or rabbit hyperimmune antiserum against a lipoproteic fraction from bovine cyst fluid. Six of these antigens were expressed in Escherichia coli and the purified recombinant proteins were tested in enzyme-linked immunosorbent assay (ELISA) for specific IgG with a panel of sera from patients with surgically confirmed (n = 58) or immunologically diagnosed (n = 71) CHD. Sera from clinically normal individuals (n = 203) and sera from individuals with other helminthic infections (n = 65) were assayed for the assessment of specificity. A cut-off value was determined by receiver-operating-characteristic plots for each antigen. A recombinant antigen B subunit (AgB8/2) presented the highest sensitivity (93.1%), considering the group of sera from patients with CHD surgically confirmed, and specificity (99.5%) and is proposed as the basis for an immunodiagnostic test. The other recombinant antigens tested presented sensitivities between 58.6% and 89.7%, and three of them were considered of complementary value. In subclass-specific ELISA, different IgG isotypes showed dominance in the response for each of the recombinant antigens. There was a clear predominance of IgG4 response for all antigens tested, indicating that this would be the subclass of choice to be assessed for these recombinant proteins.

RET genotypes comprising specific haplotypes of polymorphic variants predispose to isolated Hirschsprung disease

BACKGROUND

Hirschsprung disease (HSCR), which may be sporadic or familial, occurs in 1:5000 live births and presents with functional intestinal obstruction secondary to aganglionosis of the hindgut. Germline mutations of the RET proto-oncogene are believed to account for up to 50% of familial cases and up to 30% of isolated cases in most series. However, these series are highly selected for the most obvious and severe cases and large familial aggregations. Population based studies indicate that germline RET mutations account for no more than 3% of isolated HSCR cases. Recently, we and others have noted that specific polymorphic sequence variants, notably A45A (exon 2), are over-represented in isolated HSCR.

PURPOSE

In order to determine if it is the variant per se, a combination thereof, or another locus in linkage disequilibrium which predisposes to HSCR, we looked for association of RET haplotype(s) and disease in HSCR cases compared to region matched controls.

METHODS

Seven loci across RET were typed and haplotypes formed for HSCR cases, their unaffected parents, and region matched controls. Haplotype and genotype frequencies and distributions were compared among these groups using the transmission disequilibrium test and standard case-control statistic.

RESULTS

Twelve unique haplotypes, labelled A-L, were obtained. The distributions of haplotypes between cases and controls (chi(11)(2) =81.4, p<<0.0001) and between cases and non-transmitted parental haplotypes were significantly different (chi(2)(11)=53.1, p<0.0001). Genotypes comprising pairs of haplotypes were formed for cases and controls. There were 38 different genotypes among cases and controls combined. Inspection of the genotypes in these two groups showed that the genotype distribution between cases and controls was distinct (chi(37)(2)=93. 8, p<<0.0001). For example, BB, BC, BD, and CD, all of which contain at least one allele with the polymorphic A45A, are prominently represented among HSCR cases, together accounting for >35% of the case genotypes, yet these four genotypes were not represented among the population matched normal controls. Conversely, AA, AG, DD, GG, and GJ, none of which contains A45A, are commonly represented in the controls, together accounting for 43% of the control genotypes, and yet they are never seen among the HSCR cases.

CONCLUSIONS

Our data suggest that genotypes comprising specific pairs of RET haplotypes are associated with predisposition to HSCR either in a simple autosomal recessive manner or in an additive, dose dependent fashion.

Potential impact of American Diabetes Association (2000) criteria for diagnosis of gestational diabetes mellitus in Spain

AIMS/HYPOTHESIS

This study was carried out to determine the impact of American Diabetes Association (ADA) 2000 criteria for the diagnosis of gestational diabetes mellitus (GDM) in the Spanish population.

METHODS

Pregnant women were assigned to one of four categories: negative screenees, false-positive screenees, ADA-only-GDM (untreated) and GDM according to National Diabetes Data Group (NDDG) criteria (treated). Fetal macrosomia and Caesarean section were defined as primary outcomes, with seven additional secondary outcomes.

RESULTS

Of 9,270 pregnant women screened for GDM, 819 (8.8%) met NDDG criteria. If the threshold for defining GDM had been lowered to ADA criteria, an additional 2.8% of women would have been defined as having the condition (relative increase of 31.8%). Maternal characteristics of women with ADA-only-GDM were between those of false-positive screenees and women with NDDG-GDM. The risk of diabetes-associated complications was slightly elevated in the individuals who would have been classified as abnormal only after the adoption of ADA criteria. In addition, the ADA-only-GDM contribution to morbidity was lower than that of other variables, especially BMI.

CONCLUSIONS/INTERPRETATION

Use of the ADA criteria to identify GDM would result in a 31.8% increase in prevalence compared with NDDG criteria. However, as the contribution of these additionally diagnosed cases to adverse GDM outcomes is not substantial, a change in diagnostic criteria is not warranted in our setting.

Spoilage yeasts: What are the sources of contamination of foods and beverages?

Foods and beverages are nutrient-rich ecosystems in which most microorganisms are able to grow. Moreover, several factors, such as physicochemical characteristics, storage temperature, culinary practices, and application of technologies for storage, also define the microbial population of foods and beverages. The yeast population has been well-characterised in fresh and processed fruit and vegetables, dairy products, dry-cured meat products, and beverages, among others. Some species are agents of alteration in different foods and beverages. Since the most comprehensive studies of spoilage yeasts have been performed in the winemaking process, hence, these studies form the thread of the discussion in this review. The natural yeast populations in raw ingredients and environmental contamination in the manufacturing facilities are the main modes by which food contamination occurs. After contamination, yeasts play a significant role in food and beverage spoilage, particularly in the alteration of fermented foods. Several mechanisms contribute to spoilage by yeasts, such as the production of lytic enzymes (lipases, proteases, and cellulases) and gas, utilisation of organic acids, discolouration, and off-flavours. This review addresses the role of yeasts in foods and beverages degradation by considering the modes of contamination and colonisation by yeasts, the yeast population diversity, mechanisms involved, and the analytical techniques for their identification, primarily molecular methods.

Metal accumulation and vanadium-induced multidrug resistance by environmental isolates of Escherichia hermannii and Enterobacter cloacae

Contaminated soils from an oil refinery were screened for the presence of microorganisms capable of accumulating either nickel, vanadium, or both metals. Three strains of bacteria that belonged to the family Enterobacteriaceae were selected. Two of them were Escherichia hermannii strains, and outer membrane profile (OMP) analysis showed that they were similar to a strain of clinical origin; the other one was an Enterobacter cloacae strain that differed from clinical isolates. The selected bacteria accumulated both nickel and vanadium. Growth in the presence of vanadium induced multidrug resistance phenotypes in E. hermannii and E. cloacae. Incubation with this metal changed the OMP profile of E. hermannii but did not produce variations in the expression of the major OMPs of E. cloacae.

An EXCEL template for calculation of enzyme kinetic parameters by non-linear regression

MOTIVATION

An EXCEL template has been developed for the calculation of enzyme kinetic parameters by non-linear regression techniques. The tool is accurate, inexpensive, as well as easy to use and modify.

AVAILABILITY

The program is available from http://www.ebi.ac.uk/biocat/biocat.html

CONTACT

agustin. hernandez@bio.kuleuven.ac.be

Evaluation of a rapid immunochromatographic assay for the detection of Legionella antigen in urine samples

A new immunochromatographic membrane assay for detecting Legionella pneumophila serogroup 1 antigen in urine samples (Binax Now Legionella Urinary Antigen Test; Binax, USA) was evaluated. Its sensitivity, specificity and level of agreement with the Binax enzyme immunoassay were compared using nonconcentrated and concentrated urine samples. The overall agreement between the two tests was 98.1%; the specificity of both was 100%. The sensitivity of the immunochromatographic assay was 55.5% in nonconcentrated urine and 97.2% in concentrated urine in comparison with the enzyme immunoassay, using concentrated urine as the reference test. This immunochromatographic assay screens successfully for Legionella pneumophila serogroup 1 soluble antigen in concentrated urine samples.