Predicting enzymatic function of protein sequences with attention

MOTIVATION

There is a growing number of available protein sequences, but only a limited amount has been manually annotated. For example, only 0.25% of all entries of UniProtKB are reviewed by human annotators. Further developing automatic tools to infer protein function from sequence alone can alleviate part of this gap. In this article, we investigate the potential of Transformer deep neural networks on a specific case of functional sequence annotation: the prediction of enzymatic classes.

RESULTS

We show that our EnzBert transformer models, trained to predict Enzyme Commission (EC) numbers by specialization of a protein language model, outperforms state-of-the-art tools for monofunctional enzyme class prediction based on sequences only. Accuracy is improved from 84% to 95% on the prediction of EC numbers at level two on the EC40 benchmark. To evaluate the prediction quality at level four, the most detailed level of EC numbers, we built two new time-based benchmarks for comparison with state-of-the-art methods ECPred and DeepEC: the macro-F1 score is respectively improved from 41% to 54% and from 20% to 26%. Finally, we also show that using a simple combination of attention maps is on par with, or better than, other classical interpretability methods on the EC prediction task. More specifically, important residues identified by attention maps tend to correspond to known catalytic sites. Quantitatively, we report a max F-Gain score of 96.05%, while classical interpretability methods reach 91.44% at best.

AVAILABILITY AND IMPLEMENTATION

Source code and datasets are respectively available at https://gitlab.inria.fr/nbuton/tfpc and https://doi.org/10.5281/zenodo.7253910.

Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family

Numerous computational methods based on sequences or structures have been developed for the characterization of protein function, but they are still unsatisfactory to deal with the multiple functions of multi-domain protein families. Here we propose an original approach based on 1) the detection of conserved sequence modules using partial local multiple alignment, 2) the phylogenetic inference of species/genes/modules/functions evolutionary histories, and 3) the identification of co-appearances of modules and functions. Applying our framework to the multidomain ADAMTS-TSL family including ADAMTS (A Disintegrin-like and Metalloproteinase with ThromboSpondin motif) and ADAMTS-like proteins over nine species including human, we identify 45 sequence module signatures that are associated with the occurrence of 278 Protein-Protein Interactions in ancestral genes. Some of these signatures are supported by published experimental data and the others provide new insights (e.g. ADAMTS-5). The module signatures of ADAMTS ancestors notably highlight the dual variability of the propeptide and ancillary regions suggesting the importance of these two regions in the specialization of ADAMTS during evolution. Our analyses further indicate convergent interactions of ADAMTS with COMP and CCN2 proteins. Overall, our study provides 186 sequence module signatures that discriminate distinct subgroups of ADAMTS and ADAMTSL and that may result from selective pressures on novel functions and phenotypes.

[Organ preservation in oropharyngeal cancers treatment: What arguments for radiotherapy?]

Management of oropharyngeal cancer depends on several factors. Immediate surgery or radiotherapy may be considered. If the patient is operable, the choice depends on the extent of the disease, the contributing factors, and the expected functional results. For HPV-positive cancers, studies show comparable efficacy between surgery and radiotherapy. For early-stage cancers, unimodal treatment should be preferred. For HPV-negative cancers, the results of retrospective and observational studies are in favor of surgery. These studies have some limitations. In observational and/or retrospective studies, reclassification biases and the applicability of propensity scores weaken the validity of studies showing differences in management. Tumor and patient comparability are others majors interpretation biases. It is precipitate to conclude that surgery is superior for HPV-negative oropharyngeal cancers. Toxicity, therefore, becomes a criterion of choice for treatment. Unimodal management by surgery allows limited toxicity for the early stages. Surgery has less impact on salivation. Radiotherapy is rather less deleterious for swallowing in the early stages. For the advanced stages of HPV-induced tumors, the non-superiority of surgery should lead to the choice of radiochemotherapy. For oropharyngeal cancers, the possible benefit of surgery in HPV-negative oropharyngeal cancers must be confirmed in randomized studies. For the early stages of oropharyngeal cancer with unimodal treatment, management could be decided by shared decision making.

PPalign: optimal alignment of Potts models representing proteins with direct coupling information

Background

To assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on sequence-based homology search methods, e.g. BLAST or the current state-of-the-art methods based on profile Hidden Markov Models, which rely on significant alignments of query sequences to annotated proteins or protein families. While powerful, these approaches do not take coevolution between residues into account. Taking advantage of recent advances in the field of contact prediction, we propose here to represent proteins by Potts models, which model direct couplings between positions in addition to positional composition, and to compare proteins by aligning these models. Due to non-local dependencies, the problem of aligning Potts models is hard and remains the main computational bottleneck for their use.

Methods

We introduce here an Integer Linear Programming formulation of the problem and PPalign, a program based on this formulation, to compute the optimal pairwise alignment of Potts models representing proteins in tractable time. The approach is assessed with respect to a non-redundant set of reference pairwise sequence alignments from SISYPHUS benchmark which have lowest sequence identity (between \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$3\%$$\end{document}3% and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$20\%$$\end{document}20%) and enable to build reliable Potts models for each sequence to be aligned. This experimentation confirms that Potts models can be aligned in reasonable time (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$1'37''$$\end{document}1′37′′ in average on these alignments). The contribution of couplings is evaluated in comparison with HHalign and independent-site PPalign. Although Potts models were not fully optimized for alignment purposes and simple gap scores were used, PPalign yields a better mean \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_1$$\end{document}F1 score and finds significantly better alignments than HHalign and PPalign without couplings in some cases.

Conclusions

These results show that pairwise couplings from protein Potts models can be used to improve the alignment of remotely related protein sequences in tractable time. Our experimentation suggests yet that new research on the inference of Potts models is now needed to make them more comparable and suitable for homology search. We think that PPalign’s guaranteed optimality will be a powerful asset to perform unbiased investigations in this direction.

Estimating probabilistic context-free grammars for proteins using contact map constraints

Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when modeling collections of proteins. Yet the most popular representations of sets of related protein sequences remain the profile Hidden Markov Models. By modeling independently the distributions of the conserved columns from an underlying multiple sequence alignment of the proteins, these models are unable to capture dependencies between the protein residues. Non-local interactions can be represented by using more expressive grammatical models. However, learning such grammars is difficult. In this work, we propose to use information on protein contacts to facilitate the training of probabilistic context-free grammars representing families of protein sequences. We develop the theory behind the introduction of contact constraints in maximum-likelihood and contrastive estimation schemes and implement it in a machine learning framework for protein grammars. The proposed framework is tested on samples of protein motifs in comparison with learning without contact constraints. The evaluation shows high fidelity of grammatical descriptors to protein structures and improved precision in recognizing sequences. Finally, we present an example of using our method in a practical setting and demonstrate its potential beyond the current state of the art by creating a grammatical model of a meta-family of protein motifs. We conclude that the current piece of research is a significant step towards more flexible and accurate modeling of collections of protein sequences. The software package is made available to the community.

Amplitude spectrum distance: measuring the global shape divergence of protein fragments

Background

In structural bioinformatics, there is an increasing interest in identifying and understanding the evolution of local protein structures regarded as key structural or functional protein building blocks. A central need is then to compare these, possibly short, fragments by measuring efficiently and accurately their (dis)similarity. Progress towards this goal has given rise to scores enabling to assess the strong similarity of fragments. Yet, there is still a lack of more progressive scores, with meaningful intermediate values, for the comparison, retrieval or clustering of distantly related fragments.

Results

We introduce here the Amplitude Spectrum Distance (ASD), a novel way of comparing protein fragments based on the discrete Fourier transform of their C_α distance matrix. Defined as the distance between their amplitude spectra, ASD can be computed efficiently and provides a parameter-free measure of the global shape dissimilarity of two fragments. ASD inherits from nice theoretical properties, making it tolerant to shifts, insertions, deletions, circular permutations or sequence reversals while satisfying the triangle inequality. The practical interest of ASD with respect to RMSD, RMSD_d, BC and TM scores is illustrated through zinc finger retrieval experiments and concrete structure examples. The benefits of ASD are also illustrated by two additional clustering experiments: domain linkers fragments and complementarity-determining regions of antibodies.

Conclusions

Taking advantage of the Fourier transform to compare fragments at a global shape level, ASD is an objective and progressive measure taking into account the whole fragments. Its practical computation time and its properties make ASD particularly relevant for applications requiring meaningful measures on distantly related protein fragments, such as similar fragments retrieval asking for high recalls as shown in the experiments, or for any application taking also advantage of triangle inequality, such as fragments clustering.

ASD program and source code are freely available at: http://www.irisa.fr/dyliss/public/ASD/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0693-y) contains supplementary material, which is available to authorized users.

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions

CyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromophores (phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly annotated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characterized enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogenetic analyses of all phycobilin lyases families, describes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliography about phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluorescent markers.

[Profiles of people who return unused medicine to pharmacies in Puy-de-Dôme, and their motivations for doing so]

An unused drug (U.D.) is described as a drug which is purchased, whether according to a prescription or not, but which is not taken. In the past few years, French people have acquired the habit of returning U.D.s to pharmacies. Nevertheless, few studies have been performed to define their typical features and the motivations of these individuals. A descriptive study was carried out in 1/5 of the pharmacies in Puy de Dôme (France) over three 1 week periods between February and June 1998. 377 people (that is, 82% of those who bring U.D. back to the pharmacies) accepted to participate in this study. The main results are as follows: 1. the U.D. are primarily brought back by women (of all ages); 2. these women mainly return U.D. from the family medicine cabinet; 3. the donations result essentially from "the force of habit", "cleaning out the family medicine cabinet" and also, although in lesser proportion, for "humanitarian reasons". This behaviour is contradictory with the communication messages of Cyclamed, the official French association whose mission is to collect drug waste and unused drugs in order to preserve the environment and to promote energy development and valorisation.

[Description of unused drugs collected in pharmacies in the Puy-de-Dôme region in France]

BACKGROUND

An unused drug (UD) is defined as a drug which is purchased, after prescription or not, but which is not taken. Public health campaigns in France have requested people to return these drugs to their pharmacy. To data, few data have been available concerning the quantity of collected UD and their potential re-use. A study was performed in the pharmacies of the Puy-de-Dôme region in France to describe the UD circuit.

METHODS

A random sample of 1 out of 5 pharmacies in the Puy-de-Dôme region (France) were defined by single level stratified sampling from the list of all pharmacies operating in the region. An exhaustive record of all UD people brought back to these pharmacies was made in 1998 during three 1-week periods. The following data were recorded for each UD: the name of the drug, the pharmaceutical industry code (CIP), the price, the rate of social Security refunding, the mention of "free specimen" on the package, the inscription on the list of poisonous substances and on the list of essential drugs defined by the World Health Organization (WHO), the registration on the list of drugs reserved for hospital use, the packaging notice (opened or not), the therapeutic class, and the formulation.

RESULTS

10,254 US (717kg) were collected during the study period. The therapeutic classes of the UD were similar to those of drugs purchased in France. According to the selling price, these UD had an economic value of 405,845FF (i.e. 3.6% of Social Security refundings paid in the Puy-de-Dôme region during this same period). Only 20% of the UD were potentially reusable for humanitarian purposes. Their estimated economic value was 87,456FF (i.e. 0.78% of the annual Puy-de-Dôme Social Security refunding). Moreover, 43.4% of the reusable drugs were on the WHO list of essential drugs.

CONCLUSION

Although the volume of collected UD is high, use by humanitarian associations is on the decline because of the cost of collection and low economic yield. Furthermore, UD must be collected in a systematic manner to preserve the environment and prevent domestic accidents.

Accuracy of delayed cultures of plugged telescoping catheter samples for diagnosing bacterial pneumonia

OBJECTIVE

It is not always feasible to culture immediately bacteriologic samples of protected pulmonary specimens on a 24-hr basis before starting antibiotic treatment. We have evaluated the effect of delaying the culture of immediate plugged telescoping catheter (PTC) samples performed before starting antibiotherapy.

DESIGN

Prospective paired comparisons study.

SETTING

Intensive care unit in a university hospital.

PATIENTS

Ninety-nine PTCs were performed on 68 intensive care unit patients suspected of nosocomial or community- acquired bacterial pneumonia.

INTERVENTION

PTC samples were divided into two aliquots: one for immediate (H0) analysis and one for storage at 4 degrees C (H24) for 24 hrs before being cultured.

MEASUREMENTS AND MAIN RESULTS

The results from these delayed cultures (H24) were compared with those from immediate ones (H0). All negative H0 samples (n = 59) were also negative at H24. Forty PTCs yielded one or more microorganisms, with a total of 69 microorganisms in one or both samples. H0 and H24 cultures were concordant in 119 of 128 (97.9%) cases (kappa coefficient value 0.79) with a threshold of 103 colony-forming units (cfu)/mL. Agreement between paired cultures was very good. The bias calculated as the mean difference between paired culture results was 0.128 +/- 1.024 (Deltalog). Concordance using the 103 cfu/mL threshold (102/107 cases, kappa coefficient value 0.82) and agreement were enhanced (0.067 +/- 0.645) when possible contaminants were excluded (n = 21).

CONCLUSIONS

Storing PTC specimens for 24 hrs at 4 degrees C is an acceptable alternative when culturing cannot be performed immediately. This allows starting antibiotic treatment without any delay.

Changes in oligosaccharide content and antioxidant enzyme activities in developing bean seeds as related to acquisition of drying tolerance and seed quality

Seeds of bean (Phaseolus vulgaris cv. Vernel) were collected throughout their development on the plant and dried at 15 degrees C and 75% relative humidity to a final moisture content of about 16% (fresh weight basis) to determine whether the onset of tolerance to this drying condition was related to changes in soluble sugars or the activities of the main antioxidant enzymes, namely superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR). Measurements of soluble sugars and enzyme activities were made after drying the seeds, and drying tolerance was evaluated by the ability of dried seeds to germinate and to produce normal seedlings. Seeds became tolerant to drying at 45 d after anthesis, a time marking physiological maturity. At physiological maturity, the moisture content of seeds was about 50-55% (fresh weight basis) and seed dry matter reached about 190 mg per seed. Seed vigour, evaluated by controlled deterioration and conductivity measurements, continued to increase after seed mass maturity, but decreased when seeds remained thereafter for more than 7 d on the plant. Acquisition of drying tolerance was coincident with an accumulation of raffinose and stachyose. Dried-tolerant seeds were also characterized by a high amount of sucrose, the most abundant sugar, and by a low content of monosaccharides. The (raffinose+stachyose)/sucrose ratio increased during seed filling, reaching a value close to 1 when all the seeds became tolerant to drying, and maintaining this proportion during the final stages of maturation. Acquisition of drying tolerance was also related to a reorientation of the enzymatic antioxidant defence system. Drying-tolerant dried seeds displayed high CAT and GR activities and low SOD and APX activities, while the opposite condition was observed in immature dried seeds. The shift in antioxidant enzymes corresponded to the beginning of the maturation-drying phase. These results suggest that oligosaccharide metabolism and enzymatic antioxidant defences may be involved in acquisition of drying tolerance during bean seed development, but are not related to seed vigour.

Safety, efficacy, and cost-effectiveness of mechanical ventilation with humidifying filters changed every 48 hours: a prospective, randomized study

OBJECTIVE

To determine whether three hydrophobic and hygroscopic heat and moisture exchangers (HMEs) retain their heating and humidifying properties (assessed by psychrometric measurements of absolute humidity, relative humidity, and tracheal temperature) for 48 hrs without any drop in their bacteriologic efficiency.

DESIGN

Prospective randomized clinical trial.

PATIENTS

Sixty-one consecutive unselected mechanically ventilated intensive care unit patients.

INTERVENTIONS

Patients were randomly allocated to one of the three HMEs studied (Hygrobac-Dar from Mallinckrodt, n = 21; Humid-Vent from Gibeck, n = 20; and Clear-Thermal from Intersurgical, n = 20).

MEASUREMENTS AND MAIN RESULTS

Hygrometric parameters were measured by psychrometry after 3, 24, and 48 hrs of use. Peak airway pressure was recorded every 6 hrs and averaged over 24 hrs. Bacterial colonization of both patients and circuits was studied. Patients in all three groups were similar in terms of age, indications for, and overall duration of mechanical ventilation. Tracheal tube occlusion never occurred. Hygrometric data included 371 measurements whereas bacteriologic data included >700 samples and cultures. The Hygrobac-Dar HMEs gave a significantly higher absolute humidity whatever the time of measurement (3, 24, or 48 hrs) than the other two HMEs (p < .001). The Clear-Thermal HMEs gave the poorest hygrometric parameters (p < .01); five of them were replaced prematurely (24 hrs) because the absolute humidity was <25 mg H2O/L. This did not occur for the other HMEs. Mean peak airway pressures were identical in the three groups. The bacterial colonizations of both patient and circuit were similar (and negligible for circuits) for all three groups.

CONCLUSION

Some HMEs may be used safely for 48 hrs without change. However, this does not pertain to every brand of HME. Objective in vivo evaluation of their humidifying performances is decisive before extending their duration of use.

Efficiency and safety of mechanical ventilation with a heat and moisture exchanger changed only once a week

The cost of mechanical ventilation (MV) is high. Efforts to reduce this cost, as long as they are not detrimental for the patients, are needed. MV with heat and moisture exchangers (HME) changed every 48 h is safe, efficient, and cost-effective. Preliminary reports suggest that the life span of these filters may be prolonged. We determined prospectively whether a hygroscopic and hydrophobic HME (Hygrobac-Dar; Mallinckrodt) provided safe and efficient heating and humidification of the inspired gases when changed only once a week. Patients who were considered to require mechanical ventilation for more than 48 h were included in the study. HMEs were initially set for 7 d. Efficient airway heating and humidification were assessed by clinical parameters (number of tracheal suctionings and instillations required, peak airway pressures) and hygrometric measurements performed by psychrometry. Resistance was measured from Day 0 to Day 7. Bacterial colonization of circuits and HMEs was studied. A total of 377 days of mechanical ventilation with 60 HMEs was studied. Clinical parameters and hygrometric measurements did not change between Day 0 and Day 7. Mean absolute humidity was 30.3 +/- 1.3 mg H(2)O/L on Day 0 and 30.8 +/- 1.5 mg H(2)O/L on Day 7 (p = 0.7). Endotracheal tube occlusion never occurred. Three HMEs were replaced prematurely because of insufficient absolute humidity. This rare event occurred only in patients with COPD and after the third day of use. In addition, the absolute humidity delivered by the HMEs was significantly lower in patients with COPD than in the rest of the population. Resistance did not change from Day 0 to Day 7 (2.4 +/- 0.3 versus 2.7 +/- 0.3 cm H(2)O/L/s; p = 0.4). Bacterial samples of both circuits and ventilator sides of HMEs were sterile in most cases. We conclude that mechanical ventilation can be safely conducted in non-COPD patients using an HME changed only once a week, leading to substantial cost savings (about $110,000 per year if these findings were applied to the university-affiliated hospitals in Paris).

[Chondrosarcoma secondary to multiple cartilage diseases. Study of 29 clinical cases and review of the literature]

PURPOSE OF THE STUDY

Several studies have demonstrated better prognosis of chondrosarcomas arising in hereditary multiple exostosis or Ollier's disease. The aim of this study was to evaluate their clinical, radiological and histological features and compare their prognosis with other chondrosarcomas.

MATERIAL AND METHODS

We reviewed twenty nine secondary chondrosarcomas among seventeen patients with osteochondroma (group A), and eight with Ollier's disease (group B). These tumors represented 12 p. 100 of all chondrosarcomas treated between 1950 and 1994 in Cochin Hospital. Two group B patients successively developed three multicentric chondrosarcomas. Twenty six resections (eight intra and eighteen extra-lesional), two disarticulations and one amputation were performed as primary treatment. The average follow-up of the study was 10.5 years. The results were evaluated by means of survival curves. The significance of the difference between the curves was determined by the log-rank test.

RESULTS

The mean age of malignant change was 36 years old. The most frequent tumoral site was the innominate bone for group A and the femur for group B. In three cases, radiographs showed no malignant features. All chondrosarcomas were classified as grade 1 or 2. The ten-year survival rate was 82 p. 100 with no significant difference between the two groups. The survival rates were significantly different after carcinologic surgery (extra-lesional resection or amputation) and contaminated surgery (intralesional resection), with 5 and 88 p. 100 of local recurrences respectively.

DISCUSSION AND CONCLUSION

These secondary chondrosarcomas represent about 10 p. 100 of all chondrosarcomas. They appear 15 years earlier. According to O'Neal and Ackerman classification, most of the tumors are well-differentiated (60 p. 100 grade I, 39 p. 100 grade II and 1 p. 100 grade III). Carcinologic surgery is generally curative. Ten-year survival rate is 94 p. 100. With equivalent grade and surgery, their prognosis is better as compared to primary chondrosarcomas.

Crystallization and preliminary X-ray diffraction analysis of the homodimeric form alpha2 of the HU protein from Escherichia coli

The homodimeric form alpha(2) of the Escherichia coli DNA-binding protein HU was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystals belong to space group I222, with unit-cell parameters a = 31.09, b = 55.34, c = 117. 63 A, and contain one monomer per asymmetric unit. A full diffraction data set was collected to 2.3 A resolution on a conventional X-ray source. The molecular-replacement method, using the HU crystallographic model from Bacillus stearothermophilus as a starting point, gave a reliable solution for the rotation and translation functions.

Bedside evaluation of efficient airway humidification during mechanical ventilation of the critically ill

STUDY OBJECTIVE

To determine the correlation between simple rating of condensation seen in the flex-tube connecting the heating and humidifying device used with the endotracheal tube and hygrometric parameters (absolute and relative humidity and tracheal temperature) measured by psychrometry.

DESIGN

Prospective randomized clinical trial.

SETTING

Medical ICU of Louis Mourier Hospital, Colombes, France, a university-affiliated teaching hospital.

PATIENTS

Forty-five consecutive mechanically ventilated critically ill patients.

INTERVENTIONS

Patients undergoing mechanical ventilation were randomly assigned to receive humidification with one of the four heat and moisture exchangers (HMEs) tested or with a conventional heated humidifier.

MEASUREMENTS

The hygrometric performances of four HMEs (BB2215, BB50, and BB100 from Pall Biomedical, Saint-Germaine-en-Laye, France; and Hygrobac-Dar from Mallinckrodt, Mirandola, Italy) and a heated humidifier (Fisher & Paykel; Auckland, New Zealand) were studied after 3 h and also after 48 h of use for the Hygrobac-Dar and correlated to a clinical visual inspection rating the amount of condensation in the flex-tube of the endotracheal tube.

RESULTS

A total of 95 measurements in 45 patients were performed. The best hygrometric parameters were obtained with the heated humidifier (p < 0.001). The Hygrobac-Dar yielded significantly higher values for both humidities and tracheal temperature than the other three HMEs (p < 0.001). The performance of Hygrobac-Dar was unchanged after 48 h of use. There was a significant correlation between the condensation seen in the flex-tube and the hygrometric parameters measured by psychrometry (absolute humidity, rho = 0.7; relative humidity, rho = 0.7; tracheal temperature, rho = 0.5, p < 0.0001).

CONCLUSION

In mechanically ventilated ICU patients, visual evaluation of the condensation in the flex-tube provides an estimation of the heating and humidifying efficacy of the heating and humidifying device used, thus allowing the clinician bedside monitoring of airway humidification.

Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site

cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.

Measurement of cardiac output by transesophageal echocardiography in mechanically ventilated patients. Comparison with thermodilution

OBJECTIVE

The determination of basal cardiac output (CO) and of its variations during different therapeutic interventions liable to increase or decrease it in mechanically ventilated patients using transesophageal echocardiography (TEE).

DESIGN

To compare CO measurements simultaneously obtained by transmitral single-plane TEE and thermodilution.

SETTING

Medical intensive care unit.

PATIENTS

Twenty-two consecutive mechanically ventilated patients hospitalized for various medical conditions were included.

INTERVENTIONS

The comparisons between transmitral single-plane TEE and thermodilution measurements were made at baseline and after different therapeutic interventions affecting CO (fluids or dobutamine infusion or positive end-expiratory pressure titration).

MEASUREMENTS

Seventy-four measurements were obtained. Cardiac output using TEE was the product of the mitral valve area, the time-velocity integral of flow at the same site and the heart rate.

RESULTS

A significant correlation was observed between thermodilution and TEE measurements of CO (n = 74, r = 0.78, p < 0.001) despite wide limits of agreement (mean +/- 2SD = -0.3 +/- 3.1 l/min). Thermodilution and TEE CO determinations both had significant inverse correlation with the arterial-venous oxygen content difference in ten consecutive patients (r = 0.77, p < 0.01 and r = 0.71, p < 0.01, respectively). The correlation between variations of CO greater than 20% obtained by thermodilution and TEE was significant (r = 0.89, p < 0.001). The operative characteristics implied the ability of TEE to predict significant variations of thermodilution CO (sensitivity 85% and negative predictive values 86%). Moreover, arterial-venous oxygen content difference changes of 5% or more were better detected using TEE than thermodilution.

CONCLUSIONS

These results suggest that although transesophageal CO measurements cannot replace thermodilution ones, the determination of CO variations obtained using TEE may be useful in the management of critically ill mechanically ventilated patients. This technique may make it possible to monitor hemodynamics during initial therapeutic interventions in those patients in whom right heart catheterization cannot be performed immediately.

Validation of reconstructed bremsstrahlung spectra between 6 MV and 25 MV from measured transmission data

We have previously investigated a method of high-energy x-ray spectral reconstruction from transmission data by direct resolution of a matrix system. This technique uses the spectral vectorial algebra formalism. The resolution has previously been tested on a 12 MV photon beam. To extend and to test the validity of the results to the entire radiotherapy energy range, we have performed the method on photon beams with nominal energies of 6, 12, 15, and 25 MV. The influence on the 6 MV spectrum of a 60 degrees built-in wedge has also been investigated to test the sensitivity of the method and the results are reported. To validate our reconstructed spectra, dosimetric quantities such as tissue phantom ratios (TPR), water-to-air stopping power ratios (S/p) air water, and quality indexes TPR 10 (20) have been calculated. The results show good agreement between the measured and calculated data. Mean mass energy absorption coefficient ratios for different materials have also been computed and compared to data published recently and the results are very close (within +/- 0.5%). Primary depth dose functions in water have also been computed to deduce primary dose attenuation coefficients.

Comparison of the effects of heat and moisture exchangers and heated humidifiers on ventilation and gas exchange during weaning trials from mechanical ventilation

Heat and moisture exchangers (HME) are increasingly used to warm and humidify inspired gases in intubated ventilated patients. But these devices add dead space that may alter the alveolar ventilation. This could impair the efficiency of spontaneous ventilation (SV) during weaning trials from mechanical ventilation. Fifteen patients were tested with an HME (Hygrobac-DAR) and a heated humidifier (HH) (Fischer-Paykel MR 450) in a random order during weaning trials in SV with inspiratory pressure support. Minute ventilation VE, tidal volume), and respiratory rate were recorded and arterial blood was sampled for blood gas analysis with each device. The HME gave a significantly greater VE than the HH (9.3 +/- 0.8 L/min vs 8.1 +/- 0.8 L/min; p < 0.005), because of increased respiratory rate (21 +/- 2/min vs 19 +/- 2/min; p < 0.05). Tidal volume was unchanged for HME and HH (470 +/- 32 mL vs 458 +/- 39 mL). The higher PaCO2 with HME than with HH (44 +/- 2 mm Hg vs 42 +/- 2 mm Hg; p < 0.005) revealed an insufficient alveolar ventilation response to the increase in dead space. Arterial Po2 rose with the HME, but not significantly above the HH values (103 +/- 6 mm Hg vs 97 +/- 6 mm Hg; p = 0.055), possibly because of a positive end-expiratory pressure effect of the HME. The need to increase VE in SV when an HME is used should be taken into account during difficult weaning from mechanical ventilation.

Atrial septal aneurysm plus a patent foramen ovale. A predisposing factor for paradoxical embolism and refractory hypoxemia during pulmonary embolism

We report three consecutive cases of patients who had refractory hypoxemia and paradoxical embolism during the course of pulmonary embolism. Transesophageal echocardiography showed an atrial septal aneurysm and a patent foramen ovale in all patients. The latter was detected by an early and massive passage of contrast from the right to the left atrium. We suggest that the presence of an atrial septal aneurysm plus a patent foramen ovale greatly enhances both magnitude of shunting and the risk of systemic embolism. The presence of an atrial septal aneurysm plus a patent foramen ovale should be considered and checked using transesophageal echocardiography in every patient with significant pulmonary embolism.

[Post-traumatic thrombosis of the portal vein]

Blunt trauma to the abdomen is an exceptional cause of portal vein thrombosis. To our knowledge, 8 cases have been reported in the literature. When thrombosis of the portal vein occurs, a complete search for all the known main causes must be carried out before entertaining this diagnosis. Other causes may be cirrhosis, tumors and inflammation of the abdomen, coagulation disorders and hematologic diseases including latent myeloproliferative syndrome. We report a case in a 25-year-old man with an uneventful past history who presented with thrombosis of the portal vein after a violent blunt trauma which occurred during a rugby play. In this young man, none of the other potential causes was found, in particular bone marrow culture on medium with low growth-factor concentration allowed us to eliminate a latent myeloproliferative syndrome. The only triggering factor remaining was the recent abdominal trauma. After an 18-month follow-up, no other element has been observed which could have caused thrombosis of the portal vein.

Changing heat and moisture exchangers every 48 hours rather than 24 hours does not affect their efficacy and the incidence of nosocomial pneumonia

Heat and moisture exchangers (HME) (Dar-Hygrobac II, Peters) can safely be used every 24 h for long-term mechanical ventilation and provide a cost-saving alternative to heated humidifiers. We have prospectively determined whether changing HMEs every 48 h only affects their clinical and bacteriological efficiency in a series of consecutive nonselected ICU patients requiring long-term mechanical ventilation. Two consecutive periods were compared. During period 1, HMEs were replaced every day; during period 2, they were changed every 48 h. Patients from the two periods were similar in terms of age and indication for and overall duration of MV (10 +/- 8.6 versus 10 +/- 9 d, p = 0.9). Minute ventilation and maximum values for peak airway pressure were identical during the two periods. These values were also identical after 1 and 2 d of HME use during period 2, indicating that HME resistance was not increased by prolonged use. Obstruction of the tracheal tube occurred only once in a period 1 patient. The results of quantitative cultures indicate that the maximum and mean levels of bacterial colonization during the two periods were similar for the pharynx, trachea, Y-connector, patient, and ventilator side of the HME. More importantly, the incidence of nosocomial pneumonia was similar during the two periods (6/61 versus 8/68, p = 0.7). Thus, prolonged HME use is safe and provides a substantial reduction in the cost of mechanical ventilation.

Mechanical ventilation with heated humidifiers or heat and moisture exchangers: effects on patient colonization and incidence of nosocomial pneumonia

The contribution of ventilator circuit bacterial contamination to the occurrence of ventilator-associated pneumonia remains controversial. In a previous study, we found that the incidence of pneumonia was identical with ventilator circuit changes every 48 h and with no ventilator circuit changes. The present study prospectively assessed whether keeping ventilator circuits clean with a heat and moisture exchanger exhibiting antimicrobial barrier properties affects patient colonization and the incidence of nosocomial pneumonia in patients receiving mechanical ventilation for more than 48 h. Consecutive patients were randomly allocated to humidification with either a heat and moisture exchanger (Group 1, n = 61) or a heated humidifier (Group 2, n = 70). In both groups, no circuit changes were performed throughout ventilatory support. Duration of mechanical ventilation was identical in both groups (10 +/- 8.6 d (range: 2 to 47) in Group 1 and 12.5 +/- 14.2 d [range: 2 to 85] in Group 2). The incidence of pneumonia (positive quantitative culture of protected brush specimen) was similar in both groups (6/61 and 8/70 in Groups 1 and 2, respectively; p = 0.8), as was duration of ventilation prior to pneumonia (9 +/- 5.9 versus 8.2 +/- 5.7 d; p = 0.8). Ventilator tubing contamination was considerably reduced with the use of a heat and moisture exchanger. In contrast, bacterial colonization of the pharynx and trachea was identical in both groups. These results suggest that circuit colonization plays little or no role in the occurrence of ventilator-associated pneumonia, provided usual maintenance precautions are applied.(ABSTRACT TRUNCATED AT 250 WORDS)

Use of cross-reactive antigens of the microsporidian Glugea atherinae for the possible detection of Enterocytozoon bieneusi by western blot

The microsporidia Enterocytozoon bieneusi is reported in 10-30% of those infected with the human immunodeficiency virus. The parasite appears to be a cause of gastralgia, malabsorption, and diarrhea. A Western blot technique using another microsporidian species, Glugea atherinae, has demonstrated an antigenic similarity between this parasite and E. bieneusi. Preliminary results show the variability of the antigenic profiles obtained from the sera of immunodeficient patients infected with E. bieneusi and also of the cross-reactivity to Glugea sp. antigens of some sera from patients with cryptosporidiosis. The origin of this cross-reactivity is undetermined. The possibility of coinfection with undetected microsporidia is not excluded. These results raise questions concerning the interpretation of serologic data and of the potential immunodiagnostic value of microsporidian antigens.

Is penicillin G an adequate initial treatment for aspiration pneumonia? A prospective evaluation using a protected specimen brush and quantitative cultures

OBJECTIVE

To evaluate the bacteriology of early aspiration pneumonia using a protected specimen brush and quantitative culture techniques, and whether penicillin G is adequate as initial treatment pending culture results.

PATIENTS AND METHODS

52 patients (of which 45 required mechanical ventilation) meeting usual clinical criteria for aspiration pneumonia were prospectively included. On admission, patients were given intravenous penicillin G and a protected specimen brush was performed < or = 48 h after.

RESULTS

Cultures of the brush were negative (< 10(3) CFU/ml) in 33 patients (1 had blood cultures positive with S. pneumoniae) and positive (> or = 10(3) CFU/ml) for S. pneumoniae in 2 patients. Seventeen patients had a positive culture (> or = 10(3) CFU/ml) for at least one penicillin G resistant microorganism, with a total of 20 organisms (S. aureus: 6; H. influenzae: 2; Enterobacteriaceae: 8; P. aeruginosa: 3; C. albicans: 1). In 4 of these patients, a penicillin-sensitive pathogen was also recovered in significant concentrations (S. pneumoniae: 2; Streptococcus sp.: 2). These 17 patients with a resistant pathogen did not differ from the 35 other patients with respect to need for ventilatory support and mortality rate. By contrast, they were older (61.1 +/- 21.9 vs. 42.9 +/- 18.8 years; p < 0.005) and required longer mechanical ventilation (6.1 +/- 4.6 vs. 3.5 +/- 2.7 days; p < 0.03) and hospitalization (11.2 +/- 8.8 vs. 6.7 +/- 4.7 days; p < 0.02). Of 17 patients 12 with penicillin G resistant organisms versus 0/35 without, were in-hospital patients and/or had a digestive disorder (p < 0.001).

CONCLUSION

The broad range of offending organisms seen in early aspiration pneumonia precludes use of any single empiric regimen, making protected specimen brush mandatory in many patients. Nevertheless, the involvement of S.pneumoniae in a notable proportion of our patients suggests that routine penicillin prophylaxis after early aspiration (at least in most patients with community-acquired aspiration) is warranted given the potential severity of pneumococcal sepsis in such patients.

Clinical significance of borderline quantitative protected brush specimen culture results

In patients with clinical suspicion of pneumonia, quantitative cultures of protected brushing specimens (PBS) yielding > or = 10(3) CFU/ml of at least one microorganism have been found useful for differentiating airway colonization and lung infection, especially in mechanically ventilated patients. The amount of secretions collected by protected catheter brushing is small and difficult to determine accurately. Thus, the clinical significance of PBS cultures yielding organisms in concentrations > or = 10(2) but < 10(3) CFU/ml, in the absence of active antimicrobial treatment, is unknown. The 34 consecutive results of PBS cultures yielding organisms in concentrations > or = 10(2) but < 10(3) CFU/ml in 30 patients under mechanical ventilation or weaned for < or = 4 days were prospectively studied. No patients were receiving agents active on the organism recovered. In 5 cases, the diagnosis of pneumonia was ruled out by recovery without treatment (n = 4) or negative postmortem lung cultures (n = 1). A second PBS was cultured in 29 episodes (2.7 +/- 1.8 days after the first PBS). In 12 instances (Group 1), cultures of the second PBS yielded > or = 10(3) CFU/ml of the same organism as that found in the first PBS (S. pneumoniae, 1; S. aureus, 1; H. influenzae, 1; E. coli, 1; P. aeruginosa, 4; and A. baumannii, 4), and these patients were therefore treated with appropriate antibiotics. A total of 17 patients had a negative repeat PBS culture (no growth or trivial concentrations) and were considered free of pneumonia and given no antibiotic treatment for this episode.(ABSTRACT TRUNCATED AT 250 WORDS)

Prospective evaluation of the incidence of bacteremia after protected specimen brushing in ICU patients with and without pneumonia

To test the hypothesis that the use of protected specimen brushing (PSB) via flexible bronchoscopy does not predispose to bacteremia in ICU patients, we prospectively performed aerobic and anaerobic blood cultures immediately following bronchoscopy with PSB. A total of 123 episodes in 68 consecutive patients with suspected pneumonia were analyzed. Blood cultures were negative in 110 cases (89 percent) and positive in 13 cases (11 percent) (p < 0.001). Twelve of these 13 patients with positive blood cultures had quantitative PSB specimen cultures showing nonsignificant growth (< 10(3) CFU/ml). In nine patients, the bacteria recovered from blood cultures (coagulase-negative staphylococci or sarcina) were considered nonpathogenic according to conventional criteria. Blood cultures grew a Staphylococcus aureus in two patients with previously documented staphylococcal septicemia. In one patient with no identifiable site of infection, the blood culture yielded Enterococcus faecalis. The only patient with both a positive blood culture and PSB culture results indicating pneumonia had different organisms recovered from the two samples. Blood cultures taken after PSB in the 17 other episodes of pneumonia (PSB specimen cultures > or = 10(3) CFU/ml) were negative. At the time of brushing and blood sampling for culture, none of these patients was receiving antibiotics active on the organisms found. In conclusion, the incidence of bacteremia after PSB in ICU patients seems very low even in patients with documented pneumonia. Substantial savings would result from not performing routine blood cultures after PSB.

[Autoimmune biological anomalies in 35 patients with chronic viral hepatitis C treated over 6 months with interferon and followed-up over a year]

Several clinical or biological autoimmune disorders, particularly lupoid diseases, are associated with chronic hepatitis C. They may be exacerbated by alpha IFN, but they are not involved in the response to therapy.

[Chronic viral hepatitis C and interferon: results after a year and predictive factors of response (a multivariate study with 35 patients)]

Six months alpha IFN therapy was efficient for chronic viral hepatitis C in 31% patients after six months and in 17% after one year. Cirrhosis, low serum albumin or prealbumin levels and elevated IgA seric level were non responsiveness predictive factors.

A comparative study of the effects of almitrine bismesylate and lateral position during unilateral bacterial pneumonia with severe hypoxemia

The management of patients with unilateral pneumonia and severe hypoxemia often represents a therapeutic challenge. Mechanical ventilation with the diseased lung uppermost may improve gas exchange, but it is not devoid of adverse effects. No hemodynamic measurements have been reported in patients ventilated in this manner; therefore, whether or not the improvement in PaO2 is counterbalanced by hemodynamic deterioration remains unknown. Almitrine bismesylate is a drug that seems able to improve gas exchange in patients with chronic obstructive pulmonary disease or the adult respiratory distress syndrome. The increase in PaO2 after its administration has been attributed to an improvement in ventilation-perfusion relationships. Its use has never been reported during unilateral pneumonia with severe hypoxemia. We therefore compared its effects with those of lateral position in eight consecutive mechanically ventilated patients with unilateral pneumonia. Blood gas and hemodynamic measurements were performed both at maintenance FIO2 and at an FIO2 of 1.0. Almitrine (1 mg/kg over 1 h) had no effect on PaO2 under either FIO2 condition. Cardiac output remained unchanged, but mean pulmonary artery pressure increased from 22.5 +/- 1.2 to 26.5 +/- 1.3 mm Hg (p < 0.02). By contrast, lateral position had striking effects on PaO2, which increased from 100 +/- 14 mm Hg in supine position to 156 +/- 23 mm Hg (p < 0.01) when the abnormal lung was placed uppermost at maintenance FIO2 and from 207 +/- 21 (supine) to 300 +/- 28 mm Hg (lateral) (p < 0.01) at FIO2 1.0.(ABSTRACT TRUNCATED AT 250 WORDS)