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Embryo transfer in fallow deer (Dama dama): superovulation, embryo recovery and laparoscopic transfer of fresh and cryopreserved embryos.

Multiple ovulation-embryo transfer (MOET) protocols for farmed fallow deer (Dama dama) were investigated in a series of 3 experiments. A total of 37 donors, of either European (D.d. dama ; n = 30) or Mesopotamian hybrid (D.d. mesopotamica x D.d. dama ; n =7) genotype, each received an intravaginal silastic device containing 0.3 g progesterone (CIDR-type G device) for 14 d and injections of 0.5 units ovine FSH (8 x 0.06 unit injections from Days 10 to 14 of device insertion) and 100 IU PMSG (either with the first or last FSH injection). All donors received laparoscopic intrauterine inseminations of fresh semen (50 x 10(6) spermatozoa) from a Mesopotamian sire 36 h after withdrawal of CIDR devices. Embryos were recovered by laparotomy on Day 6 (Day 0 = estrus). Mean ovulation rates for the 3 experiments were 8.1, 9.8 and 7.0, with no effect of PMSG timing (P>0.10). However, embryo recovery rates, albeit low throughout the study (29.6%), were significantly improved with later PMSG administration (33.9 vs 20.1%; P<0.05). Hybrid and European donors performed in a similar manner. A range of embryo development stages was recovered throughout the study. In 2 experiments laparoscopic transfer of embryos to 48 recipient does treated previously with intravaginal CIDR devices for 14 d yielded a total pregnancy rate of 37.5%. In the experiment with fresh embryos, the use of clenbuterol to reduce uterine turgidity resulted in a higher proportion of does conceiving (3/4 ; 75%) compared with that of the untreated does (0/6 , 0%; P<0.05). In the second experiment, in which all the does routinely received clenbuterol, 10/19 (53%) and 5 19 (26%) does conceived following the transfer of fresh and cryopreserved embryos, respectively (P<0.05). While the overall efficiency of the MOET program was low (equivalent of 0.9 to 1.0 surrogate pregnancies per donor), improvements in the recovery rate of transferable embryos have considerable potential for genetic improvement of farm stock and captive propagation of endangered Mesopotamian fallow deer through maternal surrogacy programs.

Journal Article↗

PREDITOP: a program for antigenicity prediction.

A program (PREDITOP) for predicting the location of antigenic regions (or epitopes) on proteins is described. This program and the associated ones are written in Turbo Pascal and run on IBM-PC compatibles. The program contains 22 normalized scales, corresponding to hydrophilicity, accessibility, flexibility, or secondary structure propensities. New scales are easily implemented. An hydrophobic moment procedure has also been implemented in order to determine amphiphilic helices. The program generates a result file where the values represent a particular physicochemical aspect of the studied protein. PREDITOP can display one or several result files by simple graphical super-imposition. Curve combinations can be done by the ADDITIO or MULTIPLI routines which create a new result file by adding or multiplying previously calculated files representing several propensities. The program is useful and efficient for identifying potential antigenic regions in a protein with the aim of raising antibodies against synthesized peptides which cross-react with the native protein.

Antigens↗

A new technique for positioning tangential fields.

PURPOSE: A technique that eliminates the use of a mechanical "breast-bridge" for positioning tangential fields for treatment of the intact breast or chest wall has been developed. METHODS AND MATERIALS: Treatment set-up parameters are determined using measuring capabilities (gantry angles and source-skin distances) available on a standard simulator unit. A programmable scientific calculator is used to determine field geometry from polar coordinates for various points on the patient's skin. The calculator program determines the field size, a depth and lateral shift from a skin reference point to the isocenter for the tangential fields, and the gantry angles. The program provides additional information which facilitates the simulation process: First, the coordinates of the isocenter for the tangential fields are expressed relative to couch coordinates for an initial arbitrary isocenter so that the "auto go to" capability available on some simulators can be used. Second, the coordinates of the medial and lateral entry points can be edited when the first set of tangents are not accepted. This part of the program allows quick and efficient adjustment of the fields to obtain adequate treatment volume coverage and a minimum of irradiated lung or heart. RESULTS: Simulation of more than 300 patients has shown the technique to be a practical and efficient method for positioning tangential fields for breast or chest wall irradiation. CONCLUSION: The technique described here takes full advantage of the capabilities of the new generation of computer controlled simulators, and offers an alternative to previous methods employing a mechanical "breast-bridge."

Breast Neoplasms↗

Synthesis, stereochemistry, and antimicrobial evaluation of substituted piperidin-4-one oxime ethers.

In a wide search program toward new and efficient antimicrobial agents, a series of substituted piperidin-4-one oxime ethers (5a-5k) was synthesized and tested for their in vitro antibacterial and antifungal activities. Also, the structures of these oxime ethers and their relative stereochemistries have been investigated by nuclear magnetic resonance spectroscopy. In all the oxime ethers synthesized, the orientation of the N-O bond of the oxime ether moiety syn to C-5 (E-isomer) was deduced based on (1)H NMR and (13)C NMR spectra. It was found that the sterically less hindered compounds, either C-3 (H) and C-5 (H)- or C-3 (Me) and C-5 (H) -substituted ones 5a, 5c, 5d, 5f, 5g, 5i and 5j prefer chair conformation, whereas the sterically more hindered C-3 (Me) and C-5 (Me) -substituted ones 5b, 5e, 5h, and 5k prefer twist-boat conformation. Among the oxime ethers tested, 1,3,5-trimethyl-2,6-diphenylpiperidin-4-one O-(2-chlorophenylmethyl)oxime (5h) exhibited good antibacterial property against Bacillus subtilis, with minimum inhibitory concentration (MIC) closer to that of reference drug, streptomycin. Compounds, 1,3-dimethyl-2,6-diphenylpiperidin-4-one O-(2-chlorophenylmethyl)oxime (5g) and 1,3-dimethyl-2,6-diphenylpiperidin-4-one O-(2-bromophenylmethyl)oxime (5j) showed potent antifungal activity against Aspergillus flavus and Candida-51, respectively. The later compound 5j is more active than the reference drug while the activity of the former one 5g is similar to that of the reference drug, amphotericin B in terms of MIC. The present results may be used as key steps for the construction of novel chemical entities with better pharmacological profiles than standard drugs.

Anti-Bacterial Agents↗

Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function.

In 1978, for my PhD, I developed the efficient O(n3) dynamic programming algorithm for the-then open problem of RNA secondary structure prediction. This algorithm, now dubbed the "Nussinov algorithm", "Nussinov plots", and "Nussinov diagrams", is still taught across Europe and the U.S. As sequences started coming out in the 1980s, I started seeking genome-encoded functional signals, later becoming a bioinformatics trend. In the early 1990s I transited to proteins, co-developing a powerful computer vision-based docking algorithm. In the late 1990s, I proposed the foundational role of conformational ensembles in molecular recognition and allostery. At the time, conformational ensembles and free energy landscapes were viewed as physical properties of proteins but were not associated with function. The classical view of molecular recognition and binding was based on only two conformations captured by crystallography: open and closed. I proposed that all conformational states preexist. Proteins always have not one folded form-nor two-but many folded forms. Thus, rather than inducing fit, binding can work by shifting the ensembles between states, and this shifting, or redistributing the ensembles to maintain equilibrium, is the origin of the allosteric effect and protein, thus cell, function. This transformative paradigm impacted community views in allosteric drug design, catalysis, and regulation. Dynamic conformational ensemble shifts are now acknowledged as the origin of recognition, allostery, and signaling, underscoring that conformational ensembles-not proteins-are the workhorses of the cell, pioneering the fundamental idea that dynamic ensembles are the driving force behind cellular processes. Nussinov was recognized as pioneer in molecular biology by JMB.

Molecular Biology↗

High-throughput pharmacokinetics screen of VLA-4 antagonists by LC/MS/MS coupled with automated solid-phase extraction sample preparation.

Automation of plasma sample preparation for pharmacokinetic studies on VLA-4 antagonists has been achieved by using 96-well format solid-phase extraction operated by Beckman Coulter Biomek 2000 liquid handling system. A Biomek 2000 robot is used to perform fully automated plasma sample preparation tasks that include serial dilution of standard solutions, pipetting plasma samples, addition of standard and internal standard solutions, performing solid-phase extraction (SPE) on Waters OASIS 96-well plates. This automated sample preparation process takes less than 2 h for a typical pharmacokinetic study, including 51 samples, 24 standards, 9 quality controls, and 3-6 dose checks with minimal manual intervention. Extensive validation has been made to ensure the accuracy and reliability of this method. A two-stage vacuum pressure controller has been incorporated in the program to improve SPE efficiency. This automated SPE sample preparation approach combined with liquid chromatography coupled with the high sensitivity and selectivity of tandem mass spectrometry (LC/MS)/MS has been successfully applied on both individual and cassette dosing for pharmacokinetic screening of a large number of VLA-4 antagonists with a limit of quantitation in the range of 1-5 ng/ml. Consequently, a significant throughput increase has been achieved along with an elimination of tedious labor and its consequential tendency to produce errors.

Animals↗

A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures.

We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).

Algorithms↗

Cadmium accumulation in different rice cultivars and screening for pollution-safe cultivars of rice.

Large areas of contaminated land are being used for agricultural production in some countries due to the high demand for food. To minimize the influx of pollutants to the human food chain through consumption of agricultural products, we propose the concept of pollution-safe cultivars (PSCs), i.e. cultivars whose edible parts accumulate a specific pollutant at a level low enough for safe consumption, even when grown in contaminated soil. We tested the feasibility of the PSC concept by growing 43 cultivars of paddy rice (Oryza sativa L., including 20 normal and 23 hybrid cultivars) under a high (75.69-77.55 mg kg(-1)) and a low (1.75-1.85 mg kg(-1)) cadmium (Cd) exposure. These pot experiments took place in the spring and summer of 2004. At the low level of Cd exposure, 30 out of the 43 tested cultivars were found to be Cd-PSCs. Grain Cd concentrations were highly correlated (p<0.01) between the two experiments, suggesting that Cd accumulation in rice grain is genotype-dependent and that the selection of PSCs is possible, at least at a certain level of soil contamination. No Cd-PSCs were found under the high level of Cd exposure. Yield was enhanced in some cultivars and depressed in others in response to elevated soil Cd, indicating that farmers cannot rely on yield depression as an indicator of toxicity of the grains. It is therefore important and feasible to screen for PSCs and to establish PSC breeding programs to effectively and efficiently reduce the risk of human exposure to soil pollutants, such as Cd, through crop consumption.

Cadmium↗

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.

Genome-scale constraint-based models of several organisms have now been constructed and are being used for model driven research. A key issue that may arise in the use of such models is the existence of alternate optimal solutions wherein the same maximal objective (e.g., growth rate) can be achieved through different flux distributions. Herein, we investigate the effects that alternate optimal solutions may have on the predicted range of flux values calculated using currently practiced linear (LP) and quadratic programming (QP) methods. An efficient LP-based strategy is described to calculate the range of flux variability that can be present in order to achieve optimal as well as suboptimal objective states. Sample results are provided for growth predictions of E. coli using glucose, acetate, and lactate as carbon substrates. These results demonstrate the extent of flux variability to be highly dependent on environmental conditions and network composition. In addition we examined the impact of alternate optima for growth under gene knockout conditions as calculated using QP-based methods. It was observed that calculations using QP-based methods can show significant variation in growth rate if the flux variability among alternate optima is high. The underlying biological significance and general source of such flux variability is further investigated through the identification of redundancies in the network (equivalent reaction sets) that lead to alternate solutions. Collectively, these results illustrate the variability inherent in metabolic flux distributions and the possible implications of this heterogeneity for constraint-based modeling approaches. These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data.

Computer Simulation↗

Set theory in diagnostic reasoning.

BACKGROUND: Regarding diagnostic reasoning, the currently taught Bayesian theory is a form of hypothetical-deduction reasoning. Using set theory, we offer syllogism reasoning instead of hypothetical-deductive reasoning and establish an online diagnostic expert system model based on this diagnostic methodology. METHODS: Concepts of set theory were employed to demonstrate diagnostic reasoning. ASP, Vbscript and Microsoft Access were used to establish the expert system and data of 50 cases from Shanghai pulmonary hospital were put into the program to test its efficiency. CONCLUSION: Diagnostic procedure is type of syllogism rather than hypothetical-deductive reasoning.

Cluster Analysis↗

[Factors associated with suicidal risk among consulting young people in a preventive health center].

UNLABELLED: The association between suicidal risk and various psychological or biographical factors in teenagers or young adults is already well documented. Yet, the role of stressful life events or contexts during childhood or of the recent past, as well as the respective weight of such determinants, has to be specified. METHODS: One thousand one hundred and thirty-nine individuals, aged 16 to 25, who consecutively consulted in a preventive health center supported by the National Health Insurance System, located in Seine-Saint-Denis (a French department characterized by an unfavourable socio-economic context) on the occasion of a free work up were invited to fill out several self-administered questionnaires, aimed at assessing especially the level of psychosocial distress (Golberg's GHQ-28) and the level of hopelessness (Beck's hopelessness scale). They were also invited to meet a psychologist for a semi-structured interview, when the day of their consultation coincided with one of the three days a week the psychologist was present in the center; the interview was aimed at collecting information upon the biographical context and ancient or recent life events and to determine the level of suicidal risk, on the basis of a scale of suicidal ideation [Ducher's Suicidal Risk Scale (ERSD)]. The concurrent validity of the later has already been previously tested and positive correlation coefficients were found with Beck Depression Inventory, Hamilton's Depression Rating Scale and Beck's Hopelessness Scale. RESULTS: One thousand and four records could be analysed, as regards self-administered questionnaires, and among those, 576 as regards the interview with the psychologist and data related to suicidal risk. The studied population included 61.3% of females and 59.3% of individuals aged 20 to 25: mean age was comparable in males and females. GHQ-28 global score and sub-scores (somatisation, anxiety, social dysfunction and depressive mood) were all higher in women (all the p<0.001). A high suicidal risk (ERSD score 4) was found in 24.1% of the studied population. Subjects presenting with a high suicidal risk were characterized by higher levels of GHQ-28 psychosocial distress and GHQ-28 sub-scores as well as hopelessness (all the p<0.001). Several biographical antecedents during childhood were significantly associated with suicidal risk: unknown father (p<0.001), death of parents (p<0.001), separation from parents (p<0.001), severe quarrel between parents (p<0.001), money problems within the family (p<0.007), disorders related with alcohol consumption in parents (p<0.016), drug addiction within the family (p<0.001). Other predictors were several recent stressful events or contexts: violence within the family (p<0.001), social isolation (p<0.001), lack of self-esteem of (p<0.002), school difficulties (p<0.001), educational failure (p<0.001); as well as the notion of a consumption of drugs (p=0,001) or medications: neuroleptics (p<0.015), antidepressants (p=0.001) and tranquilizers (p<0.001). A series of univariate regression analyses allowed to compute the Odds Ratios (OR) and the 95% Confidence Intervals (95% CI) of the sub-group characterized by a high suicidal risk for each socio-demographic, psychological and biographical independent variable, linked to suicidal risk at a threshold of p<0.10. A multiple regression analysis was then performed in 2 steps: in a first step, independent variables were pooled by blocks, according to their nature (psychological characteristics, relational deficiencies among biographical antecedents, other stressful conditions among antecedents, stressful conditions among recent biographical context, recent consumption of drugs or medications); in a second step, all the independent variables which still remained associated with suicidal risk within each block were included in a final multiple regression analysis. Five variables continued to independently predict a high suicidal risk: hopelessness at Beck's scale (OR=4.09), depressive mood at GHQ-28 (OR=3.75), the notion of an unknown father (OR=2.95), the notion of a recent destabilizing event other than a school problem or an aggression (OR=1.90) and the notion of an educational failure (OR=1.78). CONCLUSION: These results confirm previous scientific data on this topic and underline that childhood context, educational course, psychological vulnerability and the occurrence of recent stressful life events combine their effects, enhancing the risk of a suicidal attempt. They can be useful for better sensitising educational as well as social and health care circles, for settling more efficient screening and preventive programs.

Adolescent↗

Ultrarapid detection of sex chromosomes with the use of fluorescence in situ hybridization with direct label DNA probes in single human blastomeres, spermatozoa, amniocytes, and lymphocytes.

OBJECTIVE: To assess the ultrarapid fluorescence in situ hybridization (FISH) procedure with a 1-minute hybridization time for gender determination. DESIGN: Fluorescence in situ hybridization with direct label fluorescence DNA probes for chromosomes X and Y were tested with the use of different hybridization times and different cell types. SETTING: Hospital-based IVF program. INTERVENTION(S): The efficiency of the FISH procedure with different hybridization times was compared with the use of male lymphocytes. The same FISH procedure, but with only 1-minute hybridization, was carried out in human blastomeres, spermatozoa, uncultured amniocytes, male lymphocytes, and female lymphocytes. MAIN OUTCOME MEASURE(S): Percentages of nuclei with positive signals. RESULT(S): The percentages of nuclei with positive signals in lymphocytes with hybridization times of 1, 3, 4, 10, 30, and 45 minutes were 97%, 97%, 98%, 98%, 98%, and 98%, respectively. The percentages of nuclei with positive signals after FISH with a 1-minute hybridization time in single blastomeres, spermatozoa, amniocytes, male lymphocytes, and female lymphocytes were 94%, 96%, 96%, 98%, and 97%, respectively. CONCLUSION(S): Chromosomes X and Y of human blastomeres. spermatozoa, uncultured amniocytes, and lymphocytes can be detected rapidly with the use of this ultrarapid FISH procedure with a 1-minute hybridization time.

Amniotic Fluid↗

Optimal coding of electrocardiograms for epidemiological studies. The performance of human coders - astatistical model.

A statistical model is introduced to characterize the ECG coding process when multiple coding is performed by human readers. Triplicate reading and arbitration of disagreements would considerably reduce the miss rate with a concomitant increase in cost and effort. The results suggest that the use of the majority rule (acceptance of the most common code from multiple, blinded individual codings) is inappropriate for ECG coding. The model proposed gives a plausible explanation to the observed high miss rate in coding of rare events in spite of duplicate reading and arbitration of disagreements. The main problem identified is the high individual miss rate in a fraction of "difficult" ECG records suggested that efficient use of computer programs and visual verification may be required to reduce coding errors to an acceptable level.

Electrocardiography↗

First and second generation cephalosporins.

Data on tissue levels of drugs are important, for they provide us with information on concentrations that can be achieved at the site of an infection. Yet many questions remain unanswered in this area such as whether it is better to achieve high levels in tissue rapidly as with bolus administration of a drug, or whether it is preferable to maintain levels of drug at lower but more prolonged levels, as with constant infusion administration of a drug. The goal in the future will be to correlate pharmacologic principles with the efficiency of various dosing programs and tissue levels in the clinical setting.

Bacteria↗

Application of electronic estrus detection technologies to reproductive management of cattle.

Artificial insemination and embryo transfer programs are dependent on efficient and accurate detection of estrus. Visual observation is accurate at detecting animals in estrus, but efficiency ranges from approximately 50 to 70%. Electronic technologies have been developed in attempts to improve estrus detection efficiency. Commercially available electronic devices for estrus detection are based on changes in physical activity (pedometers), changes in electrical resistance of reproductive tract secretions (intravaginal resistance probes) or mounting activity (mount detectors). All of the commercially available electronic estrus detection devices can improve the efficiency of estrus detection in cattle. Pedometers are most applicable to lactating dairy cattle and have greater accuracy and efficiency when combined with visual observation. Intravaginal resistance measurement is perhaps the least practical method of estrus detection because of labor and animal handling requirements. Individual resistance measurement may have practical application for confirming other inconclusive signs of estrus. Mount monitors have the broadest application to beef and dairy cattle. HeatWatch, the only real-time radiotelometric system available, requires the least labor and animal handling and provides data on the time and duration of each mount. The less expensive stand-alone mount monitors also provide the necessary information for optimum timing of insemination and embryo transfer, but are more labor intensive.

Animals↗

Effects of hCG on folliculogenesis and fecundity in mink (Mustela vision Schreb).

The endogenous hormonal response obtained after reproductive organs are challenged by exogenous hormones is increasingly being used to predict presence of functional reserves and to apply this information to improve efficiency of managed breeding programs. With that in mind, the aim of the present study was to investigate the effect of a single treatment with hCG on folliculogenesis and fertility in standard 7-month-old mink females. The extent of stimulation following treatment was determined by examining patterns of vaginal smears. Characteristics of each cycle stage were: estrus, preponderance of cornified epithelial cells; proestrus, polygonal, elongate epithelial cells; anestrus, parabasal, intermediate and leucocyte cells. Smears exhibiting a mixed population of cells were categorized as being in transition between adjacent stages anestrus-proestrus or proestrus-estrus. The initial evaluations were done on Day 6 after hCG treatment. Histomorphometric examination of ovaries and uteri was done during seasonal anestrus (November) and in the breeding season (March). Vaginal cytology patterns were correlated with changes in folliculogenesis. A mean of 1.3 mature (Graafian) follicles were counted during estrus, while the mean number seen during anestrus, anestrus-proestrus and proestrus, were 0.4, 0.3 and 1.0, respectively. During the breeding season, in females that were not treated, the numbers of growing follicles decreased and maturing follicles increased, whereas females that came in estrus after treatment with hCG in November had increased numbers of both growing and maturing follicles. Fertility after breeding in hCG-treated females was increased by 9.2% (P<0.05) as compared to untreated females. Females showing the highest fertility rise (27%) were predominantly in the group that showed estrus after hCG treatment. We conclude that monitoring the response of the mink reproductive system to hCG stimulation in November may be a useful tool for identifying females of high fertility in the spring.

Animals↗

Some factors affecting the behavioural manifestation of oestrus in cattle: a review.

The development of more efficient and cost-effective oestrous detection techniques for cattle depends on a thorough understanding of the changes in behaviour and physiology of the female during its oestrous cycle. Variability in the expression of oestrous behaviours both between individuals and over successive oestrous cycles complicates this process. This review considers many of the biological and environmental factors that influence the intensity and duration of oestrous behaviours in domestic cattle. Topics discussed include dominant-subordinate relationships, social facilitation, animal density, oestrous synchronisation, nutritional status, age and physiological state, presence of the bull and breed differences. Facility design, cattle management and various techniques used to detect oestrus (e.g. frequency, duration and timing of observations) directly influence the efficiency of oestrous detection programs. Environmental phenomena such as weather, day length, photoperiod and ambient temperature also affect the expression of oestrous behaviours.

Journal Article↗

Risk index for prediction of surgical site infection after oncology operations.

INTRODUCTION: Several studies have shown that surgical site infections represent most hospital-acquired infections, with the major impact being on average hospital stay and cost of hospitalization. METHODS: To develop a risk model for prediction of surgical site infections in cancer patients undergoing operative procedures and identify those with high probability of infection we performed a prospective cohort study in a tertiary cancer care hospital in Rio de Janeiro, Brazil. Risk factors were studied in single and multivariate analyses. RESULTS: Over a 24-month period, 1205 patients underwent operations for malignant disease. The overall surgical site infection rate was 17.3%. A multivariate stepwise logistic regression model identified six independent predictive risk factors: contaminated and infected operations, surgical duration greater than 280 minutes, male sex, prior radiotherapy, American Society of Anesthesiology class III to V, and antimicrobial prophylaxis not according to protocol. On the basis of individual risk scores, two groups of patients were identified: a low-risk (score < or = 8; surgical site infection rate 10%) and a high-risk group (score > or = 9; surgical site infection rate 33.6%; relative risk 3.4; 95% confidence interval 2.6 to 4.4). CONCLUSION: The oncology risk model allowed for the identification of a high-risk score group of patients and implementation of a more efficient and selective intervention program.

Brazil↗