Dataset of working mPEG-alkyne with scCO2

This article contains data related to the research article entitled “Carbon dioxide sorption and melting behavior of mPEG-alkyne”. The presented data gives information on the thermodynamics properties of the solvent and the polymer. The time saturation of mPEG-alkyne in supercritical carbon dioxide (scCO₂) was evaluated in a high-pressure variable volume cell in different period of time at different pressure at the same temperature.

The effects of pressure and temperature on the density of CO₂ when it is above supercritical conditions are determined with Sanchez Lacombe and Bender Equation and compared with the NIST database and values of equation of Bender. The characteristic parameters of CO₂ were determined with the equations proposed by Chengyong Wang et al. [1] and the sum of squared error was calculated for each parameter.

Furthermore in this work the solubility data of scCO₂/polymer mixture were correlated with Sanchez Lacombe Equation of State (SL EOS) and Heuristic model proposed by Irene Pasquali et al. [2]. This work describes the methodology for solving the SL EOS between the polymer and scCO₂ and the procedure of determining the solubility parameter with the group contribution method necessary to apply the heuristic model is described.

Identifying surgical site infections in electronic health data using predictive models

Objective

The objective was to prospectively derive and validate a prediction rule for detecting cases warranting investigation for surgical site infections (SSI) after ambulatory surgery.

Methods

We analysed electronic health record (EHR) data for children who underwent ambulatory surgery at one of 4 ambulatory surgical facilities. Using regularized logistic regression and random forests, we derived SSI prediction rules using 30 months of data (derivation set) and evaluated performance with data from the subsequent 10 months (validation set). Models were developed both with and without data extracted from free text. We also evaluated the presence of an antibiotic prescription within 60 days after surgery as an independent indicator of SSI evidence. Our goal was to exceed 80% sensitivity and 10% positive predictive value (PPV).

Results

We identified 234 surgeries with evidence of SSI among the 7910 surgeries available for analysis. We derived and validated an optimal prediction rule that included free text data using a random forest model (sensitivity = 0.9, PPV = 0.28). Presence of an antibiotic prescription had poor sensitivity (0.65) when applied to the derivation data but performed better when applied to the validation data (sensitivity = 0.84, PPV = 0.28).

Conclusions

EHR data can facilitate SSI surveillance with adequate sensitivity and PPV.

P13.11 Metabolomics and molecular profiling in glioma patients: an interactomic approach

BACKGROUND

A wider view of the interaction between different omic-domains is needed to identify potential biomarkers of low- and high-grade gliomas. Using an interactomic approach, we analyzed the correlation between radiological data, IDH mutation, gene expression profiling and metabolic signature in glioma samples.

MATERIAL AND METHODS

Tumor biopsies from 25 patients with clinical diagnosis of glioma were surgically collected during 2017–2019 at the senior author’s institution. Metabolomic data was obtained by high resolution 31P and 1H magnetic resonance spectroscopy (MRS, 19 metabolites quantified with LCModel). Gene expression profiling was performed using real-time qPCR of 19 genes related to energy metabolism. IDH1/2 common mutation (IDH1R132H/IDH2R172H) was verified by immunohistochemistry and amplicon sanger sequencing. All data was integrated using the R package mixOmics, and we built correlation network plot graphs and correlation maps to identify the most significant interactions, that were analyzed thereafter.

RESULTS

Mean age was 48±10 years and 72% were men. The most frequent clinical presentation was intracranial hypertension and focal deficit. Imaging revealed 88% of single lobar tumors, 96% of contrast enhancement, 52% located near eloquent areas, 48% with augmented perfusion (mean values of 300±130%) and 60% showed restricted diffusion. WHO 2016 diagnosis were glioblastoma IDH mutated (IDHmut, 16%), IDH wildtype (IDHw, 56%); anaplastic astrocytoma IDHmut (4%), IDHw (16%); diffuse astrocytoma IDHmut (4%), SEGA (4%). The genetic and metabolic profiles were normalized per sample using the total sum of all the studied variables per case. This step made the interactomic approach possible. We found no differences between the metabolic or genetic profiles of glioma grade III and IV samples. However, there was a statistical significance or near-threshold correlation between some metabolic patterns and IDH-mutation, where Alanine (4.7±1.3% IDHw vs 2.5±0.7 IDHmut, p=0.046), Glycine (2.7±0.5% vs. 1.6±0.4%, p=0.095), Glycerophosphorylcholine (3.9±0.4% vs. 6.4±0.9%, p=0.013) and Myo-inositol (4.9±1.0% vs 11.9±2.1%, p=0.004) were the most important biomarkers. Overexpression of Lactate Dehydrogenase subunit B (LDHB, 19±3% vs. 31±6%, p=0.039) and Aconitase 1 (ACO1, 0.5±0.1% vs 1.2±0.3%, p=0.08) had also a significant or near-threshold relationship with IDH-mutation. These correlations were shown as hot spots in the correlation graphs and maps.

CONCLUSION

These preliminary results indicate that metabolic patterns by high resolution 31P and 1H MRS could be a useful tool to improve our knowledge about glioma gene expression profiles and to identify potential biomarkers to tackle this pathology.

The Reference Site Collaborative Network of the European Innovation Partnership on Active and Healthy Ageing

Seventy four Reference Sites of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA) have been recognised by the European Commission in 2016 for their commitment to excellence in investing and scaling up innovative solutions for active and healthy ageing. The Reference Site Collaborative Network (RSCN) brings together the EIP on AHA Reference Sites awarded by the European Commission, and Candidate Reference Sites into a single forum. The overarching goals are to promote cooperation, share and transfer good practice and solutions in the development and scaling up of health and care strategies, policies and service delivery models, while at the same time supporting the action groups in their work. The RSCN aspires to be recognized by the EU Commission as the principal forum and authority representing all EIP on AHA Reference Sites. The RSCN will contribute to achieve the goals of the EIP on AHA by improving health and care outcomes for citizens across Europe, and the development of sustainable economic growth and the creation of jobs.

User Testing an Information Foraging Tool for Ambulatory Surgical Site Infection Surveillance

BACKGROUND

Surveillance for surgical site infections (SSIs) after ambulatory surgery in children requires a detailed manual chart review to assess criteria defined by the National Health and Safety Network (NHSN). Electronic health records (EHRs) impose an inefficient search process where infection preventionists must manually review every postsurgical encounter (< 30 days). Using text mining and business intelligence software, we developed an information foraging application, the SSI Workbench, to visually present which postsurgical encounters included SSI-related terms and synonyms, antibiotic, and culture orders.

OBJECTIVE

This article compares the Workbench and EHR on four dimensions: (1) effectiveness, (2) efficiency, (3) workload, and (4) usability.

METHODS

Comparative usability test of Workbench and EHR. Objective test metrics are time per case, encounters reviewed per case, time per encounter, and retrieval of information meeting NHSN definitions. Subjective measures are cognitive load using the National Aeronautics and Space Administration (NASA) Task Load Index (NASA TLX), and a questionnaire on system usability and utility.

RESULTS

Eight infection preventionists participated in the test. There was no difference in effectiveness as subjects retrieved information from all cases, using both systems, to meet the NHSN criteria. There was no difference in efficiency in time per case between the Workbench and EHR (8.58 vs. 7.39 minutes, p = 0.36). However, with the Workbench subjects opened fewer encounters per case (3.0 vs. 7.5, p = 0.002), spent more time per encounter (2.23 vs. 0.92 minutes, p = 0.002), rated the Workbench lower in cognitive load (NASA TLX, 24 vs. 33, p = 0.02), and significantly higher in measures of usability.

CONCLUSION

Compared with the EHR, the Workbench was more usable, short, and reduced cognitive load. In overall efficiency, the Workbench did not save time, but demonstrated a shift from between-encounter foraging to within-encounter foraging and was rated as significantly more efficient. Our results suggest that infection surveillance can be better supported by systems applying information foraging theory.

The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases

In this paper, we report a theoretical investigation of the catalytic mechanism of peptide amidases that involve a Ser-(cis)Ser-Lys catalytic triad. Previous suggestions propose that these enzymes should follow a distinct catalytic mechanism from the one that is present in the classic Ser-His-Asp catalytic triad. The theoretical and computational results obtained in this work indicate the opposite idea, showing that both mechanisms are very similar and only few differences are observed between both reactions. The results reveal that the different alignment of the Ser-(cis)Ser-Lys catalytic triad in relation to the classical Ser-His-Asp triad may provide a better stabilisation of the reaction intermediates, and therefore make these enzymes catalytically more efficient. The catalytic mechanism has been determined at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory and requires five sequential steps instead of the two that are generally proposed: (i) nucleophilic attack of serine on the carbonyl group of the substrate, forming the first tetrahedral intermediate, (ii) formation of an acyl-enzyme complex, (ii) release of an ammonia product, (iv) nucleophilic attack of a water molecule forming the second tetrahedral intermediate, and (iv) the release of the product of the reaction, the carboxylic acid. The computational results suggest that the rate-limiting step is the first one that requires an activation free energy of 15.93 kcal mol^-1. This result agrees very well with the available experimental data that predict a reaction rate of 2200 s^-1, which corresponds to a free energy barrier of 14 kcal mol^-1.

Pediatric asthma hospitalizations among urban minority children and the continuity of primary care

OBJECTIVE

To examine the effect of ambulatory health care processes on asthma hospitalizations.

METHODS

A retrospective cohort study using electronic health records was completed. Patients aged 2-18 years receiving health care from 1 of 5 urban practices between Jan 1, 2004 and Dec 31, 2008 with asthma documented on their problem list were included. Independent variables were modifiable health care processes in the primary care setting: (1) use of asthma controller medications; (2) regular assessment of asthma symptoms; (3) use of spirometry; (4) provision of individualized asthma care plans; (5) timely influenza vaccination; (6) access to primary healthcare; and (7) use of pay for performance physician incentives. Occurrence of one or more asthma hospitalizations was the primary outcome of interest. We used a log linear model (Poisson regression) to model the association between the factors of interest and number of asthma hospitalizations.

RESULTS

5,712 children with asthma were available for analysis. 96% of the children were African American. The overall hospitalization rate was 64 per 1,000 children per year. None of the commonly used asthma-specific indicators of high quality care were associated with fewer asthma hospitalizations. Children with documented asthma who experienced a lack of primary health care (no more than one outpatient visit at their primary care location in the 2 years preceding hospitalization) were at higher risk of hospitalization compared to those children with a greater number of visits (incidence rate ratio 1.39; 95% CI 1.09-1.78).

CONCLUSIONS

In children with asthma, more frequent primary care visits are associated with reduced asthma hospitalizations.

Imputing Missing Race/Ethnicity in Pediatric Electronic Health Records: Reducing Bias with Use of U.S. Census Location and Surname Data

OBJECTIVE

To assess the utility of imputing race/ethnicity using U.S. Census race/ethnicity, residential address, and surname information compared to standard missing data methods in a pediatric cohort.

DATA SOURCES/STUDY SETTING

Electronic health record data from 30 pediatric practices with known race/ethnicity.

STUDY DESIGN

In a simulation experiment, we constructed dichotomous and continuous outcomes with pre-specified associations with known race/ethnicity. Bias was introduced by nonrandomly setting race/ethnicity to missing. We compared typical methods for handling missing race/ethnicity (multiple imputation alone with clinical factors, complete case analysis, indicator variables) to multiple imputation incorporating surname and address information.

PRINCIPAL FINDINGS

Imputation using U.S. Census information reduced bias for both continuous and dichotomous outcomes.

CONCLUSIONS

The new method reduces bias when race/ethnicity is partially, nonrandomly missing.

The catalytic mechanism of carboxylesterases: a computational study

The catalytic mechanism of carboxylesterases (CEs, EC 3.1.1.1) is explored by computational means. CEs hydrolyze ester, amide, and carbamate bonds found in xenobiotics and endobiotics. They can also perform transesterification, a reaction important, for instance, in cholesterol homeostasis. The catalytic mechanisms with three different substrates (ester, thioester, and amide) have been established at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory. It was found that the reactions proceed through a mechanism involving four steps instead of two as is generally proposed: (i) nucleophilic attack of serine to the substrate, forming the first tetrahedral intermediate, (ii) formation of the acyl-enzyme complex concomitant with the release of the alcohol product, (iii) nucleophilic attack of a water or alcohol molecule forming the second tetrahedral intermediate, and (iv) the release of the second product of the reaction. The results agree very well with the available experimental data and show that the hydrolytic and the transesterification reactions are competitive processes when the substrate is an ester. In all the other studied substrates (thioester or amide), the hydrolytic and transesterification process are less favorable and some of them might not even take place under in vivo conditions.

Farnesyltransferase inhibitors: a comprehensive review based on quantitative structural analysis

Farnesyltransferase inhibitors (FTIs) have mainly been used in cancer therapy. However, more recently, investigations on these inhibitors revealed that FTIs can be used for the treatment of other diseases such as Progeria, P. falciparum resistant malaria, Trypnosomatid, etc. Hence the development of novel FTIs is an important task for the drug discovery program. Initially, numerous peptidomimetic FTIs were developed from the template of CAAX (CVIM was the first pharmacophore model used as a peptidomimetic). Later, many non-peptidomimetic FTIs have been discovered with the structural modification of the peptidomimetics. The structural analysis of those developed FTIs by various researchers suggested that the presence of a heterocycle or a polar group in place of the thiol group is required for interaction with the Zn(2+) ion. The bulky naphthyl, quinolinyl, phenyl, phenothazine, etc in this position provide better hydrophobicity to the molecules which interact with the aromatic amino acid moieties in the hydrophobic pocket. A hydrophilic region with polar groups is necessary for the polar or hydrogen bonding interactions with the amino acids or water molecules in the active site. Many FTIs have been isolated from natural products, which possessed inhibitory activity against farnesyltransferase (FTase). Among them, pepticinnamin E (9R), fusidienol (9T), gliotoxin (9V), cylindrol A (9X), etc possessed potential FTase inhibitory activities and their structural features are comparable to those of the synthetic molecules. The clinical studies progressing on FTIs showed that tipifarnib in combination with bortezomib is used for the treatment of patients with advanced acute leukemias. Successful phase I and II studies are undergoing for tipifarnib alone or in combination with other drugs/radiation for the treatment of multiple myeloma, AML, breast cancer, mantle cell lymphoma, solid tumors, non-small cell lung cancer (NSCLC), pancreatic cancer, glioblastoma, etc. Phase I pharmacokinetic (maximum tolerated dose, toxicity) and pharmacodynamic studies of AZD3409 (an orally active double prodrug) is progressing on patients with solid malignancies taking 500 mg once a day. A phase II study is undergoing on lonafarnib alone and in combination with zoledronic acid and pravastatin for the treatment of Hutchinson-Gilford Progeria syndrome (HGPS) and progeroid laminopathies. Lonafarnib therapy improved cardiovascular status of children with HGPS, by improved peripheral arterial stiffness, bone structure and audiological status in the patients. Other important FTIs such as BMS-214662, LB42908, LB42708, etc are under clinical studies for the treatment of various cancers. This review concluded that the quantitative structural analysis report with an elaborative study on the natural product compounds provides ideas for development of novel molecules for the FTase inhibitory activity. The fragment based analysis is also needed to select the substituents, which provides significant inhibitory activities and can also have good pharmacokinetic properties in the clinical studies.

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

Understanding protein-protein association and being able to determine the crucial residues responsible for their association (hot-spots) is a key issue with huge practical applications such as rational drug design and protein engineering. A variety of computational methods exist to detect hot-spots residues, but the development of a fast and accurate quantitative alanine scanning mutagenesis (ASM) continues to be crucial. Using four protein-protein complexes, we have compared a variation of the standard computational ASM protocol developed at our group, based on the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) approach, against Thermodynamic Integration (TI), a well-known and accurate but computationally expensive method. To compare the efficiency and the accuracy of the two methods, we have calculated the protein-protein binding free energy differences upon alanine mutation of interfacial residues (ΔΔGbind). In relation to the experimental ΔΔGbind values, the average error obtained with TI was 1.53 kcal/mol, while the ASM protocol resulted in an average error of 1.18 kcal/mol. The results demonstrate that the much faster ASM protocol gives results at the same level of accuracy as the TI method but at a fraction of the computational time required to run TI. This ASM protocol is therefore a strong and efficient alternative to the systematic evaluation of protein-protein interfaces, involving hundreds of amino acid residues in search of hot-spots.

Gemcitabine: a critical nucleoside for cancer therapy

Gemcitabine (dFdC, 2',2'-difluorodeoxycytidine) is a deoxycytidine nucleoside analogue of deoxycytidine in which two fluorine atoms have been inserted into the deoxyribose ring. Like other nucleoside analogues, gemcitabine is a prodrug. It is inactive in its original form, and depends on the intracellular machinery to gain pharmacological activity. What makes gemcitabine different from other nucleoside analogues is that it is actively transported across the cell membrane, it is phosphorylated more efficiently and it is eliminated at a slower rate. These differences, together with self-potentiation mechanisms, masked DNA chain termination and extensive inhibitory efficiency against several enzymes, are the source of gemcitabine's cytotoxic activity against a wide variety of tumors. This unique combination of metabolic properties and mechanistic characteristics is only found in very few other anticancer drugs, and both the FDA and the EMEA have already approved its use for clinical purposes, for the treatment of several types of tumors. In spite of the promising results associated with gemcitabine, the knowledge of its mode of action and of the enzymes it interacts with is still not fully documented. In this article we propose to review all these aspects and summarize the path of gemcitabine inside the cell.

Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds

In the present investigation, a computational analysis was performed on a data set comprised of human ether-a-go-go-related gene (hERG) blockers (triethanolamine, 1,3-thiazol-2-yl and tetrasubstituted imidazoline derivatives) in order to investigate the structural features required to reduce the hERG-induced cardiotoxicity problems in an early stage of drug discovery. The results derived from the quantitative structure-activity relationship (QSAR) analysis showed that the volume, surface area and shape descriptors (vsurf_) contributed significantly in all the models. This reveals that the hydrogen-bonding and hydrophilicity properties (vsurf_HB1, vsurf_CW4 and a_acc) on the van der Waals (vdW) surface of the molecule is negatively contributed for the hERG blocking activity and the hydrophobic property (vsurf_D6) and the total polar volume (vsurf_Wp2) on the vdW surface of the molecule are favourable for the activity. Further, the pharmacophore analysis also shows that the Aro/Hyd/Acc contour is one of the important biophore sites for the hERG blocking activity. This suggests that the presence of aromatic, hydrophobic and hydrogen-bonding groups in the molecules is favourable for interaction. In comparison with our earlier works (explaining the role of topological and hydrophobicity properties for the hERG blocking activity), these studies provided additional information on the importance of vdW surface area properties for the hERG blocking activity. These results can be used with other molecular modelling studies for the design of novel molecules that are free of cardiotoxicity.

Structural analysis of 2-piperidin-4-yl-actamide derivatives for hERG blocking and MCH R1 antagonistic activities

In the present investigation, a computational based structural analysis was performed on a series of 2-piperidin- 4-yl-acetamide derivatives to investigate the physicochemical features of the molecules responsible for the hERG blocking and melanin concentrating hormone receptor-1 (MCH R1) antagonistic activities. The QSAR models derived from MLR analysis were validated by various validation methods and they provided significant statistical results such as Q(2), F, t(test), R, predicated residual error values, etc. These significant models were constructed with different type of physicochemical descriptors which showed that the hydrophobic properties on the vdW surface of the molecules are favorable for both the activities (MCH R1 antagonistic and hERG blocking activities) and the presence of polar/electronegative groups in the molecules is detrimental for those activities. The presence of flexible aromatic rings in the molecules has favorable hERG blocking activity. The MCH R1 antagonistic activity also depends upon the vdW volume, shape and flexibility of the molecules. In addition, the presented results will guide for the optimized design of novel bioactive molecules with less/free of hERG blocking activities to avoid unwanted potential cardiotoxic side effects related with the use of these possible antiarrhythmic and anti-obesity agents in humans.

Rifampicin-miconazole-impregnated catheters save cost in jugular venous sites with tracheostomy

Antimicrobial-impregnated catheters are more expensive than standard catheters (S-C). A higher incidence of catheter-related bloodstream infection (CRBSI) has been found in jugular venous access with tracheostomy than without tracheostomy. The objective of this study was to determine central venous catheter (CVC)-related costs (considering only the cost of the CVC, diagnosis of CRBSI, and antimicrobial agents used to treat CRBSI) using rifampicin-miconazole-impregnated catheters (RM-C) or S-C in jugular venous access with tracheostomy. We performed a retrospective cohort study of patients admitted to the intensive care unit (ICU) with tracheostomy who received one or more jugular venous catheters. RM-C showed a lower incidence of CRBSI compared with S-C (0 vs. 20.16 CRBSI episodes/1,000 catheter-days; odds ratio=0.05; 95% confidence interval=0.001-0.32; p<0.001) and lower CVC-related costs (including the cost of the CVC, diagnosis, and treatment of CRBSI) (<euro>11.46 ± 6.25 vs. <euro>38.11 ± 77.25; p<0.001) in jugular venous access with tracheostomy. The use of RM-C could reduce CVC-related costs in jugular venous access with tracheostomy. The results of our study may contribute to clinical decision-making and selection of those patients who could benefit from the use of antimicrobial-impregnated catheters.

Asymptomatic carotid stenosis in patients with intermittent claudication: epidemiological study

AIM

The aim of this paper was to determine the prevalence of extracraneal carotid artery disease in patients with intermittent claudication, to describe classic cardiovascular risk factors in those with hemodynamically significant stenosis and to try to define subgroups at high risk, improving therefore the performance of non invasive testing.

METHODS

A prospective descriptive study was conducted, with 146 patients reporting an intermittent claudication of the lower limbs and without a previous cerebrovascular event or carotid surgery. An ultrasonography examination was done. Risk factors were registed (smoking, dislipemia, arterial hypertension, diabetes mellitus), also ischemic cardiopathy and myocardial revascularization procedures. Univariate and multivariate analysis was made to define the variables associated with hemodynamically significant stenosis.

RESULTS

Prevalence of hemodynamically significant stenosis was 23.2%. Smoking, dislipemia, arterial hypertension and diabetes mellitus were not significantly associated with carotid stenosis; 24.2% of patients affected of ischemic cardiopathy present a severe stenosis, and myocardial revascularization was a risk factor for carotid stenosis.

CONCLUSION

Patients with claudication and ischemic miocardiopathy, especially when myocardial revascularization is needed, must be explored with carotid ultrasonography. In this patients, probably of hemodynamically significant carotid stenosis that requires treatment is more frequent.

Substrate recognition in HIV-1 protease: a computational study

HIV-1 protease is a crucial enzyme for the life cycle of the human immunodeficiency virus, the retrovirus that triggers AIDS. It is well documented that HIV-1 protease mediates the cleavage of Gag, Gag-Pol, and Nef precursor polyproteins and is highly selective concerning the set of 12 different amino acid sequences that cleaves. However, the governing principles and physical parameters, which determine substrate recognition and specificity, remain poorly understood despite the many speculative proposals that abound in the literature. In fact, it has been difficult so far to circumvent the fact that protease's substrates share little sequence identity and lack an obvious consensus binding motif. We have used microsecond time scale MD simulations to quantitatively show that some sequences of the polyprotein Gag-Pol that are not cleaved (nonsubstrates) have in fact a higher affinity to the active site of HIV-1 protease than a substrate; i.e., recognition is not governed by affinity to the active site. On the basis of a detailed analysis of the results and experimental data, we propose that the recognition is based on the geometric specificity of PR:Gag and PR:Gag-Pol multiprotein complex, that selects which residues lie in the specific position that makes them accessible to the active site for cleavage.

Carotid bifurcation atherosclerosis in the over-65s: a prevalence study

AIM

The aim of this study was to determine the prevalence of carotid stenosis (CS) in the over-65 population segment residing in a catchment area (Gijón) served by the Asturias Health Service (Spain) as a necessary step in planning medical care for treating cerebrovascular disease in the elderly.

METHODS

In this descriptive transversal study, 232 subjects (114 men and 118 women) randomly chosen from health card data underwent colour-flow duplex scanning of the supra-aortic trunks.

RESULTS

The prevalence of CS in this sample was 21.5%. When stratified by sex and age (65-74 and >75 years of age), the CS rate was 5 points higher in the older than in the younger group, and 4 points higher among males (23.6%) than among females (19.2%).

CONCLUSION

Approximately one in every 5 subjects over 65 years of age presents with CS; CS prevalence was higher in the over-75s and among males, although the differences were not statistically significant.

Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead

Nelfinavir (Viracept) is a potent, non-peptidic inhibitor of HIV-1 Protease, which has been marketed for the treatment of HIV infected patients. However, HIV-1 develops drug-resistance which decreases the affinity of Nelfinavir for the binding pocket of Protease. We present here three new variants of Nelfinavir, which we have designed with computational tools, with greater affinity for HIV-1 Protease than Nelfinavir itself. Accordingly, we have introduced rational modifications in Nelfinavir, optimizing its affinity to the most conserved amino acids in Protease, in order to increase the efficiency of the three new inhibitors. Minimization and molecular dynamics simulations have been carried out on four complexes, HIV-1 Protease with Nelfinavir and subsequently with the new inhibitors, respectively, in order to analyze the behavior of the systems. Additionally, we have calculated the binding free energy differences Protease:inhibitor, which gave us a quantitative idea of the new molecules inhibitory efficiency in silico.

Molecular dynamics model of unliganded HIV-1 reverse transcriptase

HIV-1 RT is one of the most important antiviral targets in the treatment of acquired immunodeficiency syndrome (AIDS). Several crystallographic structures are available for this enzyme, mostly with bound inhibitors. Despite their importance for structure based drug design towards new anti-HIV retrovirals, the X-ray structures of the unliganded enzyme could only be obtained incomplete, with a low resolution and until recently even the conformation of the p66 thumb was controversial. In this work we have aligned different X-ray RT structures, and built up a computational model of RT using homology modeling, which was afterwards refined and validated through MD simulations with explicit solvent. The model enzyme was structurally stable through the whole MD simulation, showing a RMSD of 2 Angstrom from the starting geometry. The Ramanchandram plot has improved along the simulation. Both intra-domain and interdomain movements were observed. The thumb kept its closed conformation through the whole simulation. A contact map, hydration sites study and a detailed analysis of the solvation of the nucleotide binding site are also presented.

Detailed microscopic study of the full zipA:FtsZ interface

Protein-protein interaction networks are very important for a wide range of biological processes. Crystallographic structures and mutational studies have generated a large number of information that allowed the discovery of energetically important determinants of specificity at intermolecular protein interfaces and the understanding of the structural and energetic characteristics of the binding hot spots. In this study we have used the improved MMPB/SA (molecular mechanics/Poisson-Boltzmann surface area) approach that combining molecular mechanics and continuum solvent permits to calculate the free energy differences upon alanine mutation. For a better understanding of the binding determinants of the complex formed between the FtsZ fragment and ZipA we extended the alanine scanning mutagenesis study to all interfacial residues of this complex. As a result, we present new mutations that allowed the discovery of residues for which the binding free energy differences upon alanine mutation are higher than 2.0 kcal/mol. We also observed the formation of a hydrophobic pocket with a high warm spot spatial complementarity between FtsZ and ZipA. Small molecules could be designed to bind to these amino acid residues hindering the binding of FtsZ to ZipA. Hence, these mutational data can be used to design new drugs to control more efficiently bacterial infections.

NF-κB in Human Disease: Current Inhibitors and Prospects for De Novo Structure Based Design of Inhibitors

Nuclear-Factor kappa B (NF-kappaB) is an inducible transcription factor of the Rel family, sequestered in the cytoplasm by the IkappaB family of proteins. NF-kappaB exists in several dimeric forms, but the p50/p65 heterodimer is the predominant one. Activation of NF-kappaB by a range of physical, chemical, and biological stimuli leads to phosphorylation and proteasome dependent degradation of IkappaB, leading to the release of free NF-kappaB. This free NF-kappaB then binds to its target sites (kappaB sites in the DNA), to initiate transcription. This transcription has been known to be involved in a number of diseases including cancer, AIDS, and inflammatory disorders. The present article focuses on two important issues of current and future interest- firstly a review of the main human diseases which are initiated due to NF-kappaB mediated transcription is presented. Next, comprehensive information on the current inhibitors which are targeted to interfere with the NF-kappaB pathway is provided. This latter section presents a critical review on different types of latest inhibitors targeting the complex NF-kappaB pathway at several stages. The inhibitors developed till date and still under investigation, include mainly those which interfere with the activation of NF-kappaB. Based on the complexity of NF-kappaB activation, and the current knowledge of the structural biology of NF-kappaB-DNA binding, finally it is proposed that a better approach to inhibit NF-kappaB induced transcription exists. In this context, a perspective is presented in the end, proposing de novo design of inhibitors which directly interact with the DNA Binding region of the free NF-kappaB (p50 subunit), so as to generate more specific and selective leads of NF-kappaB-DNA binding.

New designs for MRI contrast agents

New designs for Magnetic Resonance Imaging contrast agents are presented. Essentially, they all are host-guest inclusion complexes between y-cyclodextrins and polyazamacrocycles of gadolinium (III) ion. Substitutions have been made to the host to optimise the host-guest association. Molecular mechanics calculations have been performed, using the UFF force field for metals, to decide on the suitability of the substitutions, and to evaluate the host-guest energies of association. Interesting general conclusions have been obtained, concerning the improvement of Magnetic Resonance Imaging contrast agents; namely, a set of rational methodologies have been deduced to improve the association between the gadolinium (III) chelates and the cyclodextrins, and their efficiency is demonstrated with a large set of substituted complexes, opening new doors to increase the diagnostic capabilities of Magnetic Resonance Imaging.

Nuclear factor kappa B: a potential target for anti-HIV chemotherapy

The Nuclear Factor Kappa B (NF-kappaB) is a lymphoid-specific transcription factor, which is sequestered in the cytoplasm by the protein IkappaB. NF-kappaB plays a major role in the regulation of HIV-1 gene expression. Upon activation, NF-kappaB is released from IkappaB, moves to the nucleus, and binds to its sites on the HIV long terminal repeat to start transcription of integrated HIV genome. The present review focuses on the NF-kappaB as a potential target for the development of chemotherapy against HIV-1. Beginning from the viral-binding to reverse transcription, integration, and gene expression, to the virion maturation, the life cycle of HIV presents drug-targets at all the stages. As a result, many drugs have been developed and have entered clinical trials. Some of the most important of these are reverse transcriptase and protease inhibitors, which have been used mostly in clinical studies in the form of combined therapy. But, this combined therapy has presented the problem of resistance, due to mutations in the virus. However, targeting NF-kappaB for the suppression of virus does not present the problem of resistance, as NF-kappaB is a normal part of the human T-4 cell, and is not subject to mutations, as is the virus. An overview of the NF-kappaB system and its role in HIV-1 is presented, followed by a critical review of its current and potential synthetic inhibitors. The drugs studied against NF-kappaB fall mainly into three categories: (1) Antioxidants, against oxidative stress conditions, which aid in NF-kappaB activation, (2) IkappaB phosphorylation and degradation inhibitors (the phosphorylation and degradation of IkappaB is necessary to make NF-kappaB free and move to the nucleus), and (3) NF-kappaB DNA binding inhibitors. The antioxidants include N-Acetyl-L-cysteine (NAC), alpha-Lipoic acid, glutathione monoester, pyrrolidine dithiocarbamate, and tepoxalin, of which NAC is the best studied. The IkappaB phosphorylation and degradation inhibitors, which have been studied in the context of HIV-1 include the salicylates (sodium salicylate, and acetylsalicylic acid (aspirin)). Finally, the NF-kappaB DNA binding inhibitors, which have received attention only recently, are reviewed. These include the most potential, aurine tricarboxylic acid (ATA), a chelating agent, which has been found to inhibit NF-kappaB DNA binding at a low concentration of 30 micro M. The probable mechanism of action of these drugs is discussed alongwith relevant suggestions and conclusions.

The search for a new model structure of beta-factor XIIa

We present the search for a new model of beta-factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modelers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and beta-factor XIIa, in particular.

Clinical significance of donor-unrecognized bacteremia in the outcome of solid-organ transplant recipients

We evaluated the clinical significance of unrecognized bacteremia in the organ donor (i.e., blood culture results that were reported to be positive after transplantation) on the outcome of transplant recipients. Twenty-nine of 569 liver and heart donors (5%) had bacteremia at the time of organ procurement, but there were no documented instances of transmission of the isolated bacteria from the donor to the recipient. Unrecognized bacteremia in the donor does not have a negative clinical impact on the outcome of organ transplant recipients.

Prevalence and risk factors of tinea unguium and tinea pedis in the general population in Spain

This study prospectively evaluated the prevalence and risk factors of tinea unguium and tinea pedis in the general adult population in Madrid, Spain. One thousand subjects were clinically examined, and samples of nails and scales from the interdigital spaces of the feet were taken from those patients presenting with signs or symptoms of onychomycosis and/or tinea pedis, respectively. In addition, a sample from the fourth interdigital space of both feet was collected from all individuals with a piece of sterilized wool carpet. Tinea unguium was defined as a positive direct examination with potassium hydroxide and culture of the etiological agent from subjects with clinically abnormal nails. Patients with positive dermatophyte cultures of foot specimens were considered to have tinea pedis. The prevalence of tinea unguium was 2.8% (4.0% for men and 1.7% for women), and the prevalence of tinea pedis was 2.9% (4.2% for men and 1.7% for women). The etiological agents of tinea unguium were identified as Trichopyton rubrum (82.1%), followed by Trichopyton mentagrophytes var. interdigitale (14.3%) and Trichopyton tonsurans (3.5%). Trichophyton rubrum (44.8%) and Trichophyton mentagrophytes (44.8%), followed by Epidermophyton floccosum (7%) and T. tonsurans (3.4%), were the organisms isolated from patients with tinea pedis. The percentage of subjects who suffered simultaneously from both diseases was 1.1% (1.7% for men and 0.6% for women). In a multivariate logistic regression analysis, age (relative risk [RR], 1.03) and gender (RR, 2.50) were independent risk factors for tinea unguium, while only gender (RR, 2.65) was predictive for the occurrence of tinea pedis. In both analyses, the presence of one of the two conditions was associated with a higher risk for the appearance of the other disease (RR, >25).

Incidence and clinical impact of fluoroquinolone-resistant Escherichia coli in the faecal flora of cancer patients treated with high dose chemotherapy and ciprofloxacin prophylaxis

This study evaluated the susceptibility of Escherichia coli to quinolones in 72 stool samples collected from 31 patients with solid tumours who had undergone high dose chemotherapy (HDC) and peripheral blood stem-cell (PBSC) rescue with ciprofloxacin prophylaxis. Samples were obtained at admission, after completing prophylaxis and three months later. All E. coli strains isolated from baseline samples were susceptible to quinolones. Fluoroquinolone-resistant E. coli strains were isolated in 10 (32%) patients in the second sample. In eight of these patients isolates were susceptible 3 months later. No patient developed infection due to fluorquinolone-resistant E. coli. No differences were observed in outcome between patients with susceptible and resistant flora.

[Five cases of zygomycosis.]

Combined histological and mycological study of tissue specimens established a proven diagnosis of cutaneous zygomycosis in four patients. All patients had been treated with wide spectrum antibiotics and one patient (liver transplantation) was in addition also treated with cyclosporine. All had acidosis and cutaneous breaks and four had also been treated with systemic corticosteroids. The infecting organisms were Absidia corymbifera (n=2), Rhizopus stolonifer (n=1) and Mucor circinelloides (n=1). Combined treatment with i.v. conventional and liposomal formulations of amphotericin B and surgical treatment lead to a favourable clinical and mycological cure in three patients (A. corymbifera and R. stolonifer infections). One lymphoma patient with suspected Rhizopus pusillus infection of the lungs (presence of hyphae in sputum and positive culture) had an unfavourable outcome. The patient had been treated with wide spectrum antibiotics, corticosteroids and showed severe neutropenia and acidosis. The clinical presentations are outlined, including the outcomes and predisposing factors and focus on the diagnostic procedures, treatment and preventive measures.

Chromophobe renal cell carcinoma: clinicopathological study of 7 cases

Chromophobe renal cell carcinoma (CRCC) may be grossly and microscopically confused with oncocytoma. It is now believed that many, if not all, of the so-called malignant oncocytomas or oncocytomas with metastases reported in the literature were indeed chromophobe renal cell carcinomas. CRCC is characteristically positive for colloidal iron and shows cytoplasmic microvesicles in electron microscopy. This study of CRCC is thought to be the first one done in Latin America. Of a total of 106 renal epithelial neoplasms, 7 (6.6%) fulfilled the criteria for chromophobe renal cell carcinoma. This frequency in Brazil is similar to that in other parts of the world. There was no difference in age, sex, and race distribution of CRCC compared to usual renal epithelial tumors. Grossly, the CRCC ranged in size from 3.5 to 20 cm (average: 10.2 cm) in greatest dimension. Most frequently, the tumor was brown on the cut surface. The growth pattern showed compact areas in all tumors and, in most of the cases, both clear and eosinophilic cellular subtypes were seen. The electron microscopic findings favor an origin of the microvesicles from outpouchings of the outer membrane of mitochondria. The strong positivity for colloidal iron in spite of the destruction of the cytoplasmic vesicles in paraffin-embedded specimens seems to indicate that the acid mucopolysaccharides are not located inside the microvesicles. By the time of diagnosis, only one case had regional lymph node metastases and this particular case was the only one mixed (associated with the usual renal cell carcinoma). The follow-up examination after nephrectomy showed that prognosis seems to be favorable in CRCC, except when the tumor coexists with the usual renal cell carcinoma.

Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein

A new approach to the molecular modelling of homologous serine proteases is adopted, by including a set of 21 buried waters known to be preserved in enzymes sharing the primary specificity of trypsin, in the homology modelling of rat submaxillary gland kallikrein. Buried waters--water molecules sequestered from bulk solvent within a protein matrix--appear to be integral conserved components of all serine proteases of known structure and should be incorporated into serine protease models built on the basis of sequence/structural homology to this family. The absence of such waters might induce errors in a force field simulation, favouring the formation of nonexistent hydrogen bonds and locally inaccurate structure. The kallikrein model refinement has led to the conclusion that an additional buried water should be added to the original rigid matrix of 21 conserved water molecules. The structurally preserved protein cavities of such waters validate the modelled structure.

The nature of trypsin-pancreatic trypsin inhibitor binding: free energy calculation of Tyr39-->Phe39 mutation in trypsin

The main goal of this work is the detailed study of the binding interactions in the trypsin-pancreatic trypsin inhibitor (PTI) complex and, here, we present how meaningful the Tyr39-Ile19 interaction is to the stability of that particular complex using free energy methods. This knowledge should be very important in the design of new inhibitors for trypsin and enzymes homologous to it. In particular, it could help to decide whether it is possible to produce selective inhibitors for these enzymes by appropriate mutations of residues in the contact region of PTI.

Evaluation of congenital dysautonomia other than Riley-Day syndrome

We report on four children, from different families, who suffer from a congenital autonomic disorder, presumably inherited. Three of them have a sensory neuropathy but do not fit any described hereditary sensory and autonomic neuropathy. All four were examined along with some of their immediate family members. We assessed the cardiovagal, sympathetic adrenergic and sympathetic cholinergic functions with a battery of non-invasive tests. Results demonstrated that sudomotor and cardiovascular orthostatic regulation exhibited the greatest abnormalities, pointing to a predominant impairment of sympathetic components, both cholinergic and adrenergic. The overall examination showed a heterogeneous group of congenital dysautonomia, exclusive of Riley-Day or other recognized hereditary sensory and autonomic neuropathies. We emphasize the importance of studying whole family groups to diagnose subclinical impairment and to provide correct genetic counselling.

Autonomic profile of subjects prone to fainting

Syncope is the most common form of fainting that may occur at least once during a life-time in up to one-third of the general population. In 50% of patients the cause remains unknown. In an attempt to identify subtle disturbances of the autonomic nervous system, we examined 70 subjects, aged from 14 to 39 years, who suffered from recurrent neurally mediated syncope. We performed a battery of non-invasive tests assessing cardiovagal, sympathetic cholinergic and sympathetic adrenergic function. We compared the results with a group of 30 healthy, non-fainting subjects matched for age and sex. Basal records were similar in both groups. Patients had preserved cardiovagal function. The multivariate cluster analysis allowed us to find a homogeneous group of cases (46%) that simultaneously presented: greater fall in systolic and diastolic blood pressure after standing, increased 15:30 ratio, exaggerated absolute heart rate rise in response to standing and subclinical reduced sudomotor function in the foot. The results suggest the existence of a subclinical autonomic profile, with subtle sympathetic postganglionic impairment, evident in lower limbs. These findings may contribute to proving the existence of different types of neurally mediated syncope, all different in their onset and mechanism but with a common final manifestation: syncopal loss of consciousness.

Sympathetic sudomotor function and aging

Many studies have reported the influence of aging on different portions of the autonomic nervous system components but only partially for the sympathetic cholinergic system. We evaluated postganglionic sudomotor function in 196 healthy subjects, 104 women and 92 men, by determining sweat gland density (SGD) per square centimeter of skin, on the dorsum of the hand and foot, with the impression mold technique. The age range was from 5 to 84 years. A significant decrease of SGD was observed in both hand and foot in relation to age (P < 0.001). The ANOVA analysis of foot data shows that age is the only significant factor for SGD reduction. In the hand, both sex and body surface area are significant covariates with age. The dorsum of the foot is the most appropriate place to examine sweating in studies of aging. The lower normal limits for SGD in the foot are 213/cm2 for subjects younger than 30 years, 199/cm2 for those from 30 to 59 years, and 123/cm2 for subjects over 59 years old.

Evaluation of recombinant Ro/SSA, La/SSB, Sm, and U1 RNP autoantigens in clinical diagnosis

This study comprises an analysis of the diagnostic usefulness of Ro/SSA, La/SSB, Sm and U1 RNP autoantigens obtained by DNA recombinant technology. We studied the presence of these autoantibodies in 33 patients with systemic lupus erythematosus (SLE) and 30 normal individuals by enzyme-linked immunosorbent assay (ELISA) using recombinant autoantigens and by Western immunoblot with these same antigens obtained from natural sources (rabbit thymus and human spleen). The strength of agreement between results found with these two techniques was moderate in the case of anti-Ro/SSA (kappa = 0.474, P < 0.001) and anti-U1 RNP (kappa = 0.566. P < 0.001) antibodies and almost perfect in the case of anti-La/SSB (kappa = 0871, P < 0.001) and anti-Sm (kappa = 0.833, P < 0.001). Furthermore, analysis of the disagreement between the two techniques evidenced a measurement bias for anti-Ro/SSA and anti-U1 RNP antibodies (Mc NEMAR'S statistic 13 and 11, respectively) whose direction, though difficult to define in the absence of a gold standard for such determinations, could be accounted for by the ELISA technique's greater tendency to produce positive results. Our conclusion is that the diagnostic usefulness of recombinant La/SSB and Sm autoantigens has been satisfactorily proven, whereas the case of the Ro/SSA and U1 RNP systems should be subject to further in-depth study of the autoepitopes recognised and the possible modifications which the latter might undergo as a result of their obtension from procariotic sources.

Model structure for the human blood coagulation agent beta-factor XIIa

An improvement to the human blood coagulation agent beta-factor XIIa three-dimensional model is proposed. The sequence alignment as well as the modeling procedures are presented and the minimized energy of the new model is reported before and after solvation of the active center.