Studying sleep: towards the identification of hypnogram features that drive expert interpretation

STUDY OBJECTIVES

Hypnograms contain a wealth of information and play an important role in sleep medicine. However, interpretation of the hypnogram is a difficult task and requires domain knowledge and "clinical intuition." This study aimed to uncover which features of the hypnogram drive interpretation by physicians. In other words, make explicit which features physicians implicitly look for in hypnograms.

METHODS

Three sleep experts evaluated up to 612 hypnograms, indicating normal or abnormal sleep structure and suspicion of disorders. ElasticNet and convolutional neural network classification models were trained to predict the collected expert evaluations using hypnogram features and stages as input. The models were evaluated using several measures, including accuracy, Cohen's kappa, Matthew's correlation coefficient, and confusion matrices. Finally, model coefficients and visual analytics techniques were used to interpret the models to associate hypnogram features with expert evaluation.

RESULTS

Agreement between models and experts (Kappa between 0.47 and 0.52) is similar to agreement between experts (Kappa between 0.38 and 0.50). Sleep fragmentation, measured by transitions between sleep stages per hour, and sleep stage distribution were identified as important predictors for expert interpretation.

CONCLUSIONS

By comparing hypnograms not solely on an epoch-by-epoch basis, but also on these more specific features that are relevant for the evaluation of experts, performance assessment of (automatic) sleep-staging and surrogate sleep trackers may be improved. In particular, sleep fragmentation is a feature that deserves more attention as it is often not included in the PSG report, and existing (wearable) sleep trackers have shown relatively poor performance in this aspect.

Cognitive functioning in survivors of hematopoietic stem cell transplantation compared with a matched general population sample – The MOSA study

Although cognitive problems can recover over time, a subgroup of hematopoietic stem cell transplantation (HCT) survivors experience persistent cognitive problems in the long term. Despite these implications, studies assessing cognitive functioning in HCT survivors are limited. The aim of the present study was (1) to quantify the prevalence of cognitive impairment in patients treated with HCT who survived at least 2 years and to compare these with a matched reference group representing the general population; (2) to identify potential determinants of cognitive functioning within the HCT survivor group. Within the single-center Maastricht Observational study of late effects after Stem cell trAnsplantation, cognitive performance was assessed by a neuropsychological test battery divided into 3 cognitive domains: memory, information processing speed, and executive function and attention. An overall cognition score was calculated as the average of the domain scores. A total of 115 HCT survivors were group-matched on a 1:4 ratio to the reference group by age, sex, and level of education. Regression analyses adjusted for different sets of covariates including demographic and health- and lifestyle-related factors were used to test for differences in cognition between HCT survivors and the reference group resembling the general population. A limited set of clinical characteristics (diagnosis, type of transplant, time since treatment, conditioning regimen with total body irradiation and age at time of transplantation) were assessed as potential determinants of neurocognitive dysfunction among HCT survivors. Cognitive impairment was defined as scores in the cognitive domains < -1.5 standard deviation (SD) from what can be expected based on someone's age, sex, and education. The mean age at time of transplantation was 50.2 (SD ± 11.2) years, and the mean number of years after transplant was 8.7 (SD ± 5.7) years. The majority of HCT survivors were treated with autologous HCT (n = 73 [64%]). The prevalence of cognitive dysfunction was 34.8% in HCT survivors and 21.3% in the reference group (p = .002.) When adjusted for age, sex, and level of education, HCT survivors had a worse overall cognition score (b = -0.35; 95% confidence interval [CI], -0.55 to -0.16; p < .001), translating into 9.0 years of higher cognitive age. Analyses of specific cognitive domain scores showed that HCT survivors scored worse on memory (b = -0.43; 95% CI, -0.73 to -0.13; p = .005), information processing speed (b = -0.33; 95% CI, -0.55 to -0.11; p = .003), and executive function and attention (b = -0.29; 95% CI, -.55 to -.03; p = .031) than the reference group. The odds of cognitive impairment were on average 2.4 times higher among HCT survivors than the reference group (odd ratio = 2.44; 95% CI, 1.47-4.07; p = .001). Within the HCT survivor group none of the tested clinical determinants of cognitive impairment were significantly associated with cognition. This cohort study showed evidence for worse cognitive functioning in HCT survivors encompassing all three cognitive domains, respectively memory, information processing speed, and executive & attention compared to a reference group that represents the general population translating into nine years of faster cognitive ageing in HCT survivors than can be expected based on their chronological age. It is important to increase awareness for signs of neurocognitive dysfunction after HCT in clinicians and HCT survivors.

Sleep Apnea is Associated With Accelerated Vascular Aging: Results From 2 European Community-Based Cohort Studies

Background The mechanisms underlying the association between obstructive sleep apnea (OSA) and cardiovascular disease may include accelerated vascular aging. The aim was to compare the magnitude of vascular aging in patients with high versus low risk of OSA. Methods and Results In 2 community-based studies, the PPS3 (Paris Prospective Study 3) and the Maastricht Study, high risk of OSA was determined with the Berlin questionnaire (a screening questionnaire for OSA). We assessed carotid artery properties (carotid intima-media thickness, Young's elastic modulus, carotid-femoral pulse wave velocity, carotid pulse wave velocity, carotid diameter using high precision ultrasound echography), and carotid-femoral pulse wave velocity (in the Maastricht Study only). Regression coefficients were estimated on pooled data using multivariate linear regression. A total of 8615 participants without prior cardiovascular disease were included (6840 from PPS3, 62% men, mean age 59.5±6.2 years, and 1775 from the Maastricht Study, 51% men, 58.9±8.1 years). Overall, high risk of OSA prevalence was 16.8% (n=1150) in PPS3 and 23.8% (n=423) in the Maastricht Study. A high risk of OSA was associated with greater carotid intima-media thickness (β=0.21; 0.17-0.26), Young's elastic modulus (β=0.21; 0.17-0.25), carotid-femoral pulse wave velocity (β=0.24; 0.14-0.34), carotid pulse wave velocity (β=0.31; 0.26-0.35), and carotid diameter (β=0.43; 0.38-0.48), after adjustment for age, sex, total cholesterol, smoking, education level, diabetes mellitus, heart rate, and study site. Consistent associations were observed after additional adjustments for mean blood pressure, body mass index, or antihypertensive medications. Conclusions These data lend support for accelerated vascular aging in individuals with high risk of OSA. This may, at least in part, underlie the association between OSA and cardiovascular disease.

Chronic obstructive pulmonary disease and atrial fibrillation: an interdisciplinary perspective

Chronic obstructive pulmonary disease (COPD) is highly prevalent among patients with atrial fibrillation (AF), shares common risk factors, and adds to the overall morbidity and mortality in this population. Additionally, it may promote AF and impair treatment efficacy. The prevalence of COPD in AF patients is high and is estimated to be ∼25%. Diagnosis and treatment of COPD in AF patients requires a close interdisciplinary collaboration between the electrophysiologist/cardiologist and pulmonologist. Differential diagnosis may be challenging, especially in elderly and smoking patients complaining of unspecific symptoms such as dyspnoea and fatigue. Routine evaluation of lung function and determination of natriuretic peptides and echocardiography may be reasonable to detect COPD and heart failure as contributing causes of dyspnoea. Acute exacerbation of COPD transiently increases AF risk due to hypoxia-mediated mechanisms, inflammation, increased use of beta-2 agonists, and autonomic changes. Observational data suggest that COPD promotes AF progression, increases AF recurrence after cardioversion, and reduces the efficacy of catheter-based antiarrhythmic therapy. However, it remains unclear whether treatment of COPD improves AF outcomes and which metric should be used to determine COPD severity and guide treatment in AF patients. Data from non-randomized studies suggest that COPD is associated with increased AF recurrence after electrical cardioversion and catheter ablation. Future prospective cohort studies in AF patients are needed to confirm the relationship between COPD and AF, the benefits of treatment of either COPD or AF in this population, and to clarify the need and cost-effectiveness of routine COPD screening.

Comorbidity clusters in patients with moderate-to-severe OSA

PURPOSE

Obstructive sleep apnea (OSA) is a prevalent and multifaceted disease. To date, the presence and severity of objectively identified comorbidities and their association with specific OSA phenotypes, CPAP adherence, and survival remain to be elucidated. The aim of this study is to cluster patients with OSA based on 10 clinically important objectively identified comorbidities, and to characterize the comorbidity clusters in terms of clinical and polysomnographic characteristics, CPAP adherence, and survival.

STUDY DESIGN AND METHODS

Seven hundred ten consecutive patients starting CPAP for moderate-to-severe OSA were included. Comorbidities were based on generally accepted cutoffs identified in the peer-reviewed literature. Self-organizing maps were used to order patients based on presence and severity of their comorbidities and to generate clusters.

RESULTS

The majority of patients were men (80%). They were generally middle-aged (52 years) and obese (BMI: 31.5 kg/m²). Mean apnea-hypopnea index (AHI) was 41 ± 20 per h of sleep. More than 94% of the patients had one or more comorbidities with arterial hypertension, dyslipidemia, and obesity being the most prevalent. Nine comorbidity clusters were identified. The clinical relevance of these comorbidity clusters was highlighted by the difference in symptoms, PSG parameters, and cardiovascular risk. Also, differences in CPAP adherence, improvements in ESS, and long-term survival were present between the clusters.

CONCLUSION

Comorbidity prevalence in patients with OSA is high, and different comorbidity clusters, demonstrating differences in cardiovascular risk, CPAP adherence, and survival, can be identified. These results further substantiate the need for a comprehensive assessment of patients with OSA beyond the AHI.

Pulmonary rehabilitation, physical activity, respiratory failure and palliative respiratory care

The CIRO Academy in Horn (the Netherlands) organised a 2-day meeting to present and discuss the studies published in 2017 pertaining to key priority areas of respiratory and critical care medicine. This review summarises studies focussing on pulmonary rehabilitation and exercise training, physical activity, chronic respiratory failure and palliative respiratory care published in 2017.

Severity of nocturnal hypoxia and daytime hypercapnia predicts CPAP failure in patients with COPD and obstructive sleep apnea overlap syndrome

BACKGROUND

Obstructive sleep apnea (OSA) and chronic obstructive pulmonary disease (COPD) are independent risk factors for cardiovascular diseases. In patients with OSA and concurrent COPD, continuous positive airway pressure (CPAP) therapy improves survival. Nevertheless, a significant proportion of such patients do not tolerate CPAP. The aim of the present study was to analyze early predictors of CPAP failure in patients with OSA and concurrent COPD, and to evaluate the effects of bilevel positive airway pressure (BiPAP) in this high-risk group of patients.

METHODS

A post hoc analysis from the database of 2100 patients diagnosed with OSA between 2012 and 2014 identified 84 subjects as having concomitant COPD and meeting inclusion criteria. Demographic data, pulmonary function tests, OSA parameters, blood gases, response to CPAP and BiPAP titration, and two months of therapy were collected. A multivariate model was generated to find determinants of CPAP failure.

RESULTS

Primary CPAP failure was found in 23% of patients who were more obese (p = 0.018), had worse lung function, lower PO₂ (p = 0.023) and higher PCO₂ while awake (p < 0.001), and more sleep time with an SpO₂ < 90% (CT90%) (p < 0.001) compared to those who responded to CPAP. In multivariate analysis, PCO₂ while awake [odds ratio (OR) 29.5, confidence interval (CI) 2.22-391, p = 0.010] and CT90% (OR 1.06, CI 1.01-1.11, p = 0.017) independently predicted CPAP failure after adjustments for covariates. The BiPAP therapy was well tolerated and effectively alleviated hypercapnia in all patients with primary CPAP failure.

CONCLUSIONS

Daytime hypercapnia and nocturnal hypoxia are independent predictors of early CPAP failure in patients with the OSA-COPD overlap syndrome.

On the preparation, characterization, and enzymatic activity of fungal protease-gold colloid bioconjugates

We present herein details pertaining to the preparation of bioconjugates of colloidal gold with aspartic protease from the fungus Aspergillus saitoi (F-prot) and their characterization and enzymatic activity. Simple mixing of the colloidal gold and protein solutions under protein-friendly conditions (pH = 3) followed by centrifugation (to remove uncomplexed gold nanoparticles and protein molecules) results in the formation of the fungal protease-gold nanoparticle conjugates. The protein-gold nanoparticle bioconjugate was redispersed in buffer solution and indicated the formation of efficient bioconjugates with intact native protein structures. The bioconjugates in solution were characterized by UV-vis spectroscopy, fluorescence spectroscopy, and biocatalytic activity measurements while drop-dried bioconjugate films on Si (111) substrates were characterized by scanning electron microscopy (SEM), energy dispersive analysis of X-rays (EDAX), and X-ray diffraction (XRD) measurements. Microscopy images do show some aggregate formation, but the intactness of the native structure of the enzyme in the bioconjugate material was verified by fluorescence and biocatalytic activity measurements. The enzyme retains substantial biocatalytic activity in the bioconjugate material and was comparable to that of free enzyme in solution.

Assembly of CdS nanoparticles in patterned structures by a novel ion-entrapment process in thermally evaporated fatty acid films

The formation of cadmium sulfide nanoparticle assemblies in a patterned manner on suitable substrates is described. The protocol for realizing such structures comprises the following steps. In the first step, patterned films of a fatty acid are thermally evaporated onto solid supports using suitable masks (e.g., a transmission electron microscope grid). Thereafter, the fatty acid film is immersed in cadmium sulfate solution and Cd2+ ions entrapped in the lipid matrix by electrostatic complexation with the carboxylate ions of the fatty acid molecules. The final step involves reaction of the entrapped Cd2+ ions with Na2S, leading to the in situ generation of cadmium sulfide nanoparticles within the patterned lipid matrix. This approach shows promise for generating patterned nanoparticle assemblies of different chemical compositions.

A new method for the generation of patterned protein films by encapsulation in arrays of thermally evaporated lipids

In this article we demonstrate a versatile method for the generation of patterned protein films by encapsulation in arrays of the lipids, octadecylamine (ODA, cationic), and arachidic acid (AA, anionic). A simple 2 x 2 array of ODA and AA was vacuum deposited on different substrates using appropriate masks. Thereafter, the enzymes pepsin and fungal protease as well as the heme-proteins cytochrome c and hemoglobin were encapsulated in the different elements of the array by sequential immersion (combined with judicious masking) of the array elements in the different protein solutions. The proteins are incorporated into the lipid elements by electrostatic interaction between charged amino acid residues on the protein surface and charged functional groups in the lipid matrix. This procedure leads to spatially distinct regions of the different proteins on one substrate and shows promise for single-chip multianalyte immunoassay/multiplex, high-throughput biosensor and catalysis applications. Fourier transform infrared spectroscopy (FTIR) was used to monitor the incorporation of the proteins in the different elements of the array as well as to ascertain whether intermixing of the proteins in a particular array element had occurred. The heme-protein composite regions were further characterized using UV-VIS spectroscopy.

Fabrication, characterization, and enzymatic activity of encapsulated fungal protease--fatty lipid biocomposite films

Encapsulation of an aspartic protease from the fungus Aspergillus saitoi (F-prot) in thermally evaporated fatty acid films by a simple beaker-based immersion technique under enzyme-friendly conditions is described. The approach is based on diffusion of the enzyme from aqueous solution, driven primarily by attractive electrostatic interaction between charged groups on the enzyme surface and ionized lipid molecules in the film. The encapsulated enzyme molecules could be "pumped out" of the biocomposite film into solution by modulating the electrostatic interaction between the enzyme and fatty acid molecules via solution pH variation. The kinetics of F-prot diffusion into the acid films was followed using quartz crystal microgravimetry measurements while the secondary and tertiary structure of the enzyme in the lipid matrix was studied using Fourier transform infrared (FT-IR) and fluorescence spectroscopies. FT-IR and fluorescence measurements indicated little perturbation to the native structure of the enzyme. A chemical analysis of the F-prot-fatty acid biocomposite film was also performed using X-ray photoelectron spectroscopy. The encapsulated F-prot molecules showed catalytic activity (as estimated by reaction with hemoglobin) comparable to free enzyme molecules in solution, indicating facile access of biological analytes/reactants in solution to the enzyme molecules. The advantages/disadvantages of this approach vis-à-vis methods currently used for encapsulation of biomolecules are briefly discussed.

Pharmacokinetics of melphalan in isolated limb perfusion

The pharmacokinetics of melphalan was studied by sampling of tissue and plasma in 72 rats that underwent isolated hyperthermic limb perfusion under different conditions. A miniaturized extracorporeal circulation system for small animals was used for perfusion of the rat hindlimb. Melphalan levels (L-phenylalanine mustard, L-PAM) were determined by high-performance liquid chromatography (HPLC). The temperature of the perfusate plasma and tissue, pH, administration method, and flow rate were modified and compared with regard to their influence on pharmacokinetic parameters. The highest tissue penetration of melphalan was observed under the following conditions: (a) pH range of the perfusate plasma between 7.3 and 7.7 (physiological environment), (b) temperature range of the perfusate from 40 degrees to 41.5 degrees C (destruction of cellular carrier systems at higher temperatures and increased inactivation by hydrolysis of melphalan above 41.5 degrees C), (c) application of melphalan as a single dose into the reservoir of the extracorporeal circuit (optimal tissue penetration), and (d) reduced perfusate flow (prolonged contact time between perfusate and tissue).

Rational design of a functional metalloenzyme: introduction of a site for manganese binding and oxidation into a heme peroxidase

The design of a series of functionally active models for manganese peroxidase (MnP) is described. Artificial metal binding sites were created near the heme of cytochrome c peroxidase (CCP) such that one of the heme propionates could serve as a metal ligand. At least two of these designs, MP6.1 and MP6.8, bind Mn2+ with Kd congruent with 0.2 mM, react with H2O2 to form stable ferryl heme species, and catalyze the steady-state oxidation of Mn2+ at enhanced rates relative to WT CCP. The kinetic parameters for this activity vary considerably in the presence of various dicarboxylic acid chelators, suggesting that the similar features displayed by native MnP are largely intrinsic to the manganese oxidation reaction rather than due to a specific interaction between the chelator and enzyme. Analysis of pre-steady-state data shows that electron transfer from Mn2+ to both the Trp-191 radical and the ferryl heme center of compound ES is enhanced by the metal site mutations, with transfer to the ferryl center showing the greatest stimulation. These properties are perplexingly similar to those reported for an alternate model for this site (1), despite rather distinct features of the two designs. Finally, we have determined the crystal structure at 1.9 A of one of our designs, MP6.8, in the presence of MnSO4. A weakly occupied metal at the designed site appears to coordinate two of the proposed ligands, Asp-45 and the heme 7-propionate. Paramagnetic nuclear magnetic resonance spectra also suggest that Mn2+ is interacting with the heme 7-propionate in MP6.8. The structure provides a basis for understanding the similar results of Yeung et al. (1), and suggests improvements for future designs.

The three-dimensional structure of Ca(2+)-bound calcyclin: implications for Ca(2+)-signal transduction by S100 proteins

BACKGROUND

Calcyclin is a member of the S100 subfamily of EF-hand Ca(2+)-binding proteins. This protein has implied roles in the regulation of cell growth and division, exhibits deregulated expression in association with cell transformation, and is found in high abundance in certain breast cancer cell lines. The novel homodimeric structural motif first identified for apo calcyclin raised the possibility that S100 proteins recognize their targets in a manner that is distinctly different from that of the prototypical EF-hand Ca2+ sensor, calmodulin. The NMR solution structure of Ca(2+)-bound calcyclin has been determined in order to identify Ca(2+)-induced structural changes and to obtain insights into the mechanism of Ca(2+)-triggered target protein recognition.

RESULTS

The three-dimensional structure of Ca(2+)-bound calcyclin was calculated with 1372 experimental constraints, and is represented by an ensemble of 20 structures that have a backbone root mean square deviation of 1.9 A for the eight helices. Ca(2+)-bound calcyclin has the same symmetric homodimeric fold as observed for the apo protein. The helical packing within the globular domains and the subunit interface also change little upon Ca2+ binding. A distinct homology was found between the Ca(2+)-bound states of the calcyclin subunit and the monomeric S100 protein calbindin D9k.

CONCLUSIONS

Only very modest Ca(2+)-induced changes are observed in the structure of calcyclin, in sharp contrast to the domain-opening that occurs in calmodulin and related Ca(2+)-sensor proteins. Thus, calcyclin, and by inference other members of the S100 family, must have a different mode for transducing Ca2+ signals and recognizing target proteins. This proposal raises significant questions concerning the purported roles of S100 proteins as Ca2+ sensors.

Solution structure of mithramycin dimers bound to partially overlapping sites on DNA

Mithramycin (MTH) is a DNA-binding antitumor agent containing A-B disaccharide and C-D-E trisaccharide segments projecting from opposite ends of an aglycone chromophore. We have previously reported on the solution structure of the MTH-DNA 6-mer complex based on a combined NMR and molecular dynamics study. This study established that the Mg(2+)-coordinated mithramycin dimer bound to a widened minor groove centered about the sequence-specific (G-C).(G-C) site and that the C-D-E trisaccharide segments from individual monomers were directed towards opposite ends of the helix spanning a six base-pair segment. This research is now extended to the binding of mithramycin dimers to partially overlapping sites on the self-complementary d(T-A-G-C-T-A-G-C-T-A) 10-mer duplex. The six base-pair mithramycin dimer footprint centered about (G-C).(G-C) steps should result in a potential steric clash in the center of the helix involving the inwardly pointing E-sugars of the pair of mithramycin dimers bound to the DNA 10-mer duplex. The MTH-d(T-A-G-C-T-A-G-C-T-A) complex (two MTH dimers per duplex) yields narrow and well-resolved NMR spectra, which have been assigned to identify intramolecular and intermolecular nuclear Overhauser enhancement (NOE) connectivities in the complex. The solution structure of the MTH-DNA 10-mer complex based on distance-restrained molecular dynamics calculations has defined the conformation of the drug and the DNA necessary for accommodation of the pair of mithramycin dimers on the DNA 10-mer helix. Specifically, the inwardly pointing E-sugars retain their face-down alignment towards the floor of the minor groove and occupy adjacent binding sites in the center of the duplex. This is achieved, in part, through torsion angle differences in the glycosidic linkage bonds along the length of the inwardly pointing aglycone-C-D-E trisaccharide segment relative to its outwardly pointing aglycone-C-D-E trisaccharide counterpart in the complex. In addition, a pronounced kink at the central (T-A).(T-A) step opens the minor groove and generates additional space to accommodate the inwardly pointing E-sugars at adjacent sites in the MTH-DNA 10-mer complex. These studies establish conformational plasticity in the C-D-E trisaccharide segment of the mithramycin dimer and deformability of the DNA helix allowing mithramycin dimers to bind to partially overlapping minor groove sites on the DNA helix.

Distinct conformational changes induced by 20-epi analogues of 1 alpha,25-dihydroxyvitamin D3 are associated with enhanced activation of the vitamin D receptor

The relative affinities of the 1 alpha,25-dihydroxyvitamin D3 (1,25-D3) analogues 20-epi-1 alpha,25-dihydroxyvitamin D3 (IE) and 20-epi-22-oxa-24a,26a,27a-tri-homo-1 alpha,25-dihydroxyvitamin D3 (ID) to the nuclear vitamin D receptor (VDR) are similar to that of 1,25-D3, but their antiproliferative action is 1000-fold greater. We tested whether the greater antiproliferative effect of these analogues is due to a differential activation of the VDR. In ROS 17/2.8 cells, the effective doses required to produce 50% maximal stimulation (ED50) of transfected reporter genes driven by either the osteocalcin or the osteopontin vitamin D-response elements (VDRE) were 5 x 10(-9) M, 10(-10) M, and 10(-11) M for 1,25-D3, ID, and IE, respectively. Similar results were obtained when recombinant human VDR was cotransfected into CV-1 cells with an osteocalcin VDRE-reporter plasmid. We found that in vitro the sensitivity of 1,25-D3-induced and analogue-induced receptors to proteases was different. The ED50 for binding to VDRE, as determined by electrophoretic mobility shift assays, was significantly higher for 1,25-D3-induced than for analogue-induced VDR. The concentration of retinoid X receptor (RXR) was significantly lower in 1,25-D3-induced than analogue-induced VDR complexes with VDRE. We therefore conclude that IE and ID augment transcriptional activity of VDR more than 1,25-D3 does, by producing conformational changes that enhance dimerization of VDR with RXR. We suggest that these conformational changes are due to differences in the contact sites of the 20-epi analogues and 1,25-D3 with the VDR.

Solution structure of the monoalkylated mitomycin C-DNA complex

Mitomycin C (MC) is a potent antitumor antibiotic which alkylates DNA through covalent linkage of its C-1" position with the exocyclic N2 amino group of guanine to yield the [MC]dG adduct at the duplex level. We report on the solution structure of the monoalkylated MC-DNA 9-mer complex where the [MC]dG5 adduct is positioned opposite dC14 in the d(A3-C4-[MC]G5-T6).d(A13-C14-G15-T16) sequence context. The solution structure was solved based on a combined NMR-molecular dynamics study including NOE intensity based refinement. The formation of the [MC]dG adduct occurs with retention of the Watson-Crick alignment at the [MC]dG5.dC14 base-pair and flanking pairs in the complex. The MC ring is positioned in the minor groove with its indoloquinone aromatic ring system at a approximately 45 degrees angle relative to the helix axis and directed towards the 3'-direction on the unmodified strand. The MC indoloquinone chromophore is asymmetrically positioned in a slightly widened minor groove so that its plane is parallel to and stacked over the d(C14-G15-T16) segment on the unmodified strand with its other face exposed to solvent. The MC five-membered ring adopts an envelope pucker with its C-2" atom displaced from the mean plane and directed away from the unmodified strand. We observe conformational perturbations in the DNA 9-mer duplex on formation of the monoalkylated MC complex. Specifically, the base-pairs are displaced by approximately -3.0 A towards the major groove on positioning the MC in the minor groove. This perturbation is accompanied by base stacking patterns similar to those observed in A-DNA while the majority of the sugars adopt puckers characteristic of B-DNA. Conformational perturbations as monitored by helix twist, sugar pucker pseudorotation and glycosidic torsion angles are also observed for the d(T6-C7-I8).d(C11-G12-A13) segment that is adjacent to but does not overlap the MC binding on the 9-mer duplex. We note that the O-10" atom on the carbamate side-chain of MC forms an intermolecular hydrogen bond with the exocyclic amino group of dG15 in two of the three refined structures of the complex. The solution structure of the complex containing this intramolecular hydrogen bond readily explains both the previously observed d(C-G).d(C-G) sequence requirement for cross-linking and the observed, somewhat less stringent, requirement of the same sequence for the initial monoalkylation step.(ABSTRACT TRUNCATED AT 400 WORDS)

Solution structure of the mithramycin dimer-DNA complex

We have characterized the NMR parameters for the complexes formed by the Mg(2+)-coordinated mithramycin dimer with self-complementary d(T-G-G-C-C-A) and d(T-C-G-C-G-A) duplexes. The solution structure of the latter complex has been determined using a combined NMR-molecular dynamics study including relaxation matrix refinement. The Mg(2+)-coordinated mithramycin dimer-d(T-C-G-C-G-A) complex exhibits a 2-fold center of symmetry with the divalent cation coordinated aglycons positioned opposite the central (G3-C4).(G3-C4) segment such that the aglycon C8 hydroxyl oxygens form symmetrical sequence-specific hydrogen bonds to guanine amino protons in the complex. The C-D-E trisaccharide segments of each monomer in the mithramycin dimer adopt extended conformations, are positioned inside the minor groove, and are directed toward either end of the duplex. The C-D saccharide component of one monomer and the aglycon of the other monomer in the mithramycin dimer share a widened minor groove with the hydrophobic edges of the C and D sugars interacting with individual strands of the duplex. The E-sugar ring is positioned in the floor of the minor groove, and its hydroxyl-bearing face interacts with both strands of the duplex through hydrogen-bonding and hydrophobic intermolecular interactions. The A-B disaccharide and the hydrophilic side chain form intermolecular contacts with the sugar-phosphate backbone in the complex. The antiparallel alignment of divalent cation coordinated monomers in the mithramycin dimer results in the two outwardly directed C-D-E trisaccharide segments generating a right-handed continuous hexasaccharide domain that spans six base pairs in the minor groove of the duplex. The solution structure of the mithramycin dimer-DNA complex reported in this study and the solution structure of the chromomycin dimer-DNA complex reported previously [Gao, X., Mirau, P., & Patel, D. J. (1992) J. Mol. Biol. 223, 259-279] show global similarities, as well as local differences that are of interest. All four nucleotides in the tetranucleotide segment of the duplex centered about the sequence-specific (G-C).(G-C) step adopt A-DNA sugar puckers and glycosidic torsion angles in the chromomycin dimer-DNA complex, while only the central cytidine adopts an A-DNA sugar pucker and glycosidic torsion angle in the mithramycin dimer-DNA complex.(ABSTRACT TRUNCATED AT 400 WORDS)

Mast cell frequency in soft tissue tumors. Relation to type and grade of malignancy

A high content of mast cells (MC) is considered characteristic of neurofibromas but not of malignant schwannomas and neurilemmomas. We examined the extent and reliability of this finding by counting MC in 61 peripheral nerve sheath tumors and in 103 non-neurogenic soft tissue sarcomas. We furthermore investigated correlations between the amount of MC and various features of the tumors (e.g. grades of malignancy). Neurofibromas had very high mast cell counts. However, this result only applied to about 70% of these tumors. Malignant schwannomas, malignant fibrous histiocytomas and leiomyosarcomas had remarkably high median values of MC counts with a wide dispersion within the histological groups. Synovial sarcomas were the only group that contained MC in every case, though often in small numbers. In univariate analyses the number of MC was negatively correlated to grades of malignancy, cellularity and mitotic activity of the sarcomas and tended to correlate positively to the amount of myxoid and collagenous connective tissue and lymphocytic infiltrates. Multiple linear regression analysis revealed a significant correlation to the grade of malignancy and the amount of connective tissue.

NMR and computational characterization of mitomycin cross-linked to adjacent deoxyguanosines in the minor groove of the d(T-A-C-G-T-A).d(T-A-C-G-T-A) duplex

Two-dimensional homonuclear and heteronuclear NMR and minimized potential energy calculations have been combined to define the structure of the antitumor agent mitomycin C (MC) cross-linked to deoxyguanosines on adjacent base pairs in the d(T1-A2-C3-G4-T5-A6).d(T7-A8-C9-G10-T11-A12) duplex. The majority of the mitomycin and nucleic acid protons in the MC-X 6-mer complex have been assigned from through-bond and through-space two-dimensional proton NMR studies in aqueous solution at 5 and 20 degrees C. The C3.G10 and G4.C9 base pairs are intact at the cross-link site and stack on each other in the complex. The amino protons of G4 and G10 resonate at 9.36 and 8.87 ppm and exhibit slow exchange with solvent H2O. The NMR experimental data establish that the mitomycin is cross-linked to the DNA through the amino groups of G4 and G10 and is positioned in the minor groove. The conformation of the cross-link site is defined by a set of NOEs between the mitomycin H1" and H2" protons and the nucleic acid imino and amino protons of G4 and the H2 proton of A8 and another set of NOEs between the mitomycin geminal H10" protons and the nucleic acid imino and amino protons of G10 and the H2 proton of A2. Several phosphorus resonances of the d(T-A-C-G-T-A) duplex shift dramatically on mitomycin cross-link formation and have been assigned from proton-detected phosphorus-proton two-dimensional correlation experiments. The proton chemical shifts and NOEs establish fraying at the ends of the d(T-A-C-G-T-A) duplex, and this feature is retained on mitomycin cross-link formation. The base-base and base-sugar NOEs exhibit similar patterns for symmetry-related steps on the two nucleic acid strands in the MC-X 6-mer complex, while the proton and phosphorus chemical shifts are dramatically perturbed at the G10-T11 step on cross-link formation. The NMR distance constraints have been included in minimized potential energy computations on the MC-X 6-mer complex. These computations were undertaken with the nonplanar five-membered ring of mitomycin in each of two pucker orientations. The resulting low-energy structures MX1 and MX2 have the mitomycin cross-linked in a widened minor groove with the chromophore ring system in the vicinity of the G10-T11 step on one of the two strands in the duplex.(ABSTRACT TRUNCATED AT 400 WORDS)

Functional irregularities of short-term and long-term memory storage in patients with Parkinson's disease and Huntington's disease

Memory performance of Parkinson's disease patients (PD patients). Huntington's disease patients (HD patients) and healthy subjects were compared by a single-trial free recall task following the presentation of a stimulus list consisting of 30 nouns. The patient groups were categorized according to the severity of the disease into mild, moderate, and severe. Healthy subjects reproduced significantly more words than PD and HD patients, while the two patient groups did not differ in the total number of words reproduced. The differences between healthy and demented subjects are attributed to the impaired functional capacity of long-term memory; there were significant differences between healthy subjects and patients as well as between PD and HD patients. When taking the severity of the disease into consideration, varied influence on the capacity of long-term memory for PD and HD patients was found. Concerning short-term memory, neither a difference between healthy subjects and patients nor between both patient groups could be established. An effect of the severity of the disease could not be proven.

Memory characteristics in Parkinson's disease

With regard to Parkinson's disease there are contradictory opinions concerning whether the severity of the disease, the patient's age, or the application of aids influence the patient's short term memory. In a 4 X 2 X 2 semifactorial design these conditions were tested on 24 healthy persons and 72 patients suffering from Parkinson's disease. The stimulus material consisted of 30 nouns belonging to 6 categories. The severity of the disease, the age of the patients, and the interaction between severity and assistance determined conditions of the patient's memory achievement.