The accelerated weight histogram method for alchemical free energy calculations

The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.

Effects of sodium bicarbonate infusion on mortality in medical-surgical ICU patients with metabolic acidosis-A single-center propensity score matched analysis

OBJECTIVE

Metabolic acidosis is associated with high mortality. Despite theoretical benefits of sodium-bicarbonate (SB), current evidence remains controversial. We investigated SB-related effects on outcomes in ICU patients with metabolic acidosis.

DESIGN

Retrospective analysis.

SETTING

Academic medical center.

PATIENTS OR PARTICIPANTS

971 ICU patients with metabolic acidosis defined as arterial pH<7.3 and CO2<45mmHg treated between 2012 and 2016. A propensity score (PS) was estimated using logistic regression. Patients were matched in pairs using the PS.

INTERVENTIONS

441 patients were treated with SB 8.4% (SB-group) and n=530 patients were not (control group).

MAIN VARIABLES OF INTEREST

Primary outcome was all-cause mortality at ICU-discharge. Average Treatment Effect (ATE), Average Treatment effect in Treated (ATT), and estimated relative survival effects at 20 days were computed.

RESULTS

In the full cohort, we observed considerable differences in pH, base excess, additional acidosis-related indices, and ICU mortality (controls 31% vs. SB-group 56%, p<.001) at baseline between the two groups. After PS-matching (n=174 in each group), no significant difference in ICU mortality was observed (controls 32% vs. SB-group 41%; p=.07). Odds ratios (OR) for ATE and ATT showed no association with ICU mortality (OR ATE: 1.08, 95%-CI 0.99-1.17; p=.08; OR ATT 1.09; 95%-CI 0.99-1.2; p=.09). Hazard ratios at 20-days (multivariable HR, matched sample n=348: 1.16, 95%-CI 0.86-1.56, p=.33) showed similar survival in the two study groups.

CONCLUSIONS

We did not observe effects of SB infusion on all-cause mortality in critically ill patients with metabolic acidosis.

Chaotic properties of spin lattices near second-order phase transitions

We perform a numerical investigation of the Lyapunov spectra of chaotic dynamics in lattices of classical spins in the vicinity of second-order ferromagnetic and antiferromagnetic phase transitions. On the basis of this investigation, we identify a characteristic of the shape of the Lyapunov spectra, the "G-index," which exhibits a sharp peak as a function of temperature at the phase transition, provided the order parameter is capable of sufficiently strong dynamic fluctuations. As part of this work, we also propose a general numerical algorithm for determining the temperature in many-particle systems, where kinetic energy is not defined.

Accelerated weight histogram method for exploring free energy landscapes

Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

Oscillatory Oxidation of Malonic Acid by Bromate

At room temperature the chemical reaction between malonic acid (0.2 M) and KBrO3 (0.06 м) in 1 м H2SO4 is catalysed by cerium ions. The oscillation of the yellow Ce4+ ions can be observed directly during the reaction. By silica-gel chromatography the brominated products of the reaction have been identified as dibromoacetic acid and bromomalonic acid.

Oscillatory Oxidation of Malonic Acid by Bromate

In order to elucidate the reaction scheme of the oscillatory malonic acid-KBrO3system in sulphuric acid the products extracted from the reaction system by ether are analysed by gas chromatography and mass spectrometry. After 2 hours reaction time implying approx. 80 to 100 cycles malonic acid, monobromomalonic acid and dibromoacetic acid are identified in a relative ratio of about 1.0, 0.14 and 0.023.

Effect of congenital heart defects on language development in toddlers with Down syndrome

BACKGROUND

Down syndrome (DS, OMIM #190685) is the most commonly identified genetic form of intellectual disability with congenital heart defect (CHD) occurring in 50% of cases. With advances in surgical techniques and an increasing lifespan, this has necessitated a greater understanding of the neurodevelopmental consequences of CHDs. Herein, we explore the impact of CHD on language development in children with DS.

METHODS

Twenty-nine children with DS were observed systematically in parent-child interactions using the Communication Play Protocol to evaluate their language use; they also completed the Mullen Scales of Early Learning and MacArthur Communication Development Inventory. Mean ages were 31.2 months for children with DS and CHD (DS + CHD, n = 12) and 32.1 months for children with DS and a structurally normal heart (DS - CHD, n = 17).

RESULTS

Compared with the DS - CHD controls, the DS + CHD group revealed lower scores in multiple areas, including fine motor skills and expressive and receptive vocabulary. Whereas most differences were not statistically significant, the Communication Development Inventory word count and symbol-infused joint engagement differed significantly (P < 0.01) and marginally (P = 0.09) between groups.

CONCLUSIONS

Finding that CHDs may account for part of the variation in language delay allows us to consider the specific mechanisms underlying the impact of CHDs on language acquisition in children with DS. Conclusions from this first study on early language outcomes of children with DS + CHD may be useful for clinicians in providing developmental surveillance and early intervention programmes with specific emphasis on language therapy as part of long-term follow-up for children with DS + CHD.

Self-organization in living cells: networks of protein machines and nonequilibrium soft matter

Microscopic self-organization phenomena inside a living cell should not represent merely a reduced copy of self-organization in macroscopic systems. A cell is populated by active protein machines that communicate via small molecules diffusing through the cytoplasm. Mutual synchronization of machine cycles can spontaneously develop in such networks - an effect which is similar to coherent laser generation. On the other hand, an interplay between reactions, diffusion and phase transitions in biological soft matter may lead to the formation of stationary or traveling nonequilibrium nanoscale structures.

Largest Lyapunov exponents for lattices of interacting classical spins

We investigate how generic the onset of chaos in interacting many-body classical systems is in the context of lattices of classical spins with nearest-neighbor anisotropic couplings. Seven large lattices in different spatial dimensions were considered. For each lattice, more than 2000 largest Lyapunov exponents for randomly sampled Hamiltonians were numerically computed. Our results strongly suggest the absence of integrable nearest-neighbor Hamiltonians for the infinite lattices except for the trivial Ising case. In the vicinity of the Ising case, the largest Lyapunov exponents exhibit a power-law growth, while further away they become rather weakly sensitive to the Hamiltonian anisotropy. We also provide an analytical derivation of these results.

An approximate model for cancellous bone screw fixation

This paper presents a finite element (FE) model to identify parameters that affect the performance of an improved cancellous bone screw fixation technique, and hence potentially improve fracture treatment. In cancellous bone of low apparent density, it can be difficult to achieve adequate screw fixation and hence provide stable fracture fixation that enables bone healing. Data from predictive FE models indicate that cements can have a significant potential to improve screw holding power in cancellous bone. These FE models are used to demonstrate the key parameters that determine pull-out strength in a variety of screw, bone and cement set-ups, and to compare the effectiveness of different configurations. The paper concludes that significant advantages, up to an order of magnitude, in screw pull-out strength in cancellous bone might be gained by the appropriate use of a currently approved calcium phosphate cement.

[Medical management of acute renal colic - there is more than hydration and Buscopan®...]

Renal colic is generated by hyperperistalsis of the obstructed ureter. Peristalsis is modulated by (among others) alpha-receptors (contraction), beta-receptors (relaxation) and prostaglandins (PG F2alpha: contraction, PG E1/E2: relaxation). Non-steroidal anti-inflammatory drugs (NSAID) are highly effective in pain relief and should always be given in the absence of contraindications. The same is true for metamizole, whereas Buscopan® is not superior to placebo. For most severe pain, opioids are indicated. alpha-blockers and calcium channel blockers dilate the distal ureter and increase the likelihood of spontaneous stone passage by up to 65%. Overhydration of patients has no advantage, but carries the risk of pelvic rupture with urine extravasation and infection. Stones of/above diameter 7 mm are unlikely to pass spontaneously and should be interventionally removed.

The structure of the core of the spiral wave in the belousov-zhabotinskii reaction

The quantitative structure of the core of the spiral-shaped traveling wave of chemical activity appearing in a thin excitable layer of the Belousov-Zhabotinskii reaction, in which the oxidation and decarboxylation of malonic acid by bromate ions is catalyzed by ferroin, was analyzed experimentally. Light absorption by ferroin as the reduced reaction catalyst and indicator was measured by means of a video-and computer-based two-dimensional spectrophotometer with 10-micrometer spatial, 2-second temporal, and 256-digital units intensity resolution. The spiral core is a singular site (diameter, 30 micrometers or less) at which intensity modulations due to ferroin-ferriin distributions are at least ten times smaller than in the surrounding area of spiral propagation. Archimedian spirals were fitted to isoconcentration lines.

Critical size and curvature of wave formation in an excitable chemical medium

The critical radius for the outward propagation of waves in an excitable solution of the Belousov-Zhabotinskii reaction was experimentally analyzed and found to be approximately 20 mum, being in a range predicted by theory. Thus, the wave initiation depends on the critical radius in an all-or-none fashion. For waves having high positive curvature of wave fronts, a linear relationship between the curvature and their normal velocity was established, allowing computation of a diffusion coefficient of 1.9 x 10(-5) cm(2)/s for the autocatalytic species, which agrees well with results previously obtained for negatively curved wave fronts. The analysis of the dispersion of wave velocity yielded the decrease of wave velocity for small initiation periods as predicted theoretically.

Transitions between oscillatory modes in a glycolytic model system

A glycolytic model system consisting of the enzymes phosphofructokinase (EC 2.7.1.11) and pyruvate kinase (EC 2.7.1.40) is analyzed when subject to periodic substrate addition. The calculations are performed by using detailed rate laws that have been derived for the enzymes of Escherichia coli. Due to linear relationships between the metabolite concentrations, the numerical solutions can be displayed inside a trapezium, so that the concentrations of four different metabolites are indicated along the trapezium edges. The analysis reveals a rich variety of time patterns, corresponding to different periodic, quasiperiodic, and chaotic attractors. These patterns undergo complex hysteresis loops when bifurcation parameters are slowly changed-for example, by modulating the input amplitude. By using this technique up to four attractors coexisting in phase space are found. The time patterns corresponding to coexisting attractors can be switched into one another by triggering the system with short substrate pulses. Furthermore, conditions exist at which the triggering is autonomous-i.e., self-sustained (intermittent) switchings occur. The time between these switchings can be set externally by the value of the input amplitude. For conditions in which the periods of the oscillations are in the order of minutes, the self-sustained switching-which modulates these oscillations-can be in the order of hours.

Influence of an electrical potential on the charge transfer kinetics of bacteriorhodopsin

The adsorption of bacteriorhodopsin(bR)-containing purple membranes (PM) to black lipid membranes (BLM) was used to study the charge translocation kinetics of bR upon flash excitation.The discharge of the PM-BLM system after charging upon illumination is found to proceed quite slowly (discharge time up to several minutes) but is considerably accelerated by addition of the protonophore FCCP.Therefore, the dependence of the proton transfer kinetics in bR on electrical potentials generated by preceding flashes of varying repetition rate and intensity was investigated. The kinetics are slowed down with increasing flash intensity as well as repetition rate. This effect is partly abolished by small amounts of FCCP.A new model is introduced which takes into account the instantaneous feedback of the electrical potential on the kinetics of the pump current. It explains the observed deviations from first-order kinetics and renders an approach with "distributed kinetics" unnecessary.

The value of phytoestrogens as a possible therapeutic option in postmenopausal women with coronary heart disease

Large epidemiological studies have proved that the risk of coronary heart disease in postmenopausal women can be decreased by oestrogen replacement therapy. The effect is triggered by metabolic processes in the liver (decrease of LDL-cholesterol, increase of HDL-cholesterol) as well as by direct impact on the arterial wall (anti-oxidation, relaxation, anti-proliferation). The therapeutical usage of oestrogens is limited by an increased incidence of breast and endometrial cancer. Cyclic application of progestogens virtually eliminates the risk. Unfortunately, progestogens may antagonise the atheroprotective effect of oestrogens. Structurally modified oestrogens as well as selective oestrogen receptor modulators were investigated in clinical trials. They might provide the desired atheroprotective effects of oestrogen without negative side effects on the mammary gland or the endometrium. In this respect isoflavones also known as phytoestrogens, were analysed. They are widespread and occur naturally in many plants, especially in soy products. Cell culture and animal experiments as well as clinical studies revealed that phytoestrogens such as genistein and daidzein act atheroprotectively in the same way as oestrogen. Effects on the mammary gland or the endometrium could not be detected, but positive side effects on the bone metabolism and the decrease of certain types of cancer could be observed. In total, the therapeutical application of phytoestrogens in postmenopausal women seems to be of real and great benefit. We conclude that in women the risk of death from coronary heart disease increases after the onset of menopause. Recently discovered properties of phyto-oestrogens seem to be of great benefit as they do not seem to have any side effects on the mammary gland and the endometrium which are limiting factors for oestrogen replacement therapy.

Energy utilization for control

When, on addition of a suitable substrate, a chemical potential is applied to an enzymic process such as glycolysis or respiration, whether in solution or membrane-bound, all components of the process pass into a nonequilibrium state, which might be steady or non-steady and which produces the following phenomena: (1) The reactants of each enzymic reaction are displaced from their equilibrium concentration, and energy is dissipated; (2) Part of each enzyme is transferred to a transition state of its catalytic function as well as isosteric and allosteric controlling functions, displaying local and gross conformation changes, and a rate-controlling state is generated; (3) In cyclic portions of a process futile events and chemical interconversion may occur; (4) In self- and cross-coupled portions of a process, oscillation with periodic changes of states and spatial propagation as well as instabilities may be observed; (5) At each step of a process, depending on the rate of flux and the specific enzymic function, a varying proportion of the free energy changes--which are concentration-dependent and derived from the overall potential of the system-is contributed to the control of flux rates. This will be exemplified for enzymes of bioenergetic pathways.

Properties of strange attractors in yeast glycolysis

The properties of periodic and aperiodic glycolytic oscillations observed in yeast extracts under sinusoidal glucose input were analyzed by the following methods. (1) Spectral analysis, rendering sharp peaks for periodic responses and enhanced broad-band noise for aperiodic oscillations. (2) Phase plane analysis, leading to closed and to open trajectories for periodic and aperiodic oscillations, respectively. (3) Rotation of a phase plane proportionally to time, revealing strange attractors associated with the aperiodic oscillations. (4) Stroboscopic plot on the phase plane, showing that the strange attractors follow a stretch-fold-press process, if the stroboscoping phase is varied. (5) Stroboscopic transfer plot, admitting a period of three transfer processes and thus implying chaos according to the Li-Yorke theorem. (6) Determination of the rate of information production by differentiation of the transfer plot, yielding approx. 0.21 bits per min for the chaotically glycolyzing yeast extract.

[Health economic consequences of the use of irbesartan in patients with type 2 diabetes, hypertension and nephropathy in Switzerland]

The irbesartan in Diabetic Nephropathy Trial (IDNT) demonstrated that treatment of patients with type 2 diabetes, hypertension and nephropathy with irbesartan resulted in a 20% relative reduction of the composite endpoint of doubling serum creatinine, end-stage renal disease or death as compared with amlodipine and placebo (antihypertensive standard therapy). The objective of this study was to investigate the long-term health economic consequences of this treatment strategy in a Swiss health care setting. This analysis used a Markov model to simulate the progression of nephropathy, life-years and treatment costs over ten years for each of the three treatment options. In additon, sensitivity analyses were performed. Treatment with irbesartan will save CHF 22681/patient as compared with amlodipine and CHF 13847 as compared with standard therapy.

Preventive treatment of nephrolithiasis with alkali citrate—a critical review

Using the keywords "urolithiasis and citrate treatment", "nephrolithaisis and citrate treatment", "kidney stones and citrate treatment", a Medline search revealed 635 articles published between 1 January 1966 and 1 December 2004. For the present analysis, only studies meeting all of the following criteria were included: (1) publications in English or German, (2) studies on preventive alkali citrate treatment in patients with calcium oxalate, uric acid and infection stone disease, (3) clinical studies including at least ten subjects, and (4) treatment phases of at least 1 week duration. A total of 43 studies met the inclusion criteria and were further subclassified according to intermediate or ultimate endpoints as well as to study design. With stone recurrence as the ultimate endpoint, 21 uncontrolled studies in almost 1,000 patients demonstrated a reduction in stone forming rate by 47-100%. In four randomized controlled trials including 227 patients, 53.5% on alkali citrate vs 35% on placebo remained stone-free after at least 1 year of treatment (P<0.0005). Similar values (66% vs 27.5% for alkali citrate vs placebo, P<0.0005) were obtained in 104 patients from two randomized trials with dissolution/clearance of residual stones as endpoint. Unfortunately, up to 48% of alkali citrate treated patients left the studies prematurely, primarily due to adverse effects such as eructation, bloating, gaseousness or frank diarrhea.

Orientation restraints in molecular dynamics simulations using time and ensemble averaging

In this article we present methodology for simulating protein dynamics while imposing restraints derived from NMR measurements on partially ordered molecules. Such measurements may include residual dipolar couplings and chemical-shift anisotropies. We define a restraint potential for use in molecular dynamics and energy minimization. The presented potential is consistent with the simultaneously optimized molecular order tensor. Restraining can be performed with time and ensemble averaging. We performed a large number of molecular dynamics simulations of the histidine containing phosphocarrier protein with restraints on backbone N-H vector orientations derived from residual dipolar couplings. From these simulations it is evident that the use of time- or ensemble-averaged restraints is essential to leave the fluctuations of the restrained vectors unaffected. Without averaging the fluctuations of the restrained vectors are reduced significantly. This also has the effect of decreasing the apparent molecular order-parameter tensor.

[Pathophysiology, diagnosis and conservative therapy in calcium kidney calculi]

Annual incidences of kidney stones are about 0.1-0.4% of the population, and lifetime prevalences in the USA and Europe range between 8 and 15%. Kidney stones occur more frequently with increasing age and among men. Within ten years, the disease usually recurs in more than 50% of patients. Nowadays, about 85% of all kidney stones contain calcium salts (calcium oxalate and/or calcium phosphate) as their main crystalline components. Because human urine is commonly supersaturated with respect to calcium salts as well as to uric acid, crystalluria is very common, i.e. healthy people excrete up to ten millions of microcrystals every day. Recurrent stone formers appear to excrete lower amounts or structurally defective forms of crystallization inhibitors which allows for the formation of large crystal aggregates as precursors of stones. Alternatively, crystal adhesion to urothelial surfaces may be enhanced in stone formers. Medical treatment of renal colic is based on nonsteroidal antiinflammatory drugs, because prostaglandins appear to play a crucial role in the pathophysiology of pain during ureteral obstruction. In addition, centrally acting analgesics such as pethidine-HCl may be required in many cases. The administration of high amounts (3-4 liters/day) of intravenous fluids should be abandoned, since it may raise intraureteral pressure whereby pain increases and kidney pelvis or fornices may rupture. All first-stone formers should undergo a simple basic evaluation, including stone analysis (x-ray diffraction or infrared spectrometry), serum values of ionized calcium (alternatively: total calcium and albumin) and creatinine, urinalysis and repeated measurements of fasting urine pH in order to detect urinary acidification disorders or low urine pH. In high-risk patients with as first stone episode (i.e. strongly positive family history, inflammatory bowel disease, short-bowel syndrome, nephrocalcinosis, bilateral stones, hypercalcemia, renal tubular acidosis, airline pilots) as well as in all recurrent stone formers, an extended metabolic evaluation should be performed. Two 24-hurines should be collected on free-choice diet not prior to three months after stone passage or urological intervention. Analysis includes measurements of volume, creatinine, calcium, oxalate, uric acid and citrate; sodium and urea as markers of salt and protein consumption are optional but clinically very helpful. Since hypercalciuria is of much less importance than increases in urinary oxalate, therapeutic efforts should primarily focus on lowering urinary oxalate excretion. Sufficient calcium intake, i.e. 1200 mg per day, is crucial, because it allows for binding of oxalate at the intestinal level whereby increases of urinary oxalate (reciprocal hyperoxaluria) can be avoided. Excess intake of flesh protein (meat, fish, poultry) is lithogenic since it increases urinary calcium, oxalate and uric acid, and lower citrate. On the other hand, a diet rich in alkali (vegetables, fruit) is associated with a lower risk of stone formation. A "common sense diet" containing sufficient amounts of fluids, 1200 mg of calcium per day and reduced amounts of flesh protein as well as salt is able to reduce the 5-year stone recurrence rate in calcium stone formers by 50%. The scientific evidence for drug treatment (thiazides, alkali citrate) is rather poor: the most widely quoted randomized thiazide trial included only 42 patients of whom 36% left the protocol prematurely, whereas 36-48% of patients included in three randomized studies with alkali citrate suffered from undesirable side-effects; nevertheless, citrate therapy reduced the stone recurrence rate by 38%, compared with 22% in patients on placebo treatment (p < 0.0005).

[Diagnostic imaging of calculi in the upper urinary tract--sonography vs. computerized tomography]

The choice of the most suitable technique for radiologic evaluation of upper urinary tract stones depends on the precise clinical questions that have to be answered. Many of these questions can still be answered by plain films of the abdomen and excretory urography. This review addresses the value of ultrasonography and computed tomography (CT) with respect to the two most important clinical questions, i.e. 1) presence/extent of obstruction/hydronephrosis and perinephric abscess in patients with acute flank pain; and 2) precise location, number and size of calculi. Because its sensitivity is comparable with CT and it is widely available, ultrasonography in the hands of experienced clinicians/radiologists may be preferred for evaluation of patients with acute flank pain. However, it must be emphasized that ultrasonography may totally miss acute ureteral obstruction/hydronephrosis within the first 12-24 hours. In children as well as in pregnant women, ultrasonography is still the technique of choice, but it may be replaced by magnetic resonance urography in the future. For precise stone location or detection of calcifications, however, the speed, safety and accuracy of unenhanced helical CT make this the most sensitive method and therefore the technique of choice. It also detects urinary calculi more accurately and exposes patients to less radiation than the traditional combined plain abdominal film/intravenous urography. Furthermore, CT can most readily reveal alternative diagnoses in patients with acute flank pain and other intraabdominal pathologies than stones.

[Pathophysiology, diagnosis and conservative therapy of non-calcium kidney calculi]

While calcium oxalate and calcium phosphate make up at least 80% of all kidney stones, infection-induced and uric acid stones occur in 10% and 8%, respectively. Although any type of stone may become infected, the term "infection stones" means that stone formation exclusively depends on urease-producing bacteria. The splitting of urea leads to a rise in urinary pH which may induce crystallization of struvite (magnesium-ammonium-phosphate), the major constituent of infection stones, or carbonate apatite. Struvite stones account for the majority of staghorn calculi. They can grow quite large and may fill the entire collecting system. Patients with struvite stones may present with acute flank pain or remain completely asymptomatic. The cure of infection stones requires complete removal of the stone material. For uric acid crystallization and stone formation, low urine pH (below 5.5) is a more important risk factor than increased urinary uric acid excretion. Main causes of low urine pH are tubular disorders (including gout), chronic diarrheal states or severe dehydration. Accordingly, the treatment of uric acid stones consists not only of hydration (urine volume above 2000 ml per day), but mainly of urine alkalinization to pH values between 6.2 and 6.8. Urinary uric acid excretion can be reduced by a low-purine diet as well as--in case of recurrent uric acid stones and/or gout--by allopurinol. Cystinuria is a rare hereditary gene disorders with impaired tubular reabsorption of cystine. Stone formation occurs as a consequence of cystine's relatively low solubility at urine pH levels below 8. Only symptomatic diet and drug treatments are currently available, with urine dilution and urine alkalinization being the most efficient ones. Cystine stones respond poorly to shockwave lithotripsy, so that invasive procedures may regularly be necessary. 2,8-dihydroxy-adenine stones occur as a consequence of an enzyme deficiency that involves purine metabolism. These resulting stones are not visible by fluoroscopy and are therefore often misinterpreted as uric acid stones. Low-purine diet and allopurinol reduce the frequency of stone formation.

[Medicamentous kidney protection in type 2 diabetic patients--is cheaper also more economical? A model calculation for Swiss health care]

Impaired renal function occurs in about 50% of patients suffering from type 2 diabetes, and diabetic nephropathy has become the leading cause of endstage renal disease. Reduction of blood pressure to levels around 120/80 mmHg is one of the most effective way to slow progression of diabetic nephropathy. Recent meta-analyses, however, have emphasized on the fact that ACE inhibitors (ACEI) and non-dihydropyridine calcium channel blockers (NDHP-CCB) exert nephro-protective effects which go beyond the effect of blood pressure reduction. This has lately been confirmed by a prospective trial in comparison to the betablocker atenolol. Based on these data, demographics of the Swiss population, literature data on mortality rates of type 2 diabetics with impaired renal function and studies on true costs of antihypertensives, we calculated the costs of a longterm intervention (20 years) with antihypertensives in 3536 middle-aged Swiss patients with type 2 diabetes and macro-albuminuria whose antihypertensive regimen was based either on the ACEI lisinopril, or the ND-HP-CCB verapamil, or the betablocker atenolol. Under atenolol, acquisition costs were lowest, whereas faster loss of renal function over time increased mortality rate and thus reduced the number of patients to be treated. Nevertheless, due to the fact that patients reached uremia and had to be dialyzed, 20 years of atenolol-based regimen with costs of 316 millions of Swiss francs turned out to be much more expensive than the lisinopril- or the verapamil-based regimen with 121 and 38 millions of Swiss francs, respectively. Thus, low acquisition cost is not necessarily the only important determinant of overall costs of drug therapy.

Mhc class I genes of swordtail fishes, Xiphophorus: variation in the number of loci and existence of ancient gene families

Swordtail fishes and platies in the genus Xiphophorus (order Cyprinodontiformes, Teleostei) encompass 22 closely related species which are the products of a recent adaptive radiation in the streams of Central America. To investigate the evolution of the major histocompatibility complex (Mhc) genes in the period immediately following speciation, the class I genes from 20 of the 22 species were cloned and characterized by sequencing. The analysis revealed the existence of multiple loci (at least seven in some individuals) whose numbers vary among the different species and probably also among individuals of the same species. The variation does not seem to bear any relationship to the taxonomy of the genus. Genes at the different loci are distinguished by their intron sequences and by the presence of characteristic motifs in exons 2 and 3. The variation in copy number of loci may have been effected in part by unequal crossing over occurring between introns of misaligned closely related genes. The sequences of the genes fall into two groups, A and B, which represent ancient lineages. The groups define two families of loci, which diverged from each other an estimated 85 million years ago, before the separation of the Acanthopterygii from the Paracanthopterygii of the advanced bony fishes. Evolution of the genes within each family can be explained by the birth-and-death process driven by gene duplications and mutational differentiation.

Methods for measuring crystallization in urolithiasis research: why, how and when?

Whereas crystalluria does not distinguish between kidney stone formers and healthy people and thus can be considered a physiologic event, kidney stone formation is a pathologic incident and reflects a specific form of biomineralization. Both single urinary crystals as well as whole kidney stones form under exquisite control of organic macromolecules. Simple crystal formation in the urinary tract is distinguished from stone formation in the kidney by the process of particle retention. The latter occurs either because nucleated crystals strongly aggregate to particles too large to pass freely through the tubules ('free particle' theory), or because crystals become abnormally adherent to tubular cell surfaces ('fixed particle' theory). Since it is impossible to mimic all the processes involved in stone formation in vitro, it is highly important to carefully chose a specific crystallization process for in vitro studies, and to select the most appropriate experimental conditions for measuring the chosen process as reliably as possible. This overview aims at critically reviewing the principles of currently available assay systems for studying crystallization processes involved in stone formation. Consensus is reached by the experts that no in vitro system really mimics what happens in renal stone formation, but that carefully designed in vitro studies will always play an important part in urolithiasis research. For such studies, it is highly important to exactly control the appropriate experimental conditions that are relevant to a specific crystallization process under investigation. Practical guidelines for researchers working with crystallization systems are provided, and it is concluded that international efforts should be made to standardize the terminology, to agree on a set of basic experimental parameters (temperature, pH, artificial urine composition), and to adopt simple tests or conditions are reference points for quality and comparative control.

Severe, isolated thrombocytopenia under polytherapy with carbamazepine and valproate

It is not known whether polytherapy with carbamazepine (CBZ) and valproate (VPA) increases the risk of thrombocytopenia. A 67-year-old woman with symptomatic epilepsy since age 6 years, classified as Lennox-Gasteau syndrome, developed severe, isolated thrombocytopenia of 5 GIGA/L (normal: 150-360 GIGA/L) after being on CBZ (1200 mg/day) for 15 days and additional VPA (300 mg/day) for 5 days in combination. After discontinuation of CBZ and VPA and two thrombocyte transfusions, the thrombocyte count normalized within 3 days. Because she had been taking VPA for only 5 days in addition to CBZ, it could not be confirmed whether it was CBZ alone or the combination of CBZ and VPA that was responsible for the severe thrombocytopenia.

Effect of testosterone on plaque development and androgen receptor expression in the arterial vessel wall

BACKGROUND

-Recent studies have suggested that testosterone has a protective effect in the arterial vascular system. However, little is known about the molecular aspects of the mechanism(s) involved in these processes. The aim of the present study was to investigate the effect of testosterone on neointimal plaque development and on the expression of the vascular androgen receptor. Methods and Results-Neointimal plaque formation was induced by endothelial denudation in the aortas of male New Zealand White rabbits. Aortic ring segments were cultured for 21 days after endothelial denudation. Testosterone was applied to the culture medium in different doses. Compared with the non-hormone-treated control group, a significant inhibition of neointimal plaque development (expressed as the intima/media ratio) was found at testosterone concentrations of 10 ng/mL (P:=0.037) and 100 ng/mL (P:=0.012; intima/media ratios: median of controls, 0.25; median of 10 ng/mL testosterone group, 0.15; median of 100 ng/mL testosterone group, 0.16). Associated with this inhibitory effect on plaque size was a 50% increase of the amount of androgen receptor mRNA in the arterial segments treated with testosterone.

CONCLUSION

-The beneficial effects of testosterone on postinjury plaque development underlines, at least in males, the important role of androgens in the vascular system. As our data suggest, the vascular androgen receptor is probably involved in these processes. Further studies are required to characterize the androgen receptor-dependent pathways in the vascular system.

CD8+ T cells recognize an inclusion membrane-associated protein from the vacuolar pathogen Chlamydia trachomatis

During infection with Chlamydia trachomatis, CD8(+) T cells are primed, even though the bacteria remain confined to a host cell vacuole throughout their developmental cycle. Because CD8(+) T cells recognize antigens processed from cytosolic proteins, the Chlamydia antigens recognized by these CD8(+) T cells very likely have access to the host cell cytoplasm during infection. The identity of these C. trachomatis proteins has remained elusive, even though their localization suggests they may play important roles in the biology of the organism. Here we use a retroviral expression system to identify Cap1, a 31-kDa protein from C. trachomatis recognized by protective CD8(+) T cells. Cap1 contains no strong homology to any known protein. Immunofluorescence microscopy by using Cap1-specific antibody demonstrates that this protein is localized to the vacuolar membrane. Cap1 is virtually identical among the human C. trachomatis serovars, suggesting that a vaccine incorporating Cap1 might enable the vaccine to protect against all C. trachomatis serovars. The identification of proteins such as Cap1 that associate with the inclusion membrane will be required to fully understand the interaction of C. trachomatis with its host cell.

Endovascular irradiation with the liquid beta-emitter Rhenium-188 to reduce restenosis after experimental wall injury

OBJECTIVE

Postinterventional irradiation is a new therapeutic concept in the prevention of restenosis. The liquid beta-emitter Rhenium-188 allows endovascular brachytherapy using a conventional balloon catheter without the problem of centering the radiation source. In an animal model of restenosis the feasibility and the dose dependent effect of intravascular brachytherapy with a Rhenium-188 filled balloon catheter was investigated.

METHODS

In 68 male New Zealand White rabbits after endothelial denudation of the right common carotid artery with a Fogarty catheter, endovascular irradiation was performed with a Rhenium-188 filled 3.0-mm balloon catheter using different dosages (0, 7.5, 15, 30, 45 and 60 Gy at the surface of the vessel). Then 4 weeks after the intervention the vessels were excised and histologically analyzed.

RESULTS

Whereas at 7.5 Gy the intimal area (median [first quartile; third quartile]) did not differ significantly from the control (0.46 mm(2) [0.33 mm(2), 0.75 mm(2)] vs. 0.49 mm(2) [0.34 mm(2), 0.66 mm(2)]), neointimal hyperplasia was decreased significantly at 15 Gy (0.15 mm(2) [0.04 mm(2), 0.17 mm(2)]) and 30 Gy (0.07 mm(2) [0.04 mm(2), 0. 10 mm(2)]), and completely inhibited at the highest dosages (45 Gy: 0 mm(2) [0 mm(2), 0.04 mm(2)]; 60 Gy: 0 mm(2) [0 mm(2), 0.01 mm(2)]).

CONCLUSIONS

Catheter transmitted endovascular irradiation with the liquid beta-emitter Rhenium-188 after vascular injury is feasible and effectively reduced neointimal hyperplasia in hypercholesterolemic rabbits. A significant reduction of the neointimal formation could be found already at a radiation absorbed dose of 15 Gy at the vessel surface. Following a surface dosage of 45 Gy the proliferative response to the vessel injury is almost completely abolished.

Similarities between principal components of protein dynamics and random diffusion

Principal component analysis, also called essential dynamics, is a powerful tool for finding global, correlated motions in atomic simulations of macromolecules. It has become an established technique for analyzing molecular dynamics simulations of proteins. The first few principal components of simulations of large proteins often resemble cosines. We derive the principal components for high-dimensional random diffusion, which are almost perfect cosines. This resemblance between protein simulations and noise implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.