Regularized Bennett and Zwanzig free energy estimators

We consider the problem of free energy estimation from the general perspective of regularization and Bayes estimation theory. We try to take advantage of an assumed a priori knowledge of the free energy. We reformulate the original Bennett acceptance ratio method, in this perspective, devise a numerical algorithm to solve it, and give a closed formula to estimate the confidence in the prior. Finally, we test the derived estimators by applying them to a toy model.

Optimal Transport for Free Energy Estimation

Optimal transport theory is a growing field of mathematics, which has recently found many applications. Here we take advantage of optimal transport for computational free energy estimation. We show analytically, and then via simulation, that this approach is effective in terms of optimizing the barriers of an alchemical transformation.

Computational analysis of the effect of [Tea][Ms] and [Tea][H2PO4] ionic liquids on the structure and stability of Aβ(17-42) amyloid fibrils

Experimental studies have reported the possibility of affecting the growth/dissolution of amyloid fibres by the addition of organic salts of the room-temperature ionic-liquid family, raising the tantalizing prospect of controlling these processes under physiological conditions. The effect of [Tea][Ms] and [Tea][H₂PO₄] at various concentrations on the structure and stability of a simple model of Aβ42 fibrils has been investigated by computational means. Free energy computations show that both [Tea][Ms] and [Tea][H₂PO₄] decrease the stability of fibrils with respect to isolated peptides in solution, and the effect is significantly stronger for [Tea][Ms]. The secondary structure of fibrils is not much affected, but single peptides in solution show a marked decrease in their β-strand character and an increase in α-propensity, again especially for [Tea][Ms]. These observations, consistent with the experimental picture, can be traced to two primary effects, i.e., the difference in the ionicity of the [Tea][Ms] and [Tea][H₂PO₄] water solutions and the remarkable affinity of peptides for [Ms]^- anions, due to the multiplicity of H-bonds.

Using Principal Paths to Walk Through Music and Visual Art Style Spaces Induced by Convolutional Neural Networks

Computational intelligence, particularly deep learning, offers powerful tools for discriminating and generating samples such as images. Deep learning methods have been used in different artistic contexts for neural style transfer, artistic style recognition, and musical genre recognition. Using a constrained manifold analysis protocol, we discuss to what extent spaces induced by deep-learning convolutional neural networks can capture historical/stylistic progressions in music and visual art. We use a path-finding algorithm, called principal path, to move from one point to another. We apply it to the vector space induced by convolutional neural networks. We perform experiments with visual artworks and songs, considering a subset of classes. Within this simplified scenario, we recover a reasonable historical/stylistic progression in several cases. We use the principal path algorithm to conduct an evolutionary analysis of vector spaces induced by convolutional neural networks. We perform several experiments in the visual art and music spaces. The principal path algorithm finds reasonable connections between visual artworks and songs from different styles/genres with respect to the historical evolution when a subset of classes is considered. This approach could be used in many areas to extract evolutionary information from an arbitrary high-dimensional space and deliver interesting cognitive insights.

Solubility Advantage of Amorphous Ketoprofen. Thermodynamic and Kinetic Aspects by Molecular Dynamics and Free Energy Approaches

Thermodynamic and kinetic aspects of crystalline (c-KTP) and amorphous (a-KTP) ketoprofen dissolution in water have been investigated by molecular dynamics simulation focusing on free energy properties. Absolute free energies of all relevant species and phases have been determined by thermodynamic integration on a novel path, first connecting the harmonic to the anharmonic system Hamiltonian at low T and then extending the result to the temperature of interest. The free energy required to transfer one ketoprofen molecule from the crystal to the solution is in fair agreement with the experimental value. The absolute free energy of the amorphous form is 19.58 kJ/mol higher than for the crystal, greatly enhancing the ketoprofen concentration in water, although as a metastable species in supersaturated solution. The kinetics of the dissolution process has been analyzed by computing the free energy profile along a reaction coordinate bringing one ketoprofen molecule from the crystal or amorphous phase to the solvated state. This computation confirms that, compared to the crystal form, the dissolution rate is nearly 7 orders of magnitude faster for the amorphous form, providing one further advantage to the latter in terms of bioavailability. The problem of drug solubility, of great practical importance, is used here as a test bed for a refined method to compute absolute free energies, which could be of great interest in biophysics and drug discovery in particular.

Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (N = 4532)

Background

Cell entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) depends on binding of the viral spike (S) proteins to angiotensin-converting enzyme 2 and on S protein priming by TMPRSS2. Inhibition of TMPRSS2 may work to block or decrease the severity of SARS-CoV-2 infections. Intriguingly, TMPRSS2 is an androgen-regulated gene that is up-regulated in prostate cancer where it supports tumor progression and is involved in a frequent genetic translocation with the ERG gene. First- or second-generation androgen-deprivation therapies (ADTs) decrease the levels of TMPRSS2. Here we put forward the hypothesis that ADTs may protect patients affected by prostate cancer from SARS-CoV-2 infections.

Materials and methods

We extracted data regarding 9280 patients (4532 males) with laboratory-confirmed SARS-CoV-2 infection from 68 hospitals in Veneto, one of the Italian regions that was most affected by the coronavirus disease 2019 (COVID-19) pandemic. The parameters used for each COVID-19-positive patient were sex, hospitalization, admission to intensive care unit, death, tumor diagnosis, prostate cancer diagnosis, and ADT.

Results

There were evaluable 9280 SARS-CoV-2-positive patients in Veneto on 1 April 2020. Overall, males developed more severe complications, were more frequently hospitalized, and had a worse clinical outcome than females. Considering only the Veneto male population (2.4 million men), 0.2% and 0.3% of non-cancer and cancer patients, respectively, tested positive for SARS-CoV-2. Comparing the total number of SARS-CoV-2-positive cases, prostate cancer patients receiving ADT had a significantly lower risk of SARS-CoV-2 infection compared with patients who did not receive ADT (OR 4.05; 95% CI 1.55–10.59). A greater difference was found comparing prostate cancer patients receiving ADT with patients with any other type of cancer (OR 4.86; 95% CI 1.88–12.56).

Conclusion

Our data suggest that cancer patients have an increased risk of SARS-CoV-2 infections compared with non-cancer patients. However, prostate cancer patients receiving ADT appear to be partially protected from SARS-CoV-2 infections.

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SARS-CoV-2-infected men have a worse clinical outcome than women.

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Cancer patients have an increased risk of SARS-CoV-2 infection.

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Prostate cancer patients receiving androgen-deprivation therapies appear to be partially protected from the infection.

Oral administration of modified live canine parvovirus type 2b induces systemic immune response

Different strategies have been proposed to overcome maternally derived antibody (MDA) interference with canine parvovirus type 2 (CPV-2) immunisation, including intranasal vaccination, which presents some practical limitations. In the present study, the results of the oral administration of a commercial CPV-2b modified live virus (MLV) vaccine in pups with MDA are reported. The CPV-2b vaccine was orally administered to 14 6-week-old pups with a bait. Blood samples and rectal swabs were collected at different days post-vaccination (dpv) to determine CPV-2 antibody titres and DNA loads. Thirteen pups were positive to serological and virological tests after the first vaccination and one pup became positive after the second vaccine administration. The findings of this study suggest that systemic immunity against CPV-2 may be achieved by the use of an MLV CPV-2b vaccine administered orally even in the presence of MDA titres that usually interfere with vaccination.

Tumor Markers and Lung Cancer: Guidelines in a Cost-limited Medical Organization

The aim of our study was to evaluate the cost of the tumor marker assays most widely used in pneumological practive and the effectiveness of the percentage of DRG-based reimbursements absorbed by these assays.

For this purpose we assessed the cost of lung tumor marker assays in Emilia Romagna compared to the DRG-based reimbursement of inpatients affected by lung diseases in whom the use of tumor markers is indicated.

As an example, we evaluated the cost/effectiveness of the CEA assay in the differential diagnosis of 68 pleural effusions from 46 patients (20 benign diseases, 26 malignant).

Because the CEA assay was not a substitute for cytology when this was not diagnostic, 41.3% of the resources were not efficiently spent. If the marker assay had been performed only in cases with negative cytology, we could have spared 14 of 46 tests.

Moreover, since the expense lies predominantly in the cost of reagents (81.23%), we suggest as a routine procedure to collect and store samples for tumor marker assay in all cases; the test should be performed in a selected population of patients with negative cytology and “suspect” clinical outcome.

Effective Surface Passivation of InP Nanowires by Atomic-Layer-Deposited Al2O3 with POx Interlayer

III/V semiconductor nanostructures have significant potential in device applications, but effective surface passivation is critical due to their large surface-to-volume ratio. For InP such passivation has proven particularly difficult, with substantial depassivation generally observed following dielectric deposition on InP surfaces. We present a novel approach based on passivation with a phosphorus-rich interfacial oxide deposited using a low-temperature process, which is critical to avoid P-desorption. For this purpose we have chosen a PO_x layer deposited in a plasma-assisted atomic layer deposition (ALD) system at room temperature. Since PO_x is known to be hygroscopic and therefore unstable in atmosphere, we encapsulate this layer with a thin ALD Al₂O₃ capping layer to form a PO_x/Al₂O₃ stack. This passivation scheme is capable of improving the photoluminescence (PL) efficiency of our state-of-the-art wurtzite (WZ) InP nanowires by a factor of ∼20 at low excitation. If we apply the rate equation analysis advocated by some authors, we derive a PL internal quantum efficiency (IQE) of 75% for our passivated wires at high excitation. Our results indicate that it is more reliable to calculate the IQE as the ratio of the integrated PL intensity at room temperature to that at 10 K. By this means we derive an IQE of 27% for the passivated wires at high excitation (>10 kW cm^-2), which constitutes an unprecedented level of performance for undoped InP nanowires. This conclusion is supported by time-resolved PL decay lifetimes, which are also shown to be significantly higher than previously reported for similar wires. The passivation scheme displays excellent long-term stability (>7 months) and is additionally shown to substantially improve the thermal stability of InP surfaces (>300 °C), significantly expanding the temperature window for device processing. Such effective surface passivation is a key enabling technology for InP nanowire devices such as nanolasers and solar cells.

Protein-ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling

In the last three decades, protein and nucleic acid structure determination and comprehension of the mechanisms, leading to their physiological and pathological functions, have become a cornerstone of biomedical sciences. A deep understanding of the principles governing the fates of cells and tissue at the molecular level has been gained over the years, offering a solid basis for the rational design of drugs aimed at the pharmacological treatment of numerous diseases. Historically, affinity indicators (i.e. Kd and IC50/EC50) have been assumed to be valid indicators of the in vivo efficacy of a drug. However, recent studies pointed out that the kinetics of the drug-receptor binding process could be as important or even more important than affinity in determining the drug efficacy. This eventually led to a growing interest in the characterisation and prediction of the rate constants of protein-ligand association and dissociation. For instance, a drug with a longer residence time can kinetically select a given receptor over another, even if the affinity for both receptors is comparable, thus increasing its therapeutic index. Therefore, understanding the molecular features underlying binding and unbinding processes is of central interest towards the rational control of drug binding kinetics. In this review, we report the theoretical framework behind protein-ligand association and highlight the latest advances in the experimental and computational approaches exploited to investigate the binding kinetics.

Atom-by-Atom Analysis of Semiconductor Nanowires with Parts Per Million Sensitivity

The functionality of semiconductor devices is determined by the incorporation of dopants at concentrations down to the parts per million (ppm) level and below. Optimization of intentional and unintentional impurity doping relies on methods to detect and map the level of impurities. Detecting such low concentrations of impurities in nanostructures is however challenging to date as on the one hand methods used for macroscopic samples cannot be applied due to the inherent small volumes or faceted surfaces and on the other hand conventional microscopic analysis techniques are not sufficiently sensitive. Here, we show that we can detect and map impurities at the ppm level in semiconductor nanowires using atom probe tomography. We develop a method applicable to a wide variety of nanowires relevant for electronic and optical devices. We expect that it will contribute significantly to the further optimization of the synthesis of nanowires, nanostructures and devices based on these structures.

Analytic model for the electrowetting properties of oil-water-solid systems

The competitive wetting of oil and aqueous electrolytes on solid surfaces depends strongly on the surface charge of the solid-water and the water-oil interface. This charge density is generally not known a priori but changes as ions adsorb or desorb from or to the interfaces, depending on the composition of the fluid and the thickness of thin films of the aqueous phase that frequently arise on hydrophilic surfaces, such as minerals. We analyze the wettability of such systems by coupling standard Derjaguin-Landau-Verwey-Overbeek theory to a linearized charge regulation model. The latter is found to play an important role. By linearizing electrostatic interactions as well, we obtain a fully analytic description of transitions between different wetting scenarios as a function of the surface potentials at infinite separation and the charge regulation parameters of the two interfaces. Depending on the specific values of the regulation parameters, charge regulation is found to extend the parameter range of partial wetting and complete wetting at the expense of pseudopartial wetting and metastable wetting configurations, respectively. A specific implementation of the model is discussed for mica-water-alkane systems that was investigated in recent experiments.

Numerical simulation of astigmatic liquid lenses tuned by a stripe electrode

We propose a new design for tuning the astigmatism of liquid micro-lenses using electric field and hydrostatic pressure as control parameters. We explore the feasibility and operating range of the lens with a self-consistent numerical calculation of the electric field distribution and the shape of the two-phase interface. Equilibrium shapes, including surface profiles parallel and perpendicular to a stripe electrode, are extracted to determine the astigmatism. The wavefronts are decomposed into Zernike polynomials under zero defocus conditions using a commercial ray-tracing software. We observe that the global curvature of the lens is primarily controlled by the hydrostatic pressure, while asphericity and astigmatism are controlled by the electric field. For optimized electrode geometries and simultaneous control of pressure and electric fields the astigmatism can be tuned from Z6 = 0…0.38 μm with minor changes in the focal length.

Aryl and heteroaryl N-[4-[4-(2,3-substituted-phenyl)piperazine-1-yl]alkyl]carbamates with improved physico-chemical properties as dual modulators of dopamine D3 receptor and fatty acid amide hydrolase

Improving the physico-chemical profile of a MTDL series.

On the shape of a droplet in a wedge: new insight from electrowetting

The equilibrium morphology of liquid drops exposed to geometric constraints can be rather complex. Even for simple geometries, analytical solutions are scarce. Here, we investigate the equilibrium shape and position of liquid drops confined in the wedge between two solid surfaces at an angle α. Using electrowetting, we control the contact angle and thereby manipulate the shape and the equilibrium position of aqueous drops in ambient oil. In the absence of contact angle hysteresis and buoyancy, we find that the equilibrium shape is given by a truncated sphere, at a position that is determined by the drop volume and the contact angle. At this position, the net normal force between drop and the surfaces vanishes. The effect of buoyancy gives rise to substantial deviations from this equilibrium configuration which we discuss here as well. We eventually show how the geometric constraint and electrowetting can be used to position droplets inside a wedge in a controlled way, without mechanical actuation.

Diameter dependence of the thermal conductivity of InAs nanowires

The diameter dependence of the thermal conductivity of InAs nanowires in the range of 40-1500 nm has been measured. We demonstrate a reduction in thermal conductivity of 80% for 40 nm nanowires, opening the way for further design strategies for nanoscaled thermoelectric materials. Furthermore, we investigate the effect of thermal contact in the most common measurement method for nanoscale thermal conductivity. Our study allows for the determination of the thermal contact using existing measurement setups. The thermal contact resistance is found to be comparable to the wire thermal resistance for wires with a diameter of 90 nm and higher.

Modeling lipid raft domains containing a mono-unsaturated phosphatidylethanolamine species

An advanced coarse-grained model for “atypical” lipid rafts was built and validated to be employed in studies of membrane-protein interactions.

Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations

Small molecules used in fragment-based drug discovery form multiple, promiscuous binding complexes difficult to capture experimentally. Here, we identify such binding poses and their associated energetics and kinetics using molecular dynamics simulations on AmpC β-lactamase. Only one of the crystallographic binding poses was found to be thermodynamically favorable; however, the ligand shows several binding poses within the pocket. This study demonstrates free-binding molecular simulations in the context of fragment-to-lead development and its potential application in drug design.

Low molecular weight, non-peptidic agonists of TrkA receptor with NGF-mimetic activity

Exploitation of the biologic activity of neurotrophins is desirable for medical purposes, but their protein nature intrinsically bears adverse pharmacokinetic properties. Here, we report synthesis and biologic characterization of a novel class of low molecular weight, non-peptidic compounds with NGF (nerve growth factor)-mimetic properties. MT2, a representative compound, bound to Trk (tropomyosin kinase receptor)A chain on NGF-sensitive cells, as well as in cell-free assays, at nanomolar concentrations and induced TrkA autophosphorylation and receptor-mediated internalization. MT2 binding involved at least two amino-acid residues within TrkA molecule. Like NGF, MT2 increased phosphorylation of extracellular signal-regulated kinase 1/2 and Akt proteins and production of MKP-1 phosphatase (dual specificity phosphatase 1), modulated p38 mitogen-activated protein kinase activation,sustained survival of serum-starved PC12 or RDG cells, and promoted their differentiation. However, the intensity of such responses was heterogenous, as the ability of maintaining survival was equally possessed by NGF and MT2, whereas the induction of differentiation was expressed at definitely lower levels by the mimetic. Analysis of TrkA autophosphorylation patterns induced by MT2 revealed a strong tyrosine (Tyr)490 and a limited Tyr785 and Tyr674/675 activation, findings coherent with the observed functional divarication. Consistently, in an NGF-deprived rat hippocampal neuronal model of Alzheimer Disease, MT2 could correct the biochemical abnormalities and sustain cell survival. Thus, NGF mimetics may reveal interesting investigational tools in neurobiology, as well as promising drug candidates.

Low molecular weight, non-peptidic agonists of TrkA receptor with NGF-mimetic activity

Exploitation of the biologic activity of neurotrophins is desirable for medical purposes, but their protein nature intrinsically bears adverse pharmacokinetic properties. Here, we report synthesis and biologic characterization of a novel class of low molecular weight, non-peptidic compounds with NGF (nerve growth factor)-mimetic properties. MT2, a representative compound, bound to Trk (tropomyosin kinase receptor)A chain on NGF-sensitive cells, as well as in cell-free assays, at nanomolar concentrations and induced TrkA autophosphorylation and receptor-mediated internalization. MT2 binding involved at least two amino-acid residues within TrkA molecule. Like NGF, MT2 increased phosphorylation of extracellular signal-regulated kinase1/2 and Akt proteins and production of MKP-1 phosphatase (dual specificity phosphatase 1), modulated p38 mitogen-activated protein kinase activation, sustained survival of serum-starved PC12 or RDG cells, and promoted their differentiation. However, the intensity of such responses was heterogenous, as the ability of maintaining survival was equally possessed by NGF and MT2, whereas the induction of differentiation was expressed at definitely lower levels by the mimetic. Analysis of TrkA autophosphorylation patterns induced by MT2 revealed a strong tyrosine (Tyr)490 and a limited Tyr785 and Tyr674/675 activation, findings coherent with the observed functional divarication. Consistently, in an NGF-deprived rat hippocampal neuronal model of Alzheimer Disease, MT2 could correct the biochemical abnormalities and sustain cell survival. Thus, NGF mimetics may reveal interesting investigational tools in neurobiology, as well as promising drug candidates.

Computational methods in the discovery and design of BACE-1 inhibitors

BACE-1 is a membrane associated aspartyl protease and is one of the enzymes responsible for the hydrolysis of the amyloid precursor protein. Due to its central role in the generation of the amyloid-β peptide, it is considered as a primary drug target for Alzheimer's disease. BACE-1 has been the focus of many drug discovery programs aimed at identifying inhibitors that effectively block this enzyme and trigger the sought therapeutic effects. Thanks to the availability of a large number of crystal structures of the catalytic domain of this enzyme, computational methods, ranging from molecular dynamics simulations, quantum mechanical calculations and ligand docking, have played a fundamental role in almost every hit discovery and hit optimization campaign performed on this target. The present article reviews the latest computational modeling and drug discovery efforts that have been carried out on this target.

Hemodialysis: yesterday, today and tomorrow

Hemodialysis was born in 1945 to treat acute renal failure, and it has progressively become a rescue therapy for patients with chronic kidney disease (CKD) stage 5, otherwise doomed to death. During the years, technological innovations have led to improved dialytic tolerance, making possible to extend the treatment to a greater number of subjects. Low- and high-flux bicarbonate dialysis are nowadays the most frequent hemodialysis techniques; hemodiafiltration with different modalities, short daily and overnight hemo-dialysis are also widespread, each of them with peculiar characteristics. A recent randomized controlled clinical trial has identified high-flux hemodialysis as the best treatment for patients with low serum levels of albumin and for diabetics in comparison to low flux dialysis. Apart from the treatment of end-stage renal disease (ESRD), hemodialysis has new and important applications, including heart failure treatment and multiple myeloma. The need to provide hemodialysis patients a better quality of life has increased the interest in developing new techniques, such as the wearable artificial kidney, although still in initial clinical development. During the last 60 years, we have seen an exciting evolution in the field of hemodialysis, which has led to important changes in the outcome of ESRD patients. The preclinical and clinical hard work ongoing in earlier stages of CKD should be able to obtain further relevant improvements and maybe avoid the need of hemodialysis itself.

[Do convective treatments significantly reduce morbidity and mortality?]

Standard hemodialysis is a far from ideal treatment for uremia since the morbidity and mortality of patients on hemodialysis are still significantly higher than those of non-hemodialyzed subjects with similar demographic characteristics. Because it has been suggested that the cause could lie in the inadequate removal of ''middle molecules'' by standard hemodialyis, two alternative treatments have been proposed: high-efficiency hemodialyis and high-flux hemodialyis. The 2002 results of the HEMO study showed that both these treatments are associated with a non-significant reduction in the relative risk of death (4% and 8%, respectively). The MPO study, which - unlike the HEMO study - enrolled only incident cases and not did not allow reuse of dialyzers, evaluated the mortality rate with high-flux and low-flux hemodialysis in a sicker population, i.e., patients with hypoalbuminemia, and showed a significant reduction in the relative risk of death especially in patients with diabetes. In an attempt to define the clinical impact of hemodiafiltration, some of the efficacy data from clinical studies are reviewed in light of a number of factors that may be related to the high mortality among hemodialysis patients. The current state of affairs suggests it is reasonable to prefer high-flux hemodialysis in sicker patients, especially diabetics. Moreover, the use of ultrapure dialysis fluid is recommended to reduce chronic inflammation and its consequences.

Identification of group A porcine rotavirus strains bearing a novel VP4 (P) Genotype in Italian swine herds

The VP4 gene of a G5 Italian porcine rotavirus strain, 344/04-1, was nontypeable by PCR genotyping. The amino acid sequence of the full-length VP4 protein had low identity (<or=76.6%) with the homologous sequences of representative strains of the remaining P genotypes, providing evidence for a novel P genotype.

Upper airway dynamics during negative expiratory pressure in apneic and non-apneic awake snorers

Background

The ability of negative expiratory pressure (NEP) technique to differentiate between awake snorers with and without obstructive sleep apnea-hypopnea (OSAH) was investigated.

Methods

Forty-eight subjects with sleep disordered breathing (SDB) and 7 healthy subjects, as non-snorer controls, underwent the NEP application of -5 and -7 cmH₂O in the seated and supine position during wakefulness, after performing a sleep study. The upper airway collapsibility was assessed by computing the volume exhaled during the first 0.5 sec. (V,NEP_0.5) and 1 sec. (V,NEP₁) following the NEP start.

Results

Patients with severe (AHI ≥ 30) (n = 19) and mild-to-moderate (AHI <30 and >5) (n = 15) OSAH had lower V,NEP_0.5 (340 ± 88 ml) as compared to snorers (AHI ≤ 5) (n = 14) (427 ± 101 ml; p < 0.01) and controls (n = 7) (492 ± 69 ml; p < 0.001) in the supine position with NEP -5 cmH₂O. Less significant differences among the different groups were observed for V,NEP_0.5 in the seated position with NEP -5 cmH₂O and in both positions with NEP -7 cmH₂O (only OSAH patients vs controls, p < 0.001). Similar results were obtained for V,NEP₁ in either position by using both NEP -5 cmH₂O and -7 cmH₂O. In spite of this, a substantial overlapping of V,NEP_0.5 and V,NEP₁ between snorers and OSAH patients did not allow to identify a reliable diagnostic cut-off level. An inverse correlation with AHI was found for V,NEP_0.5 in the supine position with NEP -5 cmH₂O (r_s = -0.46, p < 0.05) in severe OSAH patients.

Conclusion

The awake OSAH patients exhibit values of V,NEP_0.5 and V,NEP₁ lesser than those of awake snorers. The NEP technique, however, appears to have a limited usefulness as clinical tool for routine screening of the OSAH patients during wakefulness.

Antibody levels and protection to canine parvovirus type 2

The relationship between maternally derived antibody (MDA) levels and protection to canine parvovirus (CPV) infection in pups is reported. Twelve pups with a wide range of haemagglutination inhibiting (HI) titres of MDA to CPV were divided into four groups, with each group balanced for antibody titres. The dogs were inoculated with a field CPV-2b strain and clinical signs, virus shedding and antibody response were assessed. The CPV was not detected in the faeces of dogs with HI titres of 320 at any time. In dogs with HI titres up to 160, active CPV replication after challenge was demonstrated by real-time polymerase chain reaction. The successful infection of dogs with HI titres of 80 and 160 was confirmed by seroconversion, evaluated at day 14 post-infection. These findings demonstrated that CPV infection could also occur in the presence of MDA HI titres (> or =80) usually considered fully protective.

Identification of a novel VP4 genotype carried by a serotype G5 porcine rotavirus strain

Rotavirus genome segment 4, encoding the spike outer capsid VP4 protein, of a porcine rotavirus (PoRV) strain, 134/04-15, identified in Italy was sequenced, and the predicted amino acid (aa) sequence was compared to those of all known VP4 (P) genotypes. The aa sequence of the full-length VP4 protein of the PoRV strain 134/04-15 showed aa identity values ranging from 59.7% (bovine strain KK3, P8[11]) to 86.09% (porcine strain A46, P[13]) with those of the remaining 25 P genotypes. Moreover, aa sequence analysis of the corresponding VP8* trypsin cleavage fragment revealed that the PoRV strain 134/04-15 shared low identity, ranging from 37.52% (bovine strain 993/83, P[17]) to 73.6% (porcine strain MDR-13, P[13]), with those of the remaining 25 P genotypes. Phylogenetic relationships showed that the VP4 of the PoRV strain 134/04-15 shares a common evolutionary origin with porcine P[13] and lapine P[22] rotavirus strains. Additional sequence analyses of the VP7, VP6, and NSP4 genes of the PoRV strain 134/04-15 revealed the highest VP7 aa identity (95.9%) to G5 porcine strains, a porcine-like VP6 within VP6 genogroup I, and a Wa-like (genotype B) NSP4, respectively. Altogether, these results indicate that the PoRV strain 134/04-15 should be considered as prototype of a new VP4 genotype, P[26], and provide further evidence for the vast genetic and antigenic diversity of group A rotaviruses.

Lapine rotaviruses of the genotype P[22] are widespread in Italian rabbitries

An epidemiological survey was carried out to investigate the distribution of the VP7 and VP4 specificities of lapine rotaviruses (LRVs) in rabbitries from different geographical regions of Italy. Almost all the strains were characterized as P[22],G3, confirming the presence of the newly-recognized rotavirus P[22] VP4 allele in Italian rabbits. Only one P[14],G3 LRV strain was identified and two samples contained a mixed (P[14] + [22],G3) rotavirus infection. All the LRV strains analyzed exhibited a genogroup I VP6 specificity and a long dsRNA electropherotype. However, one of the P[14],G3 strains possessed a super-short pattern. Altogether, these data highlight the epidemiological relevance of the P[22] LRVs in Italian rabbitries.

Evaluation of lactogenic immunity to canine parvovirus in pups

Maternally-derived antibodies (MDA) transferred to pups through colostrum and milk are known as lactogenic immunity. In this report, we describe the kinetics of transfer of lactogenic immunity to canine parvovirus type 2 (CPV-2) from two bitches (A and B) to their offspring. At day 7 before parturition, bitches A and B had high serum antibody titers, which decreased rapidly within a few hours after parturition, in concomitance with the appearance of high HI titers in colostrum. Subsequently, the serum antibodies of the two dogs increased again, reaching approximately the initial titers. CPV-specific antibodies were observed in milk, with decreasing values, throughout the lactation period. The kinetics of MDA observed in the pups was consistent with the patterns of absorption and decline previously described.

Molecular analysis of the VP7, VP4, VP6, NSP4, and NSP5/6 genes of a buffalo rotavirus strain: identification of the rare P[3] rhesus rotavirus-like VP4 gene allele

We report the detection and molecular characterization of a rotavirus strain, 10733, isolated from the feces of a buffalo calf affected with diarrhea in Italy. Strain 10733 was classified as a P[3] rotavirus, as the VP8* trypsin cleavage product of the VP4 protein revealed a high amino acid identity (96.2%) with that of rhesus rotavirus strain RRV (P5B[3]), used as the recipient virus in the human-simian reassortant vaccine. Analysis of the VP7 gene product revealed that strain 10733 possessed G6 serotype specificity, a type common in ruminants, with an amino acid identity to G6 rotavirus strains ranging from 88 to 98%, to Venezuelan bovine strain BRV033, and Hungarian human strain Hun4. Phylogenetic analysis based on the VP7 gene of G6 rotaviruses identified at least four lineages and an apparent linkage between each lineage and the VP4 specificity, suggesting the occurrence of repeated interspecies transmissions and genetic reassortment events between ruminant and human rotaviruses. Moreover, strain 10733 displayed a bovine-like NSP4 and NSP5/6 and a subgroup I VP6 specificity, as well as a long electropherotype pattern. The detection of the rare P[3] genotype in ruminants provides additional evidence for the wide genetic and antigenic diversity of group A rotaviruses.

A severe dual infection by feline panleukopenia virus and feline calicivirus in an adult cat

A dual infection by feline panleukopenia virus (FPV) and feline calicivirus (FCV) in a 7 month-old cat is described. The animal developed a severe illness with depression, anorexia, fever, leucopoenia, nasal and ocular discharge and oral ulcers. Both FPV and FCV were isolated in cell cultures from a rectal swab and the presence of FCV was confimed by polymerase chain reaction. Antibodies to both the viruses were detected in the serum. The severity of the disease induced by the mixed viral infection highlights the need for intensifying FPV vaccination in cats.

Quality of generated diagnosis related groups in Italian Respiratory Intermediate Care Units

BACKGROUND

To date we lack official data on tipology of Diagnosis Related Groups (DRGs) and their quality in Italian Respiratory Intermediate Care Units (RICUs).

AIM

The objective of the study was to collect data on the activity of 26 Italian RICUs and to evaluate the quality of the DRGs generated.

METHODS

The primary and secondary diseases, the procedures carried out and their coding using the ICD9 system (valid Italy until 2000) were collected from the discharge forms of patients admitted to RICUs. To obtain the DRG, these codes were automatically recoded in the ICD9-CM classification system by Grouper 10. Afterwards, the same diseases and procedures were directly processed by the ICD9-CM classification system. Finally, in order to evaluate the quality of care, the DRGs generated by the ICD9 classification system were compared to DRGs generated by the ICD9-CM classification system.

RESULTS

The average weight of the patients cared for in an Italian RICU was 2.05 using the ICD9 classification system and 2.53 using the ICD9-CM classification system. Some non-complicated DRGs (80-97) or non specific DRGs (101-102) were set to zero; others, like DRG 87 appear due to the ability of the ICD9-CM classification system to recognise and accept the fifth digit of the Respiratory Failure code (518.81). The difference in terms of DRG scores generated by the two codification systems was 360.5 DRG points in favour of ICD9-CM. More than 1 million Euro of reimbursements have been lost, as the average national reimbursement for each DRG score is Euro 2,943.80.

CONCLUSION

Severe pulmonary diseases determined the case mix of patients cared for in the Italian RICUs during the observed period. The Italian RICUs offer high quality assistance and are characterised by high mean weight per treated patient. However, the activity has been under-estimated due to the low sensitivity of the ICD9 classification system used in the recognition of the real disease and in the correct generation of relative DRG. The ICD9 classification system penalised the recognition of respiratory failure in particular.

Determination of the dissociation constants (pKa) of basic acetylcholinesterase inhibitors by reversed-phase liquid chromatography

An RP-HPLC study for the pKa determination of a series of basic compounds related to caproctamine, a dibenzylaminediamide reversible inhibitor of acetylcholinesterase, is reported. The 2-substituted analogues, bearing substituents with different electronegativity, were analysed by RP-HPLC by using C18 C4 stationary phases with a mobile phase consisting of mixture of acetonitrile and triethylamine phosphate buffer (pH range comprised between 4 and 10). Typical sigmoidal curves were obtained, showing the dependence of the capacity factors upon pH. In general, the retention of the investigated basic analytes increased with increasing of the pH. The inflection point of the pH sigmoidal dependence was used for the dissociation constant determination at a fixed acetonitrile percentage. When plotting pKa vs. percent of acetonitrile in the mobile phase for two representative compounds, linear regression were obtained: the y intercept gave the aqueous pKa(w). The pKa estimation by HPLC method was found to be useful to underline the difference of benzylamine basicity produced by the ortho aromatic substituents. The variation of pKa values (6.15-7.80) within the series of compounds was correlated with the electronic properties of the ortho-substituents through the Hammett sigma parameter, whereas the ability of substituents to accept H-bond was found to play a role in determining the conformational behavior of the molecules.

Stereoselective binding of 2-(4-biphenylyl)-3-substituted-3-hydroxypropionic acids on an immobilised human serum albumin chiral stationary phase

A series of 2-(4-biphenylyl)-3,3'-hydroxy-substituted phenyl propionic acid, with anti-inflammatory properties, bearing two chiral centres, were studied by HPLC upon HSA-CSP (human serum albumin-based chiral stationary phase). The compounds were analysed in their stereoisomeric erythro and threo forms. The study involved the enantioselective analysis on HSA-CSP, the determination of the racemate lipophilicity (log k'(w)), a QSRR (quantitative structure-retention relationship) analysis and CD study for the assessment of the absolute configuration of the most retained enantiomer. Lipophilicity was found to be an important factor affecting the affinity of the compounds for the HSA stationary phase, but electronic properties seemed to play a role. The position of the substituent of the phenyl group on carbon 3 was found important to modulate stereoselective interaction, the highest value of enantioselectivities being found for the erythro ortho-substituted phenyl derivatives. The previously proposed two steps mechanism of enantiodiscrimination for cyclohexylphenyl substituted derivatives was confirmed for this series of derivatives bearing the biphenylyl moiety.

Three-dimensional model of the cyclin-dependent kinase 1 (CDK1): Ab initio active site parameters for molecular dynamics studies of CDKS

Cyclin-dependent kinase 1 (CDK1) is an interesting target for potential anticancer drugs, and its three-dimensional (3D) structure is presently unknown. The purpose of this work was to build a 3D model of CDK1, which could be used in drug design studies. The protein 3D structure was homology modeled, based on the known crystal structure of CDK2, and new nonbonded parameters for the Mg(2+) coordination complex were developed by means of ab initio quantum chemical calculations. These parameters were both obtained and validated using the CDK2 structure as reference, and then they were used for the refinement of the CDK1 model. The resulting CDK1 structure was satisfactory and stable at room temperature, as shown by the molecular dynamics simulations carried out over a 1-ns time interval on the entire protein. A number of representative kinases in the active and inactive form, including the inactive CDK1 modeled in this work, were compared. The results illustrate the conformational variability of the activation loop of the inactive form of the kinases and suggest a way for selectively targeting the single CDKs.

Acetylcholinesterase inhibitors: SAR and kinetic studies on omega-[N-methyl-N-(3-alkylcarbamoyloxyphenyl)methyl]aminoalkoxyaryl derivatives

In this work, we further investigated a class of carbamic cholinesterase inhibitors introduced in a previous paper (Rampa et al. J. Med. Chem. 1998, 41, 3976). Some new omega-[N-methyl-N-(3-alkylcarbamoyloxyphenyl)methyl]aminoalkoxyaryl analogues were designed, synthesized, and evaluated for their inhibitory activity against both acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). The structure of the lead compound (xanthostigmine) was systematically varied with the aim to optimize the different parts of the molecule. Moreover, such a structure-activity relationships (SAR) study was integrated with a kinetic analysis of the mechanism of AChE inhibition for two representative compounds. The structural modifications lead to a compound (12b) showing an IC(50) value for the AChE inhibition of 0.32 +/- 0.09 nM and to a group of BuChE inhibitors also active at the nanomolar level, the most potent of which (15d) was characterized by an IC(50) value of 3.3 +/- 0.4 nM. The kinetic analysis allowed for clarification of the role played by different molecular moieties with regard to the rate of AChE carbamoylation and the duration of inhibition. On the basis of the results presented here, it was concluded that the cholinesterase inhibitors of this class possess promising characteristics in view of a potential development as drugs for the treatment of Alzheimer's disease.

Synthesis and screening for antiacetylcholinesterase activity of (1-benzyl-4-oxopiperidin-3-ylidene)methylindoles and -pyrroles related to donepezil

The design, synthesis, and rapid evaluation of a new class of acetylcholinesterase (AChE) inhibitors related to donepezil are reported. A molecular dynamics simulation of the complex between AChE and one representative compound of the series showed a possible inhibitor binding mode in which favorable interactions are formed between the benzylpiperidinone moiety and some active-site residues. The biochemical evaluation of this newly synthesized series was performed using a chemiluminescent method suitable for high-throughput screening.

Control of the efficiency of agonist-induced information transfer and stability of the ternary complex containing the delta opioid receptor and the alpha subunit of G(i1) by mutation of a receptor/G protein contact interface

Fusion proteins were constructed between the delta opioid receptor and forms of the alpha subunit of G(i1) in which cysteine(351) was mutated to a range of amino acids. GDP reduced the binding of the agonist [(3)H]DADLE but not the antagonist [(3)H]naltrindole to both the receptor alone and all the delta opioid receptor-Cys(351)XaaG(i1)alpha fusion proteins. For the fusion proteins the pEC(50) for GDP was strongly correlated with the n-octanol/H(2)O partition co-efficient of G protein residue(351). Fusion proteins in which this residue was either isoleucine or glycine had similar observed binding kinetics for [(3)H]DADLE. However, the rate of dissociation of [(3)H]DADLE was substantially greater for the glycine-containing fusion protein than that containing isoleucine, indicating that more hydrophobic residues imbued greater stability to the agonist-receptor-G protein ternary complex. This resulted in a higher affinity of binding of [(3)H]DADLE to the fusion protein containing isoleucine(351). In expectation with the binding data, maximal DADLE-stimulated GTP hydrolysis by the isoleucine(351)-containing fusion protein was two-fold greater and the potency of DADLE seven-fold higher than for the version containing glycine. These results demonstrate that the stability of the ternary complex between delta opioid receptor, G(i1)alpha and an agonist (but not antagonist) ligand is dependent upon the nature of residue(351) of the G protein and that this determines the effectiveness of information flow from the receptor to the G protein.