Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening

The dynamic character of proteins strongly influences biomolecular recognition mechanisms. With the development of the main models of ligand recognition (lock-and-key, induced fit, conformational selection theories), the role of protein plasticity has become increasingly relevant. In particular, major structural changes concerning large deviations of protein backbones, and slight movements such as side chain rotations are now carefully considered in drug discovery and development. It is of great interest to identify multiple protein conformations as preliminary step in a screening campaign. Protein flexibility has been widely investigated, in terms of both local and global motions, in two diverse biological systems. On one side, Replica Exchange Molecular Dynamics has been exploited as enhanced sampling method to collect multiple conformations of Lactate Dehydrogenase A (LDHA), an emerging anticancer target. The aim of this project was the development of an Ensemble-based Virtual Screening protocol, in order to find novel potent inhibitors. On the other side, a preliminary study concerning the local flexibility of Opioid Receptors has been carried out through ALiBERO approach, an iterative method based on Elastic Network-Normal Mode Analysis and Monte Carlo sampling. Comparison of the Virtual Screening performances by using single or multiple conformations confirmed that the inclusion of protein flexibility in screening protocols has a positive effect on the probability to early recognize novel or known active compounds.

The application of a new psychotherapeutic strategy for enhancing eudaimonic well-being in children with mood and anxiety disorders

The aim of the dissertation was to test the feasibility of a new psychotherapeutic protocol for treating children and adolescents with mood and anxiety disorders: Child-Well-Being Therapy (CWBT). It originates from adult Well-Being Therapy protocol (WBT) and represents a conceptual innovation for treating affective disorders. WBT is based on the multidimensional model of well-being postulated by Ryff (eudaimonic perspective), in sequential combination with cognitive-behavioral therapy (CBT). Results showed that eudaimonic well-being was impaired in children with affective disorders in comparison with matched healthy students. A first open investigation aimed at exploring the feasibility of a 8-session CWBT protocol in a group of children with emotional and behavioural disorders has been implemented. Data showed how CWBT resulted associated to symptoms reduction, together with the decrease of externalizing problems, maintained at 1-year follow-up. CWBT triggered also an improvement in psychological well-being as well as an increasing flourishing trajectory over time. Subsequently, a modified and extended version of CWBT (12-sessions) has been developed and then tested in a controlled study with 34 patients (8 to 16 years) affected by mood and anxiety disorders. They were consecutively randomized into 3 different groups: CWBT, CBT, 6-month waiting list (WL). Both treatments resulted effective in decreasing distress and in improving well-being. Moreover, CWBT was associated with higher improvement in anxiety and showed a greater recovery rate (83%) than CBT (54%). Both groups maintained beneficial effects and CWBT group displayed a lower level of distress as well as a higher positive trend in well-being scores over time. Findings need to be interpret with caution, because of study limitations, however important clinical implications emerged. Further investigations should determine whether the sequential integration of well-being and symptom-oriented strategies could play an important role in children and adolescents’ psychotherapeutic options, fostering a successful adaptation to adversities during the growth process.

Ottimizzazione di un protocollo di anticoagulazione regionale con citrato in CRRT

Ottimizzazione di un protocollo di anticoagulazione regionale con citrato in CRRT Introduzione: La necessità di un'anticoagulazione continua e l'ipofosforemia in corso di trattamento sono problemi costranti in corso di CRRT. Il nostro studio ha cercato di dimostrare l'efficacia e la sicurezza dell'anticoagulazione regionale con citrato in CVVH basato sull'utilizzo di una soluzione di citrato (18 mmol/L) associata ad una soluzione di reinfusione contenente fosfato, recentemente disponibile in commercio, al fine di ridurre l'ipofosfatemia in corso di CRRT. Metodi: Abbiamo utilizzato il nostro protocollo basato sull'utilizzo di una concentrazione di citrato contenente 18 mmol/l associata ad una soluzione di reinfusione contenente fosfato in un piccolo gruppo di pazienti ricoverati in terapia intensiva post-cardiochirurgica, sottoposti a CRRT per insufficienza renale acuta. Risultati: Il nostro protocollo ha garantito un'adeguata durata del circuito ed un ottimo controllo dell'equilibrio acido-base in ogni paziente. E' stata necessaria solo una minima supplementazione di fosforo in alcuni dei pazienti trattati. Conclusioni: Il nostro protocollo basato sull' utilizzo di una soluzione a concentrazione di citrato maggiore (18 mmol/l), permette un miglior controllo dell'equilibrio acido-base rispetto all'utilizzo della soluzione a più bassa concentrazione di citrato. L'uso di una minore dose di citrato ed il mantenimento di un target maggiore di calcio ionizzato all'interno del circuito sono comunque associati ad un'adeguata durata del circuito. I livelli di fosforemia sono rimasti sostanzialmente stabili nella maggior parte dei pazienti trattati, grazie alla presenza di fosfato nella soluzione utilizzata come reinfusione in post-diluizione.

New Application of Piezoelectric Ultrasounds in Maxillo-facial bone surgery

Background: Piezoelectric instrumentation seems to offer 3 important advantages for cutting bone structures. Be more precise because it is produced by micro-vibrations from the cutting insert. Be safer because the ultrasonic frequency used does not affect soft tissue. Thirdly, the less invasive cutting action produces minor tissue damage and consequently probably a better healing Aim of the Study: The aim of this study is to evaluate the effectiveness of piezoelectric device capability in maxillo-facial surgery, in order to take advantage of these favourable capacity. Material and Methods: Considering the several potential application of the piezoelectric technology in Orthognathic, Oncologic and Extractive surgery, we would like to design protocols in order to verify how this new device can modify the surgical technique, the surgical time, the patients healing and its quality of life. Results: Due to the precise Piezosurgery cut, we can manage the Cad-Cam-Custom Made plates protocol in Oncologic Surgery and in Orthognatic Surgery increasing our percentage of comparison between the 3D preoperative plan and the surgical execution. We also found a better quality of life impaction in Patient who underwent and extractive surgery Conclusion: Piezosurgery device seems to be a strong surgical aid were safe and precise cut are needed and its capability to reduce the discomfort Patients need to be study in deep also in major surgery like Orthognatic and Oncologic surgery.

Connectivity management and dynamic context grouping in mobile heterogenous systems

In the last 10 years the number of mobile devices has grown rapidly. Each person usually brings at least two personal devices and researchers says that in a near future this number could raise up to ten devices per person. Moreover, all the devices are becoming more integrated to our life than in the past, therefore the amount of data exchanged increases accordingly to the improvement of people's lifestyle. This is what researchers call Internet of Things. Thus, in the future there will be more than 60 billions of nodes and the current infrastructure is not ready to keep track of all the exchanges of data between them. Therefore, infrastructure improvements have been proposed in the last years, like MobileIP and HIP in order to facilitate the exchange of packets in mobility, however none of them have been optimized for the purpose. In the last years, researchers from Mid Sweden University created The MediaSense Framework. Initially, this framework was based on the Chord protocol in order to route packets in a big network, but the most important change has been the introduction of PGrids in order to create the Overlay and the persistence. Thanks to this technology, a lookup in the trie takes up to 0.5*log(N), where N is the total number of nodes in the network. This result could be improved by further optimizations on the management of the nodes, for example by the dynamic creation of groups of nodes. Moreover, since the nodes move, an underlaying support for connectivity management is needed. SCTP has been selected as one of the most promising upcoming standards for simultaneous multiple connection's management.

Pancuronium dose refinement in experimental pigs used in cardiovascular research

To quantify the dose of pancuronium required to obtain moderate neuromuscular blockade as monitored by acceleromyography (NMB(mod) : train-of-four count of ≤2) as a part of a balanced anaesthetic protocol in pigs used in cardiovascular research.

Genitourinary applications of diffusion-weighted MR imaging in the pelvis

Diffusion-weighted (DW) magnetic resonance (MR) imaging has a large number of potential clinical applications in the female and male pelvis and can easily be added to any routine MR protocol. In the female pelvis, DW imaging allows improvement of staging in endometrial and cervical cancer, especially in locally advanced disease and in patients in whom contrast medium administration should be avoided. It can also be helpful in characterizing complex adnexal masses and in depicting recurrent tumor after treatment of various gynecologic malignancies. DW imaging shows promising results in monitoring treatment response in patients undergoing radiation therapy of cervical cancer. An increase in apparent diffusion coefficient (ADC) values of responders precedes changes in size and may therefore allow early assessment of treatment success. In the male pelvis, the detection of prostate cancer in the peripheral zone is relatively easier than in the central gland based on the underlying ADC values, whereas overlapping values reported in the central gland still need further research. DW imaging might also be applied in the noninvasive evaluation of bladder cancer to differentiate between superficial and muscle-invasive tumors. Initial promising results have been reported in differentiating benign from malignant pelvic lymph nodes based on the ADC values; however, larger-scale studies will be needed to allow the detection of lymph node metastases in an individual patient. Prerequisites for successfully performing DW imaging of the female and male pelvis are standardization of the DW imaging technique, including the choice of b values, administration of an antiperistaltic drug, and comparison of DW findings with those of morphologic MR imaging.

Nerve excitability changes in critical illness polyneuropathy

Patients in intensive care units frequently suffer muscle weakness and atrophy due to critical illness polyneuropathy (CIP), an axonal neuropathy associated with systemic inflammatory response syndrome and multiple organ failure. CIP is a frequent and serious complication of intensive care that delays weaning from mechanical ventilation and increases mortality. The pathogenesis of CIP is not well understood and no specific therapy is available. The aim of this project was to use nerve excitability testing to investigate the changes in axonal membrane properties occurring in CIP. Ten patients (aged 37-76 years; 7 males, 3 females) were studied with electrophysiologically proven CIP. The median nerve was stimulated at the wrist and compound action potentials were recorded from abductor pollicis brevis muscle. Strength-duration time constant, threshold electrotonus, current-threshold relationship and recovery cycle (refractoriness, superexcitability and late subexcitability) were recorded using a recently described protocol. In eight patients a follow-up investigation was performed. All patients underwent clinical examination and laboratory investigations. Compared with age-matched normal controls (20 subjects; aged 38-79 years; 7 males, 13 females), CIP patients exhibited reduced superexcitability at 7 ms, from -22.3 +/- 1.6% to -7.6 +/- 3.1% (mean +/- SE, P approximately 0.0001) and increased accommodation to depolarizing (P < 0.01) and hyperpolarizing currents (P < 0.01), indicating membrane depolarization. Superexcitability was reduced both in patients with renal failure and without renal failure. In the former, superexcitability correlated with serum potassium (R = 0.88), and late subexcitability was also reduced (as also occurs owing to hyperkalaemia in patients with chronic renal failure). In patients without renal failure, late subexcitability was normal, and the signs of membrane depolarization correlated with raised serum bicarbonate and base excess, indicating compensated respiratory acidosis. It is inferred that motor axons in these CIP patients are depolarized, in part because of raised extracellular potassium, and in part because of hypoperfusion. The chronic membrane depolarization may contribute to the development of neuropathy.

Gene expression in working skeletal muscle

A number of molecular tools enable us to study the mechanisms of muscle plasticity. Ideally, this research is conducted in view of the structural and functional consequences of the exercise-induced changes in gene expression. Muscle cells are able to detect mechanical, metabolic, neuronal and hormonal signals which are transduced over multiple pathways to the muscle genome. Exercise activates many signaling cascades--the individual characteristic of the stress leading to a specific response of a network of signaling pathways. Signaling typically results in the transcription of multiple early genes among those of the well known for and jun family, as well as many other transcription factors. These bind to the promoter regions of downstream genes initiating the structural response of muscle tissue. While signaling is a matter of minutes, early genes are activated over hours leading to a second wave of transcript adjustments of structure genes that can then be effective over days. Repeated exercise sessions thus lead to a concerted accretion of mRNAs which upon translation results in a corresponding protein accretion. On the structural level, the protein accretion manifests itself for instance as an increase in mitochondrial volume upon endurance training or an increase in myofibrillar proteins upon strength training. A single exercise stimulus carries a molecular signature which is typical both for the type of stimulus (i.e. endurance vs. strength) as well as the actual condition of muscle tissue (i.e. untrained vs. trained). Likewise, it is clearly possible to distinguish a molecular signature of an expressional adaptation when hypoxic stress is added to a regular endurance exercise protocol in well-trained endurance athletes. It therefore seems feasible to use molecular tools to judge the properties of an exercise stimulus much earlier and at a finer level than is possible with conventional functional or structural techniques.

Suitability comparison of rainwater harvesting and piped water systems in the Dominican Republic

Rainwater harvesting (RWH) has a long history and has been supported as an appropriate technology and relatively cheap source of domestic water supply. This study compares the suitability of RWH and piped water systems in three rural Dominican communities seeking to improve their water systems. Ethnographic methods considering the views of residents and feasibility and cost analysis of the options were used to conclude that RWH is not a feasible or cost-effective solution for domestic water needs of all households in the communities studied. RWH investment is best left to individual households that can implement informal RWH with incremental increases in storage volume. Piped water distribution (PWD) systems perceived as too large or expensive to implement have much lower capital costs and are more supported by residents as a solution because they provide large quantities of water needed to maintain water services beyond mere survival levels.

Myocardial salvage through coronary collateral growth by granulocyte colony-stimulating factor in chronic coronary artery disease: a controlled randomized trial

BACKGROUND: The efficacy of granulocyte colony-stimulating factor (G-CSF) for coronary collateral growth promotion and thus impending myocardial salvage has not been studied so far, to our best knowledge. METHODS AND RESULTS: In 52 patients with chronic stable coronary artery disease, age 62+/-11 years, the effect on a marker of myocardial infarct size (ECG ST segment elevation) and on quantitative collateral function during a 1-minute coronary balloon occlusion was tested in a randomized, placebo-controlled, double-blind fashion. The study protocol before coronary intervention consisted of occlusive surface and intracoronary lead ECG recording as well as collateral flow index (CFI, no unit) measurement in a stenotic and a > or =1 normal coronary artery before and after a 2-week period with subcutaneous G-CSF (10 microg/kg; n=26) or placebo (n=26). The CFI was determined by simultaneous measurement of mean aortic, distal coronary occlusive, and central venous pressure. The ECG ST segment elevation >0.1 mV disappeared significantly more often in response to G-CSF (11/53 vessels; 21%) than to placebo (0/55 vessels; P=0.0005), and simultaneously, CFI changed from 0.121+/-0.087 at baseline to 0.166+/-0.086 at follow-up in the G-CSF group, and from 0.152+/-0.082 to 0.131+/-0.071 in the placebo group (P<0.0001 for interaction of treatment and time). The absolute change in CFI from baseline to follow-up amounted to +0.049+/-0.062 in the G-CSF group and to -0.010+/-0.060 in the placebo group (P<0.0001). CONCLUSIONS: Subcutaneous G-CSF is efficacious during a short-term protocol in improving signs of myocardial salvage by coronary collateral growth promotion.

Molecular Surface Features in Modeling the HIV-1 RT Inhibitory Activity of 2-(2,6-Disubstituted phenyl)-3-(substituted pyrimidin-2-yl)-thiazolidin-4-ones

The human immunodeficiency virus-1 reverse transcriptase inhibitory activity of 2-(2,6-disubstituted phenyl)-3-(substituted pyrimidin-2-yl)-thiazolidin-4-ones have been analyzed using combinatorial protocol in multiple linear regression (CP-MLR) with several electronic and molecular surface area features of the compounds obtained from Molecular Operating Environment (MOE) software. The study has indicated the role of different charged molecular surface areas in modeling the inhibitory activity of the compounds. The derived models collectively suggested that the compounds should be compact without bulky substitutions on its peripheries for better HIV-1 RT inhibitory activity. It also emphasized the necessity of hydrophobicity and compact structural features for their activity. The scope of the descriptors identified for these analogues have been verified by extending the dataset with different 2-(disubstituted phenyl)-3-(substituted pyridin-2-yl)-thiazolidin-4-ones. The joint analysis of extended dataset highlighted the information content of identified descriptors in modeling the HIV-1 RT inhibitory activity of the compounds.

CP-MLR Directed QSAR Studies on the Antimycobacterial Activity of Functionalised Alkenols - Topological Descriptors in Modeling the Activity

The antimycobacterial activity of nitro/ acetamido alkenol derivatives and chloro/ amino alkenol derivatives has been analyzed through combinatorial protocol in multiple linear regression (CP-MLR) using different topological descriptors obtained from Dragon software. Among the topological descriptor classes considered in the study, the activity is correlated with simple topological descriptors (TOPO) and more complex 2D autocorrelation descriptors (2DAUTO). In model building the descriptors from other classes, that is, empirical, constitutional, molecular walk counts, modified Burden eigenvalues and Galvez topological charge indices have made secondary contribution in association with TOPO and / or 2DAUTO classes. The structure-activity correlations obtained with the TOPO descriptors suggest that less branched and saturated structural templates would be better for the activity. For both the series of compounds, in 2DAUTO the activity has been correlated to the descriptors having mass, volume and/ or polarizability as weighting component. In these two series of compounds, however, the regression coefficients of the descriptors have opposite arithmetic signs with respect to one another. Outwardly these two series of compounds appear very similar. But in terms of activity they belong to different segments of descriptor-activity profiles. This difference in the activity of these two series of compounds may be mainly due to the spacing difference between the C1 (also C6) substituents and rest of the functional groups in them.

Topological Descriptors in Modeling the HIV Inhibitory Activity of 2-Aryl-3-pyridyl-thiazolidin-4-ones

The HIV-1 RT inhibitory activity of 2-(2,6-dihalophenyl)-3-(substituted pyridin-2-yl)-thiazolidin-4-ones has been analyzed with different topological descriptors obtained from DRAGON software. Here, simple topological descriptors (TOPO), Galvez topological charge indices (GVZ) and 2D autocorrelation descriptors (2DAUTO) have been found to yield good predictive models for the activity of these compounds. The correlations obtained from the TOPO class descriptors suggest that less extended or compact saturated structural templates would be better for the activity. The participating GVZ class descriptors suggest that they have same degree of influence on the activity. In 2DAUTO class, the large participation of descriptors of lags seven and three indicate the association of activity information with the seven and three centered structural fragments of these compounds. The physicochemical weighting components of these descriptors suggest homogeneous influence of mass, volume, electronegativity and/ or polarizability on the activity.

Topological Descriptors in Modeling the Antimalarial Activity of 4-(3’, 5’-Disubstitutedanilino)quinolines

Two series of closely related antimalarial agents, 7-chloro-4-(3’,5’-disubstitutedanilino) quinolines, have been analyzed using Combinatorial Protocol in Multiple Linear Regression (CP-MLR) for the structure-activity relations with more than 450 topological descriptors for each set. The study clearly suggested that 3’- and 5’- substituents of the anilino moiety map different domains in the activity space. While one domain favors the compact structural frames having aromatic, heterocyclic ring(s) substituted with closely spaced F, NO2 and O functional groups, the other prefers structural frames enriched with unsaturation, loops, branches, electronic content and devoid of carbonyl function. Also, this study gives an indication in favour of the electron rich centres in the aniline substituent groups for better antimalarial activity; an observation in line with several of the previous reports too. The models developed and the participating descriptors suggest that the substituent groups of the 4-anilino moiety of the 4-(3’, 5’-disubstitutedanilino)quinolines hold scope for further modification in the optimisation of the antimalarial activity.