Measuring Ultrashort Laser Pulses Using Frequency-Resolved Optical Gating in Conjunction with Genetic and Iterative Algorithms

Precise ultrashort light pulse measurements are critical in many physics experiments using ultrafast lasers. A Frequency-Resolved Optical Gating (FROG) system can efficiently and accurately record these desired measurements. FROGs split the input laser beam, delay half of the beam, and overlap both halves in a nonlinear medium. The resulting beam allows the retrieval of phase and duration information. A data file is created by the FROG software that includes beam intensity measurements. By using genetic and iterative algorithms, the intensity data can be manipulated in order to retrieve the pulse duration and phase information. One focus of this research was to align the FROG and crosscheck the measurements with a commercially-built FROG. The other component of this research was to determine a way to interpret intensity data from the laser using genetic and iterative algorithms together. Correct interpretations of the intensity data result in pulse duration and phase measurements

Kinase-independent phosphoramidate S1P1 receptor agonist benzyl ether derivatives

Previously published S1P receptor modulator benzyl ether derivatives have shown potential as being viable therapeutics for the treatment of neurodegenerative diseases, however, two of the most S1P1-selective compounds are reported as being poorly phosphorylated by kinases in vivo. Phosphoramidates of BED compounds (2a, 2b) were synthesised with the aim of producing kinase-independent S1P receptor modulators. Carboxypeptidase, human serum and cell lysate processing experiments were conducted. ProTide BED analogues were found to have an acceptable level of stability in acidic and basic conditions and in vitro metabolic processing experiments showed that they are processed to the desired pharmacologically active monophosphate. The research describes the development of an entirely novel family of therapeutic agents

The molecular determinants of small-molecule ligand binding at P2X receptors

P2X receptors are trimeric eukaryotic ATP-gated cation channels. Extracellular ATP - their physiological ligand - is released as a neurotransmitter and in conditions of cell damage such as inflammation, and substantial evidence implicates P2X receptors in diseases including neuropathic pain, cancer and arthritis. In 2009, the first P2X crystal structure, Danio rerio P2X4 in the apo- state, was published, and this was followed in 2012 by the ATP-bound structure. These structures transformed our understanding of the conformational changes induced by ATP binding and the mechanism of ligand specificity, and enabled homology modelling of mammalian P2X receptors for ligand docking and rational design of receptor modulators. P2X receptors are attractive drug targets, and a wide array of potent, subtype-selective modulators (mostly antagonists) have been developed. In 2016, crystal structures of human P2X3 in complex with the competitive antagonists TNP-ATP and A-317491, and Ailuropoda melanoleuca P2X7 in complex with a series of allosteric antagonists were published, giving fascinating insights into the mechanism of channel antagonism. In this article we not only summarize current understanding of small-molecule modulator binding at P2X receptors, but also use this information in combination with previously published structure-function data and molecular docking experiments, to hypothesise a role for the dorsal fin loop region in differential ATP potency, and describe novel, testable binding conformations for both the semi-selective synthetic P2X7 agonist 2’-(3’)-O-(4-benzoyl)benzoyl ATP (BzATP), and the P2X4-selective positive allosteric modulator ivermectin. We find that the distal benzoyl group of BzATP lies in close proximity to Lys-127, a residue previously implicated in BzATP binding to P2X7, potentially explaining the increased potency of BzATP at rat P2X7 receptors. Furthermore, to our knowledge, we present the first molecular docking of ivermectin to rat P2X4 receptors, illustrating a plausible binding conformation between the first and second transmembrane domains which not only tallies with previous mutagenesis studies, but would also likely have the effect of stabilizing the open channel structure, consistent with the mode of action of this positive allosteric modulator. From our docking simulations and analysis of sequence homology we propose a series of mutations likely to confer ivermectin sensitivity to human P2X1

A Comparison of Criminal Sexual Conduct Defendants Based on Victim Age*

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75428/1/j.1556-4029.2007.00571.x.pd

L’applicazione della cluster analysis per la segmentazione dei consumatori e il ruolo del marketing: la ricerca di mercato sulla “Fouta”

Il punto di partenza della tesi è stato l’analisi del contesto di “vendita” potenziale: l’avvento di Internet e l’evoluzione del Web. Vediamo come dal Web 1.0 al 3.0 sono aumentate le forme di interazione, la qualità e la quantità di connessioni che esistono tra gli utenti, mettendo in rilievo i temi della multicanalità e della convergenza digitale, che acquistano così una valenza tangibile quando, ad esempio, acquistiamo con mobile/tablet. Il Web ha portato numerosi cambiamenti, dai mezzi di comunicazione, ai luoghi virtuali come le comunità social, ma hanno soprattutto influenzato i comportamenti e i bisogni dei consumatori, e, conseguentemente, anche il marketing stesso. Vediamo come da una logica di marketing mix che puntava sulle “4P” siamo passati oggi ad una logica delle “4C”, consumatore, costo, convenienza, comunicazione (più contenuto e comunità per gli e-commerce). Un altro esempio può essere rappresentato dalle tecniche di pricing, che ora devono operare online, dal Versioning o Bundling al Dynamic exchange, oppure ancora dalle tecniche di segmentazione che operando sul web cambiano le proprie chiavi di lettura, partendo da dati collezionati online (Webmining) e segmentando attraverso le nuove metriche (KPI). Le modificazioni però sono anche di carattere generale; abbiamo visto infatti come il marketing 3.0 utilizza le leve di comunicazione rivoluzionando il quadro d’azione: il marketing culturale, collaborativo e spirituale. In ognuno di questi contesti diventa importantissimo avere una presenza sociale, sia online che offline. A tal scopo abbiamo specificato l’importanza che acquisisce la social media analysis e le tecniche di search engine per la visibilità delle pagine web. Sono stati così introdotti i concetti di web marketing e web analytics come i nuovi orizzonti in cui operare. Infine sono state introdotte delle considerazioni personali sul futuro del marketing; data l’ingente importanza che ha assunto il contesto, la nascita di nuovi ed efficienti strumenti di vendita, di fruizione delle informazioni e di comunicazione, il web marketing diventerà la leva d’azione del Web 3.0. Questa supposizione ben si associa al concetto di Inbound marketing inteso come tutte le tecniche di marketing che si possono attuare sul web per comunicare fuori dall’azienda (social, blog, video, viral, email ecc.). Successivamente sono stati introdotti gli e-commerce, i volumi d’affari degli ultimi anni, e una profilazione del potenziale consumatore online italiano. Prima di arrivare a questo prototipo però abbiamo analizzato un livello ancora più generale, parlando dei consumatori del web, di come si sono rivoluzionati i bisogni (da Maslow alla piramide COSMA), di come agiscono le logiche di problem solving e di vendita sul web e di come si comportano gli stessi consumatori di fronte a pagine web e venditori online. Una volta definiti dettagliatamente il contesto, i consumatori e il marketing, siamo passati ad descrivere il prodotto preso in esame per attuare la ricerca di mercato: la “Fouta”. Per questo bene sono state descritte le caratteristiche, il target, le tematiche di distribuzione, con l’inserimento di potenziali matrici di posizionamento ed infine il prezzo. Una volta introdotto il prodotto siamo passati alla ricerca di mercato vera e propria. La ricerca è stata divisa in un’analisi quantitativa ed una qualitativa di ricerca. La fase qualitativa implica l’utilizzo del Focus Group per generare idee e capire gli atteggiamenti legati al prodotto, sia per un’analisi preliminare, sia per la stipulazione facilitata di un questionario. L’analisi quantitativa invece parte dalla spiegazione delle tecniche d’indagine vera e propria, come ad esempio il campionamento. Una volta spiegato come sono stati ottenuti i dati, sono stati analizzati. Sono stati calcolati diversi indici per il calcolo delle relazioni tra variabili e sono state descritte più approfonditamente le relazioni con alta significatività, sia in termini statistici che di importanza strategica. Terminata l’analisi descrittiva si è proceduto alla creazione dei cluster per la segmentazione della clientela. Sono state esposte le motivazioni che hanno portato ad utilizzare la cluster analysis per la ricerca, cioè il bisogno di trovare segmenti di consumatori con caratteristiche simili all’interno e caratteristiche diverse tra i gruppi stessi al fine di un utilizzo molto più efficiente del marketing in una logica di marketing differenziato one to one. Nel secondo capitolo sono stati esposti i concetti di distanza e similarità e le cluster analysis gerarchica e non gerarchica. Sono stati individuati i cluster, costruiti tramite il software SPSS, ognuno con caratteristiche distinte. Nel terzo capitolo infine sono stati riportati i risultati tradotti in termini di marketing, cioè le basi per la creazione delle strategie di marketing (il target e il marketing mix). Dalla ricerca si sono evinti un consumatore medio, che rappresenta il target di una strategia di marketing concentrata, e diversi gruppi di consumatori necessari per attuare una strategia differenziata

Erratum to ‘Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni’:[IJP Drugs Drug Resist. 8 (2018) 559–570]

Schistosomiasis endangers the lives of greater than 200 million people every year and is predominantly controlled by a single class chemotherapy, praziquantel (PZQ). Development of PZQ replacement (to combat the threat of PZQ insensitivity/resistance arising) or combinatorial (to facilitate the killing of PZQ-insensitive juvenile schistosomes) chemotherapies would help sustain this control strategy into the future. Here, we re-categorise two families of druggable epigenetic targets in Schistosoma mansoni, the histone methyltransferases (HMTs) and the histone demethylases (HDMs). Amongst these, a S. mansoni Lysine Specific Demethylase 1 (SmLSD1, Smp_150560) homolog was selected for further analyses. Homology modelling of SmLSD1 and in silico docking of greater than four thousand putative inhibitors identified seven (L1 – L7) showing more favourable binding to the target pocket of SmLSD1 vs Homo sapiens HsLSD1; six of these seven (L1 – L6) plus three structural analogues of L7 (L8 – L10) were subsequently screened against schistosomula using the Roboworm anthelmintic discovery platform. The most active compounds (L10 - pirarubicin > L8 – danunorubicin hydrochloride) were subsequently tested against juvenile (3 wk old) and mature (7 wk old) schistosome stages and found to impede motility, suppress egg production and affect tegumental surfaces. When compared to a surrogate human cell line (HepG2), a moderate window of selectivity was observed for the most active compound L10 (selectivity indices - 11 for schistosomula, 9 for juveniles, 1.5 for adults). Finally, RNA interference of SmLSD1 recapitulated the egg-laying defect of schistosomes co-cultivated in the presence of L10 and L8. These preliminary results suggest that SmLSD1 represents an attractive new target for schistosomiasis; identification of more potent and selective SmLSD1 compounds, however, is essential. Nevertheless, the approaches described herein highlight an interdisciplinary strategy for selecting and screening novel/repositioned anti-schistosomals, which can be applied to any druggable (epigenetic) target encoded by the parasite's genome. Keywords: Anthelmintic drug discovery, Neglected tropical diseases, Schistosoma mansoni, Epigenetics, Lysine specific demethylas

Antivirals in medical biodefense

The viruses historically implicated or currently considered as candidates for misuse in bioterrorist events are poxviruses, filoviruses, bunyaviruses, orthomyxoviruses, paramyxoviruses and a number of arboviruses causing encephalitis, including alpha- and flaviviruses. All these viruses are of concern for public health services when they occur in natural outbreaks or emerge in unvaccinated populations. Recent events and intelligence reports point to a growing risk of dangerous biological agents being used for nefarious purposes. Public health responses effective in natural outbreaks of infectious disease may not be sufficient to deal with the severe consequences of a deliberate release of such agents. One important aspect of countermeasures against viral biothreat agents are the antiviral treatment options available for use in post-exposure prophylaxis. These issues were adressed by the organizers of the 16th Medical Biodefense Conference, held in Munich in 2018, in a special session on the development of drugs to treat infections with viruses currently perceived as a threat to societies or associated with a potential for misuse as biothreat agents. This review will outline the state-of-the-art methods in antivirals research discussed and provide an overview of antiviral compounds in the pipeline that are already approved for use or still under development

Modeling Epac1 interactions with the allosteric inhibitor AM-001 by co-solvent molecular dynamics

The exchange proteins activated by cAMP (EPAC) are implicated in a large variety of physiological processes and they are considered as promising targets for a wide range of therapeutic applications. Several recent reports provided evidence for the therapeutic effectiveness of the inhibiting EPAC1 activity cardiac diseases. In that context, we recently characterized a selective EPAC1 antagonist named AM-001. This compound was featured by a non-competitive mechanism of action but the localization of its allosteric site to EPAC1 structure has yet to be investigated. Therefore, we performed cosolvent molecular dynamics with the aim to identify a suitable allosteric binding site. Then, the docking and molecular dynamics were used to determine the binding of the AM-001 to the regions highlighted by cosolvent molecular dynamics for EPAC1. These analyses led us to the identification of a suitable allosteric AM-001 binding pocket at EPAC1. As a model validation, we also evaluated the binding poses of the available AM-001 analogues, with a different biological potency. Finally, the complex EPAC1 with AM-001 bound at the putative allosteric site was further refined by molecular dynamics. The principal component analysis led us to identify the protein motion that resulted in an inactive like conformation upon the allosteric inhibitor binding