Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

Designing the System of Remote Knowledge Diagnosing for Students of Technical Specialties

In the article the theoretical aspects of planning of the systems of the controlled from distance diagnosing of level of know ledges of students are resulted on the basis of modern pedagogical theoretical and technological approaches. The practical results of creation of the systems of this type are resulted for organization of testing both in the structure of local networks of higher educational establishments and with access through the global network of Internet.

AstroWeb – A Graphical Representation of an Astronomical WFPDB Database Using a Web-Based Open Source Geographical Information System

ACM Computing Classification System (1998): H.5.2, H.2.8, J.2, H.5.3.

Bulgarian Digital Mathematical Library BulDML and Czech Digital Mathematical Library DML-CZ as parts of the European Digital Mathematics Library EuDML

The paper presents in brief the Bulgarian Digital Mathematical Library BulDML and the Czech Digital Mathematical Library DML-CZ. Both libraries use the open source software DSpace and both are partners in the European Digital Mathematics Library EuDML. We describe their content and metadata schemas; outline the architecture system and overview the statistics of its use.

Fifty shades of innovation – from open toward user, and open collaborative forms of innovation – an overview

Starting from the Schumpeterian producer-driven understanding of innovation, followed by user-generated solutions and understanding of collaborative forms of co-creation, scholars investigated the drivers and the nature of interactions underpinning success in various ways. Innovation literature has gone a long way, where open innovation has attracted researchers to investigate problems like compatibilities of external resources, networks of innovation, or open source collaboration. Openness itself has gained various shades in the different strands of literature. In this paper the author provides with an overview and a draft evaluation of the different models of open innovation, illustrated with some empirical findings from various fields drawn from the literature. She points to the relevance of transaction costs affecting viable forms of (open) innovation strategies of firms, and the importance to define the locus of innovation for further analyses of different firm and interaction level formations.

Database-backed library web sites: a case study of the use of PHP and MySQL at the University of Nottingham

This paper discusses the advantages of database-backed websites and describes the model for a library website implemented at the University of Nottingham using open source software, PHP and MySQL. As websites continue to grow in size and complexity it becomes increasingly important to introduce automation to help manage them. It is suggested that a database-backed website offers many advantages over one built from static HTML pages. These include a consistency of style and content, the ability to present different views of the same data, devolved editing and enhanced security. The University of Nottingham Library Services website is described and issues surrounding its design, technological implementation and management are explored.

Ottimizzazione mediante codici di calcolo open source di componenti per il settore aerospaziale

Lo scopo della presente tesi è sviluppare un ambiente per l'ottimizzazione strutturale di componenti per applicazione aerospaziale utilizzando codici open-source. In particolare, il codice Salome viene utilizzato per il disegno automatico delle strutture, il programma Code Aster permette di effettuare l'analisi agli elementi finiti del componente, mentre Octave viene utilizzato per svolgere l'ottimizzazione basata su un algoritmo euristico e per integrare fra di loro i differenti codici. Le tecniche di ottimizzazione dei componenti stanno rivestendo sempre più importanza visto che le moderne tecniche di Additive Manufacturing permettono di realizzare strutture molto complesse che un tempo non era conveniente (o possibile) realizzare con asportazione di materiale. Nella prima parte della tesi si descrivono gli strumenti software utilizzati e la loro integrazione al fine di parametrizzare la generazione di geometrie ed effettuare in modo automatico analisi strutturali. Successivamente si descrivono tre casi di studio in cui la metodologia è stata sperimentata: un primo caso di validazione in cui si è applicato il metodo alla definizione della geometria di minimo peso per una trave a sbalzo con carico concentrato, un secondo test di ottimizzazione di un longherone per aeromobile, un terzo caso applicativo legato alla ottimizzazione di un serbatoio per fluidi in pressione da utilizzare su un satellite.

Un sistema di domotica per il controllo energetico domestico con tecnologie open-source.

Data la sempre maggiore richiesta di fabbisogno energetico, si è sviluppata una nuova filosofia nella gestione dei consumi energetici, il DSM (demand side management), che ha lo scopo di incoraggiare il consumatore ad usare energia in modo più intelligente e coscienzioso. Questo obiettivo, unito all’accumulo di energia da fonti rinnovabili, permetterà un abbassamento dell’utilizzo dell’energia elettrica proveniente dal consumo di fonti non rinnovabili e altamente inquinanti come quelle a combustibili fossili ed una diminuzione sia del consumo energetico, sia del costo per produrre energia che dell’energia stessa. L’home automation e la domotica in ambiente domestico rappresentano un esempio di DSM. L’obiettivo di questa tesi è quello di creare un sistema di home automation utilizzando tecnologie opensource. Sono stati utilizzati device come board Arduino UNO, Raspberry Pi ed un PC con sistema operativo GNU/Linux per creare una simulazione di un sistema di home automation abbinato alla gestione di celle fotovoltaiche ed energy storaging. Il sistema permette di poter spegnere un carico energetico in base a delle particolari circostanze come, per esempio, il superamento di una certa soglia di consumo di energia elettrica. Il software utilizzato è opensource e mira a poter ottimizzare il consumo energetico secondo le proprie finalità. Il tutto a dimostrare che si può creare un sistema di home automation da abbinare con il presente e futuro delle fonti rinnovabili utilizzando tecnologie libere in modo tale da preservare privacy e security oltre che customizzazione e possibilità di adattamento a diverse circostanze. Nella progettazione del sistema è stato implementato un algoritmo per gestire varie situazioni all’interno di un ambiente domestico. La realizzazione di tale algoritmo ha prodotto ottimi risultati nella raggiungimento degli obiettivi prefissati. Il progetto di questa tesi può essere ulteriormente ampliato ed il codice è reperibile in un repository pubblico.

Acumen : an open-source testbed for cyber-physical systems research

Developing Cyber-Physical Systems requires methods and tools to support simulation and verification of hybrid (both continuous and discrete) models. The Acumen modeling and simulation language is an open source testbed for exploring the design space of what rigorousbut- practical next-generation tools can deliver to developers of Cyber- Physical Systems. Like verification tools, a design goal for Acumen is to provide rigorous results. Like simulation tools, it aims to be intuitive, practical, and scalable. However, it is far from evident whether these two goals can be achieved simultaneously. This paper explains the primary design goals for Acumen, the core challenges that must be addressed in order to achieve these goals, the “agile research method” taken by the project, the steps taken to realize these goals, the key lessons learned, and the emerging language design.

Big Code Applications and Approaches

The availability of a huge amount of source code from code archives and open-source projects opens up the possibility to merge machine learning, programming languages, and software engineering research fields. This area is often referred to as Big Code where programming languages are treated instead of natural languages while different features and patterns of code can be exploited to perform many useful tasks and build supportive tools. Among all the possible applications which can be developed within the area of Big Code, the work presented in this research thesis mainly focuses on two particular tasks: the Programming Language Identification (PLI) and the Software Defect Prediction (SDP) for source codes. Programming language identification is commonly needed in program comprehension and it is usually performed directly by developers. However, when it comes at big scales, such as in widely used archives (GitHub, Software Heritage), automation of this task is desirable. To accomplish this aim, the problem is analyzed from different points of view (text and image-based learning approaches) and different models are created paying particular attention to their scalability. Software defect prediction is a fundamental step in software development for improving quality and assuring the reliability of software products. In the past, defects were searched by manual inspection or using automatic static and dynamic analyzers. Now, the automation of this task can be tackled using learning approaches that can speed up and improve related procedures. Here, two models have been built and analyzed to detect some of the commonest bugs and errors at different code granularity levels (file and method levels). Exploited data and models’ architectures are analyzed and described in detail. Quantitative and qualitative results are reported for both PLI and SDP tasks while differences and similarities concerning other related works are discussed.

Analysis Of The Contribution Of Immunologically-detectable Her2, Steroid Receptors And Of The Triple-negative" Tumor Status To Disease-free And Overall Survival Of Women With Epithelial Ovarian Cancer."

We assessed associations between steroid receptors including: estrogen-alpha, estrogen-beta, androgen receptor, progesterone receptor, the HER2 status and triple-negative epithelial ovarian cancer (ERα-/PR-/HER2-; TNEOC) status and survival in women with epithelial ovarian cancer. The study included 152 women with primary epithelial ovarian cancer. The status of steroid receptor and HER2 was determined by immunohistochemistry. Disease-free and overall survival were calculated and compared with steroid receptor and HER2 status as well as clinicopathological features using the Cox Proportional Hazards model. A mean follow-up period of 43.6 months (interquartile range=41.4 months) was achieved where 44% of patients had serous tumor, followed by mucinous (23%), endometrioid (9%), mixed (9%), undifferentiated (8.5%) and clear cell tumors (5.3%). ER-alpha staining was associated with grade II-III tumors. Progesterone receptor staining was positively associated with a Body Mass Index≥25. Androgen receptor positivity was higher in serous tumors. In stand-alone analysis of receptor contribution to survival, estrogen-alpha positivity was associated with greater disease-free survival. However, there was no significant association between steroid receptor expression, HER2 status, or TNEOC status, and overall survival. Although estrogen-alpha, androgen receptor, progesterone receptor and the HER2 status were associated with key clinical features of the women and pathological characteristics of the tumors, these associations were not implicated in survival. Interestingly, women with TNEOC seem to fare the same way as their counterparts with non-TNEOC.

Knoop microhardness and FT-Raman evaluation of composite resins: influence of opacity and photoactivation source

The aim of this study was to evaluate the degree of conversion by Knoop microhardness (KHN) and FT-Raman spectroscopy (FTIR) of one nanofilled (Filtek Supreme-3M-ESPE [FS]) and one microhybrid composite (Charisma-Heraeus-Kulzer [CH]), each with different opacities, namely enamel, dentin, and translucent, which were photo-activated by a quartz-tungsten-halogen lamp (QTH) and a light-emitting diode (LED). Resin was bulk inserted into a disc-shaped mold that was 2.0 mm thick and 4 mm in diameter, obtaining 10 samples per group. KHN and FTIR values were analyzed by two-way ANOVA and Tukey's tests (α = 0.05). Nanofilled resin activated by a LED presented higher microhardness values than samples activated by a QTH for dentin opacity (p < 0.05). The microhybrid resin showed no differences in KHN or FTIR values with different activation sources or opacity. The nanofilled dentin and enamel resins showed lower FTIR values than the translucent resin. The KHN values of the translucent resins were not influenced by the light source.

Fermentation of Groundnut Shell Enzymatic Hydrolysate for Fuel Ethanol Production by Free and Sorghum Stalks Immobilized Cells of Pichia stipitis NCIM 3498

Groundnut shell (GS), after separation of pod, is readily available as a potential feedstock for production of fermentable sugars. The substrate was delignified with sodium sulfite. The delignified substrate released 670 mg/g of sugars after enzymatic hydrolysis (50 degrees C, 120 rpm, 50 hrs) using commercial cellulases (Dyadic Xylanase PLUS, Dyadic Inc. USA). The groundnut shell enzymatic hydrolysate (45.6 g/L reducing sugars) was fermented for ethanol production with free and sorghum stalks immobilized cells of Pichia stipitis NCIM 3498 under submerged cultivation conditions. Immobilization of yeast cells on sorghum stalks were confirmed by scanning electron microscopy (SEM). A maximum of ethanol production (17.83 g/L, yield 0.44 g/g and 20.45 g/L, yield 0.47 g/g) was observed with free and immobilized cells of P. stipitis respectively in batch fermentation conditions. Recycling of immobilized cells showed a stable ethanol production (20.45 g/L, yield 0.47 g/g) up to 5 batches followed by a gradual downfall in subsequent cycles.

Sequential spectrofluorimetric determination of free and total glycerol in biodiesel in a multicommuted flow system

A new procedure for spectrofluorimetric determination of free and total glycerol in biodiesel samples is presented. It is based on the oxidation of glycerol by periodate, forming formaldehyde, which reacts with acetylacetone, producing the luminescent 3,5-diacetyl-1,4-dihydrolutidine. A flow system with solenoid micro-pumps is proposed for solution handling. Free glycerol was extracted off-line from biodiesel samples with water, and total glycerol was converted to free glycerol by saponification with sodium ethylate under sonication. For free glycerol, a linear response was observed from 5 to 70 mg L(-1) with a detection limit of 0.5 mg L(-1), which corresponds to 2 mg kg(-1) in biodiesel. The coefficient of variation was 0.9% (20 mg L(-1), n = 10). For total glycerol, samples were diluted on-line, and the linear response range was 25 to 300 mg L(-1). The detection limit was 1.4 mg L(-1) (2.8 mg kg(-1) in biodiesel) with a coefficient of variation of 1.4% (200 mg L(-1), n = 10). The sampling rate was ca. 35 samples h(-1) and the procedure was applied to determination of free and total glycerol in biodiesel samples from soybean, cottonseed, and castor beans.

Nitrogen removal in a sequencing batch biofilm reactor with liquid circulation: Effect of feed strategy and carbon source in the denitrifying step

Ammonium nitrogen removal from a synthetic wastewater by nitrification and denitrification processes were performed in a sequencing batch biofilm reactor containing immobilized biomass on polyurethane foam with circulation of the liquid-phase. It was analyzed the effect of four external carbon sources (ethanol, acetate, carbon synthetic medium and methanol) acting as electron donors in the denitrifying process. The experiments were conducted with intermittent aeration and operated at 30+/-1 degrees C in 8-h cycles. The synthetic wastewater (100 mgCOD/L and 50 mgNH(4)(+)-N/L) was added batch-wise, while the external carbon sources were added fed-batch-wise during the periods where aeration was suspended. Ammonium nitrogen removal efficiencies obtained were 95.7, 94.3 and 97.5% for ethanol, acetate and carbon synthetic medium, respectively. As to nitrite, nitrate and ammonium nitrogen effluent concentrations, the results obtained were, respectively: 0.1, 5.7 and 1.4 mg/L for ethanol; 0.2, 4.1 and 1.8 mg/L for acetate and 0.2, 6.7 and 0.8 for carbon synthetic medium. On the other hand using methanol, even at low concentrations (50% of the stoichiometric value calculated for complete denitrification), resulted in increasing accumulation of nitrate and ammonium nitrogen in the effluent over time.