Holistic recommender systems for software engineering

The knowledge possessed by developers is often not sufficient to overcome a programming problem. Short of talking to teammates, when available, developers often gather additional knowledge from development artifacts (e.g., project documentation), as well as online resources. The web has become an essential component in the modern developer’s daily life, providing a plethora of information from sources like forums, tutorials, Q&A websites, API documentation, and even video tutorials. Recommender Systems for Software Engineering (RSSE) provide developers with assistance to navigate the information space, automatically suggest useful items, and reduce the time required to locate the needed information. Current RSSEs consider development artifacts as containers of homogeneous information in form of pure text. However, text is a means to represent heterogeneous information provided by, for example, natural language, source code, interchange formats (e.g., XML, JSON), and stack traces. Interpreting the information from a pure textual point of view misses the intrinsic heterogeneity of the artifacts, thus leading to a reductionist approach. We propose the concept of Holistic Recommender Systems for Software Engineering (H-RSSE), i.e., RSSEs that go beyond the textual interpretation of the information contained in development artifacts. Our thesis is that modeling and aggregating information in a holistic fashion enables novel and advanced analyses of development artifacts. To validate our thesis we developed a framework to extract, model and analyze information contained in development artifacts in a reusable meta- information model. We show how RSSEs benefit from a meta-information model, since it enables customized and novel analyses built on top of our framework. The information can be thus reinterpreted from an holistic point of view, preserving its multi-dimensionality, and opening the path towards the concept of holistic recommender systems for software engineering

Phosphoinositide 3-kinase activates Rac by entering in a complex with Eps8, Abi1, and Sos-1

Class I phosphoinositide 3-kinases (PI3Ks) are implicated in many cellular responses controlled by receptor tyrosine kinases (RTKs), including actin cytoskeletal remodeling. Within this pathway, Rac is a key downstream target/effector of PI3K. However, how the signal is routed from PI3K to Rac is unclear. One possible candidate for this function is the Rac-activating complex Eps8–Abi1–Sos-1, which possesses Rac-specific guanine nucleotide exchange factor (GEF) activity. Here, we show that Abi1 (also known as E3b1) recruits PI3K, via p85, into a multimolecular signaling complex that includes Eps8 and Sos-1. The recruitment of p85 to the Eps8–Abi1–Sos-1 complex and phosphatidylinositol 3, 4, 5 phosphate (PIP3), the catalytic product of PI3K, concur to unmask its Rac-GEF activity in vitro. Moreover, they are indispensable for the activation of Rac and Rac-dependent actin remodeling in vivo. On growth factor stimulation, endogenous p85 and Abi1 consistently colocalize into membrane ruffles, and cells lacking p85 fail to support Abi1-dependent Rac activation. Our results define a mechanism whereby propagation of signals, originating from RTKs or Ras and leading to actin reorganization, is controlled by direct physical interaction between PI3K and a Rac-specific GEF complex

Identifying and Describing Information Seeking Tasks

A software developer works on many tasks per day, frequently switching between these tasks back and forth. This constant churn of tasks makes it difficult for a developer to know the specifics of when they worked on what task, complicating task resumption, planning, retrospection, and reporting activities. In a first step towards an automated aid to this issue, we introduce a new approach to help identify the topic of work during an information seeking task — one of the most common types of tasks that software developers face — that is based on capturing the contents of the developer’s active window at regular intervals and creating a vector representation of key information the developer viewed. To evaluate our approach, we created a data set with multiple developers working on the same set of six information seeking tasks that we also make available for other researchers to investigate similar approaches. Our analysis shows that our approach enables: 1) segments of a developer’s work to be automatically associated with a task from a known set of tasks with average accuracy of 70.6%, and 2) a word cloud describing a segment of work that a developer can use to recognize a task with average accuracy of 67.9%

An effector region in Eps8 is responsible for the activation of the Rac-specific GEF activity of Sos-1 and for the proper localization of the Rac-based actin-polymerizing machine

Genetic and biochemical evidence demonstrated that Eps8 is involved in the routing of signals from Ras to Rac. This is achieved through the formation of a tricomplex consisting of Eps8-E3b1-Sos-1, which is endowed with Rac guanine nucleotide exchange activity. The catalytic subunit of this complex is represented by Sos-1, a bifunctional molecule capable of catalyzing guanine nucleotide exchange on Ras and Rac. The mechanism by which Sos-1 activity is specifically directed toward Rac remains to be established. Here, by performing a structure-function analysis we show that the Eps8 output function resides in an effector region located within its COOH terminus. This effector region, when separated from the holoprotein, activates Rac and acts as a potent inducer of actin polymerization. In addition, it binds to Sos-1 and is able to induce Rac-specific, Sos-1-dependent guanine nucleotide exchange activity. Finally, the Eps8 effector region mediates a direct interaction of Eps8 with F-actin, dictating Eps8 cellular localization. We propose a model whereby the engagement of Eps8 in a tricomplex with E3b1 and Sos-1 facilitates the interaction of Eps8 with Sos-1 and the consequent activation of an Sos-1 Rac-specific catalytic ability. In this complex, determinants of Eps8 are responsible for the proper localization of the Rac-activating machine to sites of actin remodeling

Evaluation of bioactive sphingolipids in 4-HPR-resistant leukemia cells

<p>Abstract</p> <p>Background</p> <p><it>N</it>-(4-hydroxyphenyl)retinamide (4-HPR, fenretinide) is a synthetic retinoid with potent pro-apoptotic activity against several types of cancer, but little is known regarding mechanisms leading to chemoresistance. Ceramide and, more recently, other sphingolipid species (e.g., dihydroceramide and dihydrosphingosine) have been implicated in 4-HPR-mediated tumor cell death. Because sphingolipid metabolism has been reported to be altered in drug-resistant tumor cells, we studied the implication of sphingolipids in acquired resistance to 4-HPR based on an acute lymphoblastic leukemia model.</p> <p>Methods</p> <p>CCRF-CEM cell lines resistant to 4-HPR were obtained by gradual selection. Endogenous sphingolipid profiles and in situ enzymatic activities were determined by LC/MS, and resistance to 4-HPR or to alternative treatments was measured using the XTT viability assay and annexin V-FITC/propidium iodide labeling.</p> <p>Results</p> <p>No major crossresistance was observed against other antitumoral compounds (i.e. paclitaxel, cisplatin, doxorubicin hydrochloride) or agents (i.e. ultra violet C, hydrogen peroxide) also described as sphingolipid modulators. CCRF-CEM cell lines resistant to 4-HPR exhibited a distinctive endogenous sphingolipid profile that correlated with inhibition of dihydroceramide desaturase. Cells maintained acquired resistance to 4-HPR after the removal of 4-HPR though the sphingolipid profile returned to control levels. On the other hand, combined treatment with sphingosine kinase inhibitors (unnatural (dihydro)sphingosines ((dh)Sph)) and glucosylceramide synthase inhibitor (PPMP) in the presence or absence of 4-HPR increased cellular (dh)Sph (but not ceramide) levels and were highly toxic for both parental and resistant cells.</p> <p>Conclusions</p> <p>In the leukemia model, acquired resistance to 4-HPR is selective and persists in the absence of sphingolipid profile alteration. Therapeutically, the data demonstrate that alternative sphingolipid-modulating antitumoral strategies are suitable for both 4-HPR-resistant and sensitive leukemia cells. Thus, whereas sphingolipids may not be critical for maintaining resistance to 4-HPR, manipulation of cytotoxic sphingolipids should be considered a viable approach for overcoming resistance.</p

Identifying reputation collectors in community question answering (CQA) sites: Exploring the dark side of social media

YesThis research aims to identify users who are posting as well as encouraging others to post low-quality and duplicate contents on community question answering sites. The good guys called Caretakers and the bad guys called Reputation Collectors are characterised by their behaviour, answering pattern and reputation points. The proposed system is developed and analysed over publicly available Stack Exchange data dump. A graph based methodology is employed to derive the characteristic of Reputation Collectors and Caretakers. Results reveal that Reputation Collectors are primary sources of low-quality answers as well as answers to duplicate questions posted on the site. The Caretakers answer limited questions of challenging nature and fetches maximum reputation against those questions whereas Reputation Collectors answers have so many low-quality and duplicate questions to gain the reputation point. We have developed algorithms to identify the Caretakers and Reputation Collectors of the site. Our analysis finds that 1.05% of Reputation Collectors post 18.88% of low quality answers. This study extends previous research by identifying the Reputation Collectors and 2 how they collect their reputation points

Antineoplastic Drugs as a Potential Risk Factor in Occupational Settings: Mechanisms of Action at the Cell Level, Genotoxic Effects, and Their Detection Using Different Biomarkers

U članku je prikazana osnovna podjela antineoplastičnih lijekova prema mehanizmima djelovanja na razini stanice. Objašnjeni su mehanizmi genotoksičnosti najvažnijih vrsta lijekova koji se primjenjuju u okviru uobičajenih protokola za liječenje zloćudnih novotvorina. Navedena je važeća klasifi kacija antineoplastika prema kancerogenom potencijalu, podaci o mutagenom potencijalu te je prikazana njihova podjela u skladu s anatomsko-terapijsko-kemijskim sustavom klasifi kacije. Sustavno su prikazani najvažniji rezultati svjetskih i hrvatskih istraživanja na populacijama radnika izloženih antineoplasticima, provedenih u razdoblju 1980.-2009. s pomoću četiri najčešće primjenjivane metode: analize izmjena sestrinskih kromatida, analize kromosomskih aberacija, mikronukleus-testa i komet-testa. Objašnjena su osnovna načela navedenih metoda te raspravljene njihove prednosti i nedostaci. Biološki pokazatelji daju važne podatke o individualnoj osjetljivosti profesionalno izloženih ispitanika koji mogu poslužiti unaprjeđenju postojećih uvjeta rada i upravljanju rizicima pri izloženosti genotoksičnim agensima. Na osnovi prednosti i nedostataka citogenetičkih metoda zaključeno je da je mikronukleus-test, koji podjednako uspješno dokazuje klastogene i aneugene učinke, jedna od najboljih metoda dostupnih za otkrivanje štetnih djelovanja antineoplastičnih lijekova koji su u aktivnoj primjeni.This article brings an overview of the mechanisms of action of antineoplastic drugs used in the clinical setting. It also describes the genotoxic potentials of the most important classes of antineoplastic drugs involved in standard chemotherapy protocols. Classifi cation of antineoplastic drugs according to the IARC monographs on the evaluation of carcinogenic risks to humans is accompanied by data on their mutagenicity and the most recent updates in the Anatomical Therapeutic Chemical (ATC) Classifi cation System. We report the main fi ndings of biomonitoring studies that were conducted in exposed healthcare workers all over the world between 1980 and 2009 using four biomarkers: sister chromatid exchanges, chromosome aberrations, micronuclei. and the comet assay. The methods are briefl y explained and their advantages and disadvantages discussed. Biomarkers provide important information on individual genome sensitivity, which eventually might help to improve current working practices and to manage the risks related with exposure to genotoxic agents. Taking into consideration all known advantages and drawbacks of the existing cytogenetic methods, the micronucleus assay, which is able to detect both clastogenic and aneugenic action, is the most suitable biomarker for assessing harmful effects of antineoplastic drugs currently used in health care

Studi sulla persistenza dei sister choromatid exchanges, spontanei e indotti, attraverso tre cicli cellulari, a livello di singola cellula

Dottorato di ricerca in scienze genetiche. 8. ciclo. A.a. 1994-95. Tutore R. Barale. Coordinatore I. BarraiConsiglio Nazionale delle Ricerche - Biblioteca Centrale - P.le Aldo Moro, 7, Rome; Biblioteca Nazionale Centrale - P.za Cavalleggeri, 1, Florence / CNR - Consiglio Nazionale delle RichercheSIGLEITItal

Caratterizzazione chimica e valutazione delle prestazioni di un impianto di bonifica elettrocinetica di sedimenti marini

Utilizzo della tecnica elettrocinetica per la decontaminazione dei sedimenti dragati dal porto di Livorno: il progetto Life+ SEKRET si propone l'obiettivo di dimostrare come la tecnica suddetta possa avere effetti migliori rispetto alle tradizionali tecniche di bonifica di matrici solide caratterizzate da determinate peculiarità, tra le quali una bassa permeabilità. Il lavoro di tesi è finalizzato alla valutazione delle prestazioni avute dall'impianto dimostrativo di progetto nonché alla verifica dei risultati ottenuti mediante la caratterizzazione chimica di alcune delle componenti facenti parte del processo di decontaminazione