86,603 research outputs found
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
No full textBackground: Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen as the future for genomic data storage and processing, with MapReduce-Hadoop as leaders. Somewhat surprisingly, none of the specialized FASTA/Q compressors is available within Hadoop. Indeed, their deployment there is not exactly immediate. Such a State of the Art is problematic. Results: We provide major advances in two different directions. Methodologically, we propose two general methods, with the corresponding software, that make very easy to deploy a specialized FASTA/Q compressor within MapReduce-Hadoop for processing files stored on the distributed Hadoop File System, with very little knowledge of Hadoop. Practically, we provide evidence that the deployment of those specialized compressors within Hadoop, not available so far, results in better space savings, and even in better execution times over compressed data, with respect to the use of generic compressors available in Hadoop, in particular for FASTQ files. Finally, we observe that these results hold also for the Apache Spark framework, when used to process FASTA/Q files stored on the Hadoop File System. Conclusions: Our Methods and the corresponding software substantially contribute to achieve space and time savings for the storage and processing of FASTA/Q files in Hadoop and Spark. Being our approach general, it is very likely that it can be applied also to FASTA/Q compression methods that will appear in the future. Availability: The software and the datasets are available at https://github.com/fpalini/fastdoop
Alignment-free Genomic Analysis via a Big Data Spark Platform
No full textMotivation: Alignment-free distance and similarity functions (AF functions, for short) are a well-established alternative to pairwise and multiple sequence alignments for many genomic, metagenomic and epigenomic tasks. Due to data-intensive applications, the computation of AF functions is a Big Data problem, with the recent literature indicating that the development of fast and scalable algorithms computing AF functions is a high-priority task. Somewhat surprisingly, despite the increasing popularity of Big Data technologies in computational biology, the development of a Big Data platform for those tasks has not been pursued, possibly due to its complexity.Results: We fill this important gap by introducing FADE, the first extensible, efficient and scalable Spark platform for alignment-free genomic analysis. It supports natively eighteen of the best performing AF functions coming out of a recent hallmark benchmarking study. FADE development and potential impact comprises novel aspects of interest. Namely, (i) a considerable effort of distributed algorithms, the most tangible result being a much faster execution time of reference methods like MASH and FSWM; (ii) a software design that makes FADE user-friendly and easily extendable by Spark non-specialists; (iii) its ability to support data- and compute-intensive tasks. About this, we provide a novel and much needed analysis of how informative and robust AF functions are, in terms of the statistical significance of their output. Our findings naturally extend the ones of the highly regarded benchmarking study, since the functions that can really be used are reduced to a handful of the eighteen included in FADE
Differences in blood and semen oxidative status in fertile and infertile men, and their relationship with sperm quality.
No full textReprod Biomed Online. 2012 Sep;25(3):300-6. doi: 10.1016/j.rbmo.2012.05.011. Epub 2012 May 30.
Differences in blood and semen oxidative status in fertile and infertile men, and their relationship with sperm quality.
Benedetti S1, Tagliamonte MC, Catalani S, Primiterra M, Canestrari F, De Stefani S, Palini S, Bulletti C.
Author information
Abstract
Oxidative stress plays a fundamental role in the aetiology of male infertility by negatively affecting sperm quality and function. Assessment of blood and seminal plasma oxidative profiles might be a valuable tool to improve evaluation of sperm reproductive capacity and functional competence. This study examined the lipid-soluble antioxidant profile and levels of lipid peroxidation both in blood and seminal plasma samples of infertile and fertile males, in relation to semen parameters. Total antioxidant capacity (TAC) and vitamin E concentrations were significantly (P<0.05) lower in seminal plasma of infertile men compared with fertile subjects; concurrently, a significant accumulation of malondialdehyde was found in infertile patients (P=0.032 compared with controls), which was negatively correlated with sperm motility and morphology. In blood samples, infertile men presented lower concentrations of TAC, carotenoids and vitamin E than fertile subjects; TAC and carotenoids were positively correlated with sperm motility, morphology and concentration. Finally, blood TAC and vitamin E concentrations were positively correlated with the corresponding seminal values, confirming the close relationship between blood and semen antioxidants. All these results indicated the possibility of using not only seminal antioxidants but also blood antioxidants as biochemical markers to support sperm quality evaluation. Oxidative stress induced by reactive oxygen species (ROS) has been widely recognized as one of the major causes of male infertility; indeed, excessive ROS production can negatively impact sperm quality and function. The assessment of blood and seminal plasma oxidative profiles has been suggested as a valuable tool to improve the evaluation of sperm reproductive capacity and functional competence in infertile men. With this in mind, in the present study we examined the lipid soluble antioxidant profile (carotenoids and vitamins A and E) and the levels of lipid peroxidation (malondialdehyde; MDA) both in blood and seminal plasma samples of infertile and fertile males, in correlation with semen parameters namely motility, morphology and concentration. As a result, we obtained evidence that the total antioxidant capacity (TAC) and the concentrations of vitamin E of seminal plasma samples were significantly lower in infertile men than in fertile subjects; at the same time, a significant accumulation of MDA was found in infertile patients. MDA, in turn, negatively correlated with sperm motility and morphology, thus confirming that oxidative damage to lipids impairs sperm quality. In blood samples, infertile men presented lower TAC and lower concentrations of carotenoids and vitamin E than fertile subjects; interestingly, TAC and carotenoid concentrations were positively correlated with sperm motility, morphology, and concentration, confirming the close relationship between blood antioxidants and sperm quality. In conclusion, all these results suggested that the examination of blood and semen oxidative profiles might furnish useful information on sperm quality and function in infertile men
Using software visualization to support the teaching of distributed programming
No full textIn this paper, we introduce MARVEL, a system designed to simplify the teaching
of MapReduce, a popular distributed programming paradigm, through software
visualization. At its core, it allows a teacher to describe and recreate a MapReduce
application by interactively requesting, through a graphical interface, the execution
of a sequence of MapReduce transformations that target an input dataset. Then, the
execution of each operation is illustrated on the screen by playing an appropriate
graphical animation stage, highlighting aspects related to its distributed nature. The
sequence of all animation stages, played back one after the other in a sequential
order, results in a visualization of the whole algorithm. The content of the resulting visualization is not simulated or fctitious, but refects the real behavior of the
requested operations, thanks to the adoption of an architecture based on a real
instance of a distributed system running on Apache Spark. On the teacher’s side, it
is expected that by using MARVEL he/she will spend less time preparing materials
and will be able to design a more interactive lesson than with electronic slides or a
whiteboard. To test the efectiveness of the proposed approach on the learner side,
we also conducted a small scientifc experiment with a class of volunteer students
who formed a control group. The results are encouraging, showing that the use of
software visualization guarantees students a learning experience at least equivalent
to that of conventional approaches
Correction to: FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
No full textFollowing publication of the original article [1], the authors identified that the affiliations of Giuseppe Cattaneo and Raffaele Giancarlo were interchanged. The correct affiliations are given below.
The correct affiliation of Giuseppe Cattaneo is:
2Dipartimento di Informatica, Università di Salerno, Fisciano, Italy.
The correct affiliation of Raffaele Giancarlo is:
3Dipartimento di Matematica ed Informatica, Università di Palermo, Palermo, Italy.
The original article [1] has been corrected
The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis
No full textMotivation: Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either missing or limited. Results: By concentrating on a representative set of word-frequency-based AF functions, we perform the first coherent and uniform evaluation of the power, involving also Type I error for completeness. Two alternative models of important genomic features (CIS Regulatory Modules and Horizontal Gene Transfer), a wide range of sequence lengths from a few thousand to millions, and different values of k have been used. As a result, we provide a characterization of those AF functions that is novel and informative. Indeed, we identify weak and strong points of each function considered, which may be used as a guide to choose one for analysis tasks. Remarkably, of the 15 functions that we have considered, only four stand out, with small differences between small and short sequence length scenarios. Finally, to encourage the use of our methodology for validation of future AF functions, the Big Data platform supporting it is public
Variations on the Author
No full text“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
A natural human-drone embodied Interface: empirical comparison with a traditional interface
No full textDespite the importance of usability in human-machine interaction (HMI), most commonly used devices are not usable by all potential users. In particular, users with low or null technological experience, or with special needs, require carefully designed systems and easy-to-use interfaces supporting recognition over recall. To this purpose, Natural User Interfaces (NUIs) represent an effective strategy as the user's learning is facilitated by features of the interface that mimic the human “natural” sensorimotor embodied interactions with the environment. This paper compares the usability of a new NUI (based on an eye-tracker and hand gesture recognition) with a traditional interface (keyboard) for the distal control of a simulated drone flying in a virtual environment. The whole interface relies on “dAIsy”, a new software allowing the flexible use of different input devices and the control of different robotic platforms. The 59 users involved in the study were required to complete two tasks with each interface, while their performance was recorded: (a) exploration: detecting trees embedded in an urban environment; (b) accuracy: guiding the drone as accurately and fast as possible along a predefined track. Then they were administered questionnaires regarding the user's background, the perceived embodiment of the device, and the perceived quality of the virtual experience while either using the NUI or the traditional interface. The results appear controversial and call for further investigation: (a) contrary to our hypothesis, the specific NUI used led to lower performance than the traditional interface; (b) however, the NUI was evaluated as more natural and embodied. The final part of the paper discusses the possible causes underlying these results that suggest possible future improvements of the NUI
Challenging abdominal incisional hernia repaired with platelet-rich plasma and bone marrow-derived mesenchymal stromal cells. A case report
No full textIntroduction The necessity to develop new treatment options for challenging procedures in hernia surgery is becoming even more evident and tissue engineering and biological technologies offer even newer strategies to improve fascial healing. The present case reports a patient-tailored surgical technique performed to repair a grade IV abdominal incisional hernia, with a combined use of platelet-rich plasma and bone marrow-derived mesenchymal stromal cells, implanted on a biological mesh. Presentation of the case A 71 year-old female patient complained of an abdominal incisional hernia, complicated by enterocutaneous fistula, four-months following laparostomy. Contrast enhanced computed tomography showed an incisional hernia defect of 15.5 × 20 cm, with a subcutaneous abscess and an intestinal loop adherent to the anterior abdominal wall, with a concomitant enterocutaneous fistula. Surgery involved abdominal wall standardized technique closure, with in addition platelet-rich plasma and bone marrow-derived mesenchymal stromal cells implanted on a biological mesh. Two years follow up showed no recurrences of incisional hernia. Discussion Coating surgical meshes with patient's own cells may improve biocompatibility, by reducing inflammation and adhesion formation. Moreover, platelet-rich plasma is a good source of growth factors for wound healing, as well as a good medium for bone marrow multinucleate cells introduction into fascial repair. Conclusion This approach is likely to improve abdominal wall repair in high grade (IV) incisional hernia, with the real possibility of improving prosthetic compatibility and reducing future recurrences. The authors agree with the necessity of further studies and trials to assure the safety profile and superiority of this procedure
- …
