PPG: online generation of protein pictures and animations.
Ontology highlight
ABSTRACT:
SUBMITTER: Binisti C
PROVIDER: S-EPMC1160153 | biostudies-literature | 2005 Jul
REPOSITORIES: biostudies-literature
Publications
PPG: online generation of protein pictures and animations.
Binisti Cédric C Salim Ahmed Ali AA Tufféry Pierre P
Nucleic acids research 20050701 Web Server issue
The protein picture generator (PPG) is an online service to generate pictures of a protein structure. Its design was conceived as an answer to the need expressed by a part of the community to have some means to produce simply complex pictures to insert in publications or in presentations. PPG can produce static or animated pictures. It can be accessed at http://bioserv.rpbs.jussieu.fr/cgi-bin/PPG. ...[more]
Similar Datasets
Project description:The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html.
| S-EPMC1933120 | biostudies-literature
Project description:BackgroundMental ill-health is one of the most significant health and social issues affecting young people globally. To address the mental health crisis, a number of cross-sectoral research and action priorities have been identified. These include improving mental health literacy, translating research findings into accessible public health outputs, and the use of digital technologies. There are, however, few examples of public health-oriented knowledge transfer activities involving collaborations between researchers, the Arts, and online platforms in the field of youth mental health.ObjectiveThe primary aim of this project was to translate qualitative research findings into a series of online public mental health animations targeting young people between the ages of 16 and 25 years. A further aim was to track online social media engagement and viewing data for the animations for a period of 12 months.MethodsQualitative data were collected from a sample of 17 youth in Ireland, aged 18-21 years, as part of the longitudinal population-based Adolescent Brain Development study. Interviews explored the life histories and the emotional and mental health of participants. The narrative analysis revealed 5 thematic findings relating to young people's emotional and mental health. Through a collaboration between research, the Arts, and the online sector, the empirical thematic findings were translated into 5 public health animations. The animations were hosted and promoted on 3 social media platforms of the Irish youth health website called SpunOut. Viewing data, collected over a 12-month period, were analyzed to determine the reach of the animations.ResultsNarrative thematic analysis identified anxiety, depression, feeling different, loneliness, and being bullied as common experiences for young people. These thematic findings formed the basis of the animations. During the 12 months following the launch of the animations, they were viewed 15,848 times. A majority of views occurred during the period of the social media ad campaign at a cost of €0.035 (approximately US $0.042) per view. Animations on feeling different and being bullied accounted for the majority of views.ConclusionsThis project demonstrates that online animations provide an accessible means of translating empirical research findings into meaningful public health outputs. They offer a cost-effective way to provide targeted online information about mental health, coping, and help-seeking to young people. Cross-sectoral collaboration is required to leverage the knowledge and expertise required to maximize the quality and potential reach of any knowledge transfer activities. A high level of engagement is possible by targeting non-help-seeking young people on their native social media platforms. Paid promotion is, therefore, an important consideration when budgeting for online knowledge translation and dissemination activities in health research.
| S-EPMC7902194 | biostudies-literature
Project description:To the best of our knowledge, there is no annotated database of PPG signals recorded by smartphone publicly available. This article introduces Brno University of Technology Smartphone PPG Database (BUT PPG) which is an original database created by the cardiology team at the Department of Biomedical Engineering, Brno University of Technology, for the purpose of evaluating photoplethysmographic (PPG) signal quality and estimation of heart rate (HR). The data comprises 48 10-second recordings of PPGs and associated electrocardiographic (ECG) signals used for determination of reference HR. The data were collected from 12 subjects (6 female, 6 male) aged between 21 and 61. PPG data were collected by smartphone Xiaomi Mi9 with sampling frequency of 30 Hz. Reference ECG signals were recorded using a mobile ECG recorder (Bittium Faros 360) with a sampling frequency of 1,000 Hz. Each PPG signal includes annotation of quality created manually by biomedical experts and reference HR. PPG signal quality is indicated binary: 1 indicates good quality for HR estimation, 0 indicates signals where HR cannot be detected reliably, and thus, these signals are unsuitable for further analysis. As the only available database containing PPG signals recorded by smartphone, BUT PPG is a unique tool for the development of smart, user-friendly, cheap, on-the-spot, self-home-monitoring of heart rate with the potential of widespread using.
| S-EPMC8440059 | biostudies-literature
Project description:A pentablock copolymer was prepared via the atom transfer radical polymerization of 2-hydroxyethyl methacrylate (HEMA) initiated by 2-bromoisobutyryl end-capped PPO-PEO-PPO as a macroinitiator in DMF. Attaching PHEMA blocks altered the self-assembly process of the pentablock copolymer with γ-CDs in aqueous solution. Before attaching the PHEMA, the macroinitiator was preferentially bent to pass through the inner cavity of γ-CDs to give rise to tight-fit double-chain stranded polypseudorotaxanes (PPRs). After attaching the PHEMA, the resulting pentablock copolymer was single-chain stranded into the interior of γ-CDs to form more stable, loose-fit PPRs. The results of (1)H NMR, WXRD, DSC, TGA, (13)C CP/MAS NMR and FTIR analyses indicated that γ-CDs can accommodate and slip over PHEMA blocks to randomly distribute along the entire pentablock copolymer chain. This results in unique, single-chain stranded PPRs showing no characteristic channel-type crystal structure.
| S-EPMC4222382 | biostudies-literature
Project description:CyAnimator (http://apps.cytoscape.org/apps/cyanimator) is a Cytoscape app that provides a tool for simple animations of Cytoscape networks. The tool allows you to take a series of snapshots (CyAnimator calls them frames) of Cytoscape networks. For example, the first frame might be of a network shown from a "zoomed out" viewpoint and the second frame might focus on a specific group of nodes. Once these two frames are captured by the tool, it can animate between them by interpolating the changes in location, zoom, node color, node size, edge thickness, presence or absence of annotations, etc. The animations may be saved as a series of individual frames, animated GIFs, or H.264/MP4 movies. CyAnimator is available from within the Cytoscape App Manager or from the Cytoscape app store.
| S-EPMC4752027 | biostudies-literature
Project description:Toxoplasma gondii is a protozoan parasite that is the causative agent of toxoplasmosis, an infection with high prevalence worldwide. Most of the infected individuals are either asymptomatic or have mild symptoms, but T. gondii can cause severe neurologic damage and even death of the fetus when acquired during pregnancy. It is also a serious condition in immunodeficient patients. The life-cycle of T. gondii is complex, with more than one infective form and several transmission pathways. In two animated videos, we describe the main aspects of this cycle, raising questions about poorly or unknown issues of T. gondii biology. Original plates, based on electron microscope observations, are also available for teachers, students and researchers. The main goal of this review is to provide a source of learning on the fundamental aspects of T. gondii biology to students and teachers contributing for better knowledge and control on this important parasite, and unique cell model. In addition, drawings and videos point to still unclear aspects of T. gondii lytic cycle that may stimulate further studies.
| S-EPMC7686686 | biostudies-literature
Project description:We introduce a dataset to provide insights about the photoplethysmography (PPG) signal captured from the wrist in presence of motion artifacts and the accelerometer signal, simultaneously acquired from the same wrist. The data presented were collected by the electronics research team of the Department of Information Engineering, Polytechnic University of Marche, Ancona, Italy. This article describes data recorded from 7 subjects and includes 105 PPG signals (15 for each subject) and the corresponding 105 tri-axial accelerometer signals measured with a sampling frequency of 400 Hz. These data can be reused for testing machine learning algorithms for human activity recognition.
| S-EPMC6971339 | biostudies-literature
Project description:Recent studies have shown that guanine-rich (G-rich) sequences with the potential to form quadruplexes might play a role in normal transcription as well as overexpression of oncogenes. Chemical tools that allow examination of the specific roles of G-quadruplex formation in vivo, and their association with gene regulation will be essential to understanding the functions of these quadruplexes and might lead to beneficial therapies. Properly designed peptide nucleic acids (PNAs) can invade G-rich DNA duplexes and induce the formation of a G-quadruplex in the free DNA strand. Replacing guanines in the PNA sequence with pyrazolo[3,4-d]pyrimidine guanine (PPG) nucleobases eliminates G-quadruplex formation with PNA and promotes invasion of the target DNA.
| S-EPMC4180717 | biostudies-literature
Project description:Understanding speech becomes a demanding task when the environment is noisy. Comprehension of speech in noise can be substantially improved by looking at the speaker's face, and this audiovisual benefit is even more pronounced in people with hearing impairment. Recent advances in AI have allowed to synthesize photorealistic talking faces from a speech recording and a still image of a person's face in an end-to-end manner. However, it has remained unknown whether such facial animations improve speech-in-noise comprehension. Here we consider facial animations produced by a recently introduced generative adversarial network (GAN), and show that humans cannot distinguish between the synthesized and the natural videos. Importantly, we then show that the end-to-end synthesized videos significantly aid humans in understanding speech in noise, although the natural facial motions yield a yet higher audiovisual benefit. We further find that an audiovisual speech recognizer (AVSR) benefits from the synthesized facial animations as well. Our results suggest that synthesizing facial motions from speech can be used to aid speech comprehension in difficult listening environments.
| S-EPMC8766421 | biostudies-literature
Project description:The neuronal system underlying learning, generation and recognition of song in birds is one of the best-studied systems in the neurosciences. Here, we use these experimental findings to derive a neurobiologically plausible, dynamic, hierarchical model of birdsong generation and transform it into a functional model of birdsong recognition. The generation model consists of neuronal rate models and includes critical anatomical components like the premotor song-control nucleus HVC (proper name), the premotor nucleus RA (robust nucleus of the arcopallium), and a model of the syringeal and respiratory organs. We use Bayesian inference of this dynamical system to derive a possible mechanism for how birds can efficiently and robustly recognize the songs of their conspecifics in an online fashion. Our results indicate that the specific way birdsong is generated enables a listening bird to robustly and rapidly perceive embedded information at multiple time scales of a song. The resulting mechanism can be useful for investigating the functional roles of auditory recognition areas and providing predictions for future birdsong experiments.
| S-EPMC3240584 | biostudies-literature