scholarly journals Topaz-Denoise: general deep denoising models for cryoEM and cryoET

2019 ◽  
Author(s):  
Tristan Bepler ◽  
Kotaro Kelley ◽  
Alex J. Noble ◽  
Bonnie Berger
Keyword(s):  
Data Collection ◽  
Protein Structures ◽  
Electron Dose ◽  
Cryo Electron Microscopy ◽  
Data Collection Process ◽  
Wide Range ◽  
Open Structures ◽  
Downstream Analysis ◽  
First Time ◽  
Particle Orientations

AbstractCryo-electron microscopy (cryoEM) is becoming the preferred method for resolving protein structures. Low signal-to-noise (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations. Denoising cryoEM images can not only improve downstream analysis but also accelerate the time-consuming data collection process by allowing lower electron dose micrographs to be used for analysis. Here, we present Topaz-Denoise, a deep learning method for reliably and rapidly increasing the SNR of cryoEM images and cryoET tomograms. By training on a dataset composed of thousands of micrographs collected across a wide range of imaging conditions, we are able to learn models capturing the complexity of the cryoEM image formation process. The general model we present is able to denoise new datasets without additional training. Denoising with this model improves micrograph interpretability, enabling us to solve the first 3D single particle closed and partially open structures of clustered protocadherin, an elongated particle with previously-elusive views. We then show for the first time that low dose collection, enabled by Topaz-Denoise, improves downstream analysis in addition to reducing data collection time. We also present the first general 3D denoising model for cryoET. Topaz-Denoise and pre-trained general models are now included in Topaz. We expect that Topaz-Denoise will be of broad utility to the cryoEM community for improving micrograph and tomogram interpretability and accelerating analysis.

scholarly journals Topaz-Denoise: general deep denoising models for cryoEM and cryoET

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Tristan Bepler ◽  
Kotaro Kelley ◽  
Alex J. Noble ◽  
Bonnie Berger
Keyword(s):  
Data Collection ◽  
Signal To Noise Ratio ◽  
Protein Structures ◽  
Electron Dose ◽  
Cryo Electron Microscopy ◽  
Data Collection Process ◽  
Wide Range ◽  
Downstream Analysis ◽  
Particle Orientations ◽  
Imaging Conditions

Abstract Cryo-electron microscopy (cryoEM) is becoming the preferred method for resolving protein structures. Low signal-to-noise ratio (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations. Denoising cryoEM images can not only improve downstream analysis but also accelerate the time-consuming data collection process by allowing lower electron dose micrographs to be used for analysis. Here, we present Topaz-Denoise, a deep learning method for reliably and rapidly increasing the SNR of cryoEM images and cryoET tomograms. By training on a dataset composed of thousands of micrographs collected across a wide range of imaging conditions, we are able to learn models capturing the complexity of the cryoEM image formation process. The general model we present is able to denoise new datasets without additional training. Denoising with this model improves micrograph interpretability and allows us to solve 3D single particle structures of clustered protocadherin, an elongated particle with previously elusive views. We then show that low dose collection, enabled by Topaz-Denoise, improves downstream analysis in addition to reducing data collection time. We also present a general 3D denoising model for cryoET. Topaz-Denoise and pre-trained general models are now included in Topaz. We expect that Topaz-Denoise will be of broad utility to the cryoEM community for improving micrograph and tomogram interpretability and accelerating analysis.

scholarly journals Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography

2009 ◽  
Vol 42 (6) ◽  
pp. 1165-1175 ◽  
Author(s):  
Kazuya Hasegawa ◽  
Kunio Hirata ◽  
Tetsuya Shimizu ◽  
Nobutaka Shimizu ◽  
Takaaki Hikima ◽  
...  
Keyword(s):  
Data Collection ◽  
Dynamic Range ◽  
Protein Structures ◽  
Protein Crystallography ◽  
New Method ◽  
Oxide Semiconductor ◽  
X Ray ◽  
Rotation Method ◽  
Continuous Rotation ◽  
Wide Range

A new shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The principle of operation and the basic performance of the X-ray CMOS detector (Hamamatsu Photonics KK C10158DK) have been shown to be appropriate to the shutterless continuous rotation method. The data quality of the continuous rotation method is comparable to that of the conventional oscillation method using a CCD detector and, furthermore, the combination with fine φ slicing improves the data accuracy without increasing the data-collection time. The new method is more sensitive to diffraction intensity because of the narrow dynamic range of the CMOS detector. However, the strong diffraction spots were found to be precisely measured by recording them on successive multiple images by selecting an adequate rotation step. The new method has been used to successfully determine three protein structures by multi- and single-wavelength anomalous diffraction phasing and has thereby been proved applicable in protein crystallography. The apparatus and method may become a powerful tool at synchrotron protein crystallography beamlines with important potential across a wide range of X-ray wavelengths.

scholarly journals “Out” in the field. Reflecting on the dilemmas of insider status on data collection and conducting interviews with gay men

2014 ◽  
Vol 33 (5) ◽  
pp. 451-461 ◽  
Author(s):  
Simon Roberts
Keyword(s):  
Data Collection ◽  
Gay Men ◽  
Ethical Issues ◽  
Sexual Attraction ◽  
Power Balance ◽  
Structured Interviews ◽  
Content Type ◽  
Data Collection Process ◽  
Wide Range ◽  
The Impact

Purpose – The purpose of this paper is to explore using a reflexive approach the impact of author's personal positioning on issues of power balance between the interviewer and the interviewee, dealing with sensitive stories and concerns of difference and sameness between participants and the researcher in both the data collection process and also during the interviews. Design/methodology/approach – Initial data were gathered from 45 semi-structured interviews with self-identified gay men in a wide range of occupations and ages working in the seaside resort of Bournemouth on the south coast of England. Findings – The paper highlights some of the dilemmas of insider status and doing research on gay men. These include: ethical issues of closeness and involvement with participants, dealing with author's own personal frustrations, tackling the power imbalance between the interviewer and the interviewee and the impact of author's personal positioning on the data collection. Originality/value – Little research has been done on the impact of men doing research on issues of diversity. In particular, this paper re-examines the power balance between the interviewer and interviewee as being one sided as previous studies have suggested in the researcher's favour. It also uncovers ethical dilemmas such as sexual attraction and involvement that has had scant coverage in the literature.

Pemanfaatan Sistem Informasi Sebagai Alat Untuk Pendataan Masyarakat Di Pasuruan

2020 ◽  
Vol 2 (3) ◽  
pp. 145-150
Author(s):  
Syaifuddin Syaifuddin ◽  
Wildan Suharso
Keyword(s):  
Information System ◽  
Data Collection ◽  
Human Resources ◽  
Regional Government ◽  
Community Based ◽  
Collection Process ◽  
Data Collection Process ◽  
Service Activity ◽  
Development Plans ◽  
Collection Time

Pendataan yang bersifat manual menjadikan permasalahan pada proses dilakukannya pendataan, hal ini juga terjadi pada Dinas Pendidikan dan Kebudayaan Kota Pasuruan dimana pendataan masih bersifat manual dengan keterbatasan jumlah Sumber Daya Manusia (SDM) yang ditugaskan untuk melakukan pendataan, oleh karena itu pada kegiatan pengabdian ini dilakukan pelatihan sistem informasi untuk meningkatkan waktu pendataan dan mengurangi kompleksitas dalam proses pendataan pada pegawai di Dinas Pendidikan dan Kebudayaan Kota Pasuruan. Pelatihan sistem informasi yang dimaksud adalah sistem informasi pendataan berbasis masyarakat, yang berisikan data dasar yang diperlukan oleh Pemerintah Daerah dalam rangka penyusunan rencana pembangunan. Data informasi tidak akan memberikan manfaat jika tidak dijadikan sebagai bahan acuan dalam penyusunan rencana pembangunan sehingga pelatihan dan pendampingan perlu dilakukan untuk tercapainya tujuan.Kata Kunci : Sistem Informasi, Berbasis Masyarakat, PendataanABSTRACT Manual data collection causes problems in the data collection process, this also occurs in the Pasuruan City Education and Culture Office where data collection is still manual with a limited number of Human Resources (HR) assigned to collect data, therefore this service activity is carried out information system training to increase data collection time and reduce complexity in the data collection process for employees at the Pasuruan City Education and Culture Office. The information system training referred to is a community-based data collection information system, which contains basic data required by the Regional Government in the framework of formulating development plans. Information data will not provide benefits if it is not used as a reference in the preparation of development plans so that training and assistance are needed to achieve the goals.Keywords : Information System, Community Based, Data Collection 

Management Strategy for Distributing Questionnaires and Interview Guidelines in the Research Data Collection Process

2018 ◽  
Vol 2 (2) ◽  
pp. 104-111
Author(s):  
Po. Abas Sunarya ◽  
George Iwan Marantika ◽  
Adam Faturahman
Keyword(s):  
Focus Group ◽  
Data Collection ◽  
Management Strategy ◽  
Research Data ◽  
Accurate Information ◽  
Focus Group Interviews ◽  
Good Management ◽  
Research Activities ◽  
Data Collection Process ◽  
Group Interviews

Writing can mean lowering or describing graphic symbols that describe a languageunderstood by someone. For a researcher, management of research preparation is a veryimportant step because this step greatly determines the success or failure of all researchactivities. Before a person starts with research activities, he must make a written plan commonlyreferred to as the management of research data collection. In the process of collecting researchdata, of course we can do the management of questionnaires as well as the preparation ofinterview guidelines to disseminate and obtain accurate information. With the arrangement ofplanning and conducting interviews: the ethics of conducting interviews, the advantages anddisadvantages of interviews, the formulation of interview questions, the schedule of interviews,group and focus group interviews, interviews using recording devices, and interview bias.making a questionnaire must be designed with very good management by giving to theinformation needed, in accordance with the problem and all that does not cause problems at thestage of analysis and interpretation.

FUNCTIONAL COORDINATION OF METHODS OF ORGANIZATION OF ADAPTIVE DATA COLLECTION PROCESSES AND METHODS OF SPATIAL SELF-ORGANIZATION OF MOBILE AGENTS

2017 ◽  
Vol 2 (1) ◽  
pp. 27-32
Author(s):  
Botchkaryov. A. ◽  
Keyword(s):  
Data Collection ◽  
Key Words ◽  
Motion Control ◽  
Mobile Agent ◽  
Mobile Agents ◽  
Parallel Execution ◽  
Self Organization ◽  
Data Collection Process ◽  
Speed Up ◽  
Adaptive Data Collection

The way of functional coordination of methods of organization adaptive data collection processes and methods of spatial self-organization of mobile agents by parallel execution of the corresponding data collection processes and the process of motion control of a mobile agent using the proposed protocol of their interaction and the algorithm of parallel execution planning is proposed. The method allows to speed up the calculations in the decision block of the mobile agent by an average of 40.6%. Key words: functional coordination, adaptive data collection process, spatial self-organization, mobile agents

Life Cycle Development of Successful Women-owned Enterprises

2020 ◽  
Vol 3 (4) ◽  
pp. 142-152
Author(s):  
Mohammad Waliul Hasanat ◽  
Kamna Anum ◽  
Ashikul Hoque ◽  
Mahmud Hamid ◽  
Sandy Francis Peris ◽  
...  
Keyword(s):  
Life Cycle ◽  
Data Collection ◽  
Research Work ◽  
Primary Data ◽  
Small Scale ◽  
Data Collection Process ◽  
Theoretical Finding ◽  
Successful Women ◽  
Two Phases ◽  
Life Cycle Development

In developing countries, the role of women in the business sector is continuously improving. As a result, female enterprises have also been encouraged in Pakistan. This study is based on life cycle development phases from which women-owned enterprises have to go through in order to become successful. As a primary data source, face-to-face interviews with owners of successful women-owned enterprises were preferred. The data collection process was divided into two phases i.e. Phase-I and Phase-II. After data collection, qualitative analysis has been performed using NVIVO. Findings provide both generic and specific factors involved in life cycle development of women-owned enterprises. This study provides a detailed view of life cycle development model followed by successful women enterprises. The outcome of this research work is a theoretical finding which can be utilized by entrepreneurs owning small scale enterprises to improve their level of performance. Findings can also be helpful for potentially talented women interested in setting up their own business.

Safety assessment of biological raw materials in the system of medicines quality assurance

2020 ◽  
pp. 63-72
Author(s):  
Yu. Olefir ◽  
E. Sakanyan ◽  
I. Osipova ◽  
V. Dobrynin ◽  
M. Smirnova ◽  
...  
Keyword(s):  
Raw Materials ◽  
State Level ◽  
The State ◽  
Spongiform Encephalopathy ◽  
Safety Standards ◽  
Wide Range ◽  
The Russian Federation ◽  
Key Aspects ◽  
First Time ◽  
Medicines Quality

The entry of a wide range of biotechnological products into the pharmaceutical market calls for rein-forcement of the quality, efficacy and safety standards at the state level. The following general monographs have been elaborated for the first time to be included into the State Pharmacopoeia of the Russian Federation, XIV edition: "Viral safety" and "Reduction of the risk of transmitting animal spongiform encephalopathy via medicinal products". These general monographs were elaborated taking into account the requirements of foreign pharmacopoeias and the WHO recommendations. The present paper summarises the key aspects of the monographs.

Innovation in Byzantine Medicine

2020 ◽  
Author(s):  
Petros Bouras-Vallianatos
Keyword(s):  
Human Physiology ◽  
Medical Literature ◽  
Cultural Exchange ◽  
Significant Degree ◽  
Medieval Medicine ◽  
Medieval Latin ◽  
Main Thesis ◽  
Wide Range ◽  
Comprehensive Examination ◽  
First Time

Byzantine medicine is still a little-known and misrepresented field not only in the wider arena of debates on medieval medicine but also among Byzantinists. Byzantine medical literature is often viewed as ‘stagnant’ and mainly preserving ancient ideas; and our knowledge of it continues to be based to a great extent on the comments of earlier authorities, which are often repeated uncritically. This book presents the first comprehensive examination of the medical corpus of, arguably, the most important late Byzantine physician John Zacharias Aktouarios (c.1275–c.1330). The main thesis is that John’s medical works show an astonishing degree of openness to knowledge from outside Byzantium combined with a significant degree of originality, in particular, in the fields of uroscopy, pharmacology, and human physiology. The analysis of John’s edited (On Urines and On Psychic Pneuma) and unedited (Medical Epitome) works is supported for the first time by the consultation of a large number of manuscripts. The study is also informed by evidence from a wide range of medical sources, including previously unpublished ones, and texts from other genres, such as epistolography and merchants’ accounts. The contextualization of John’s works sheds new light on the development of Byzantine medical thought and practice, and enhances our understanding of the late Byzantine social and intellectual landscape. Finally, John’s medical observations are also examined in the light of examples from the medieval Latin and Islamic worlds, placing his medical theories in the wider Mediterranean milieu and highlighting the cultural exchange between Byzantium and its neighbours.

Rebels, Believers, Survivors

2020 ◽  
Author(s):  
Noel Malcolm
Keyword(s):  
Catholic Church ◽  
Religious Conversion ◽  
Late Nineteenth Century ◽  
Napoleonic Wars ◽  
Conversion To Islam ◽  
Wide Range ◽  
History Of ◽  
External Powers ◽  
First Time ◽  
Modern Myth

This book of essays covers a wide range of topics in the history of Albania and Kosovo. Many of the essays illuminate connections between the Albanian lands and external powers and interests, whether political, military, diplomatic or religious. Such topics include the Habsburg invasion of Kosovo in 1689, the manoeuvrings of Britain and France towards the Albanian lands during the Napoleonic Wars, the British interest in those lands in the late nineteenth century, and the Balkan War of 1912. On the religious side, essays examine ‘crypto-Christianity’ in Kosovo during the Ottoman period, the stories of conversion to Islam revealed by Inquisition records, the first theological treatise written in Albanian (1685), and the work of the ‘Apostolic Delegate’ who reformed the Catholic Church in early twentieth-century Albania. Some essays bring to life ordinary individuals hitherto unknown to history: women hauled before the Inquisition, for example, or the author of the first Albanian autobiography. The longest essay, on Ali Pasha, tells for the first time the full story of the role he played in the international politics of the Napoleonic Wars. Some of these studies have been printed before (several in hard-to-find publications, and one only in Albanian), but the greater part of this book appears here for the first time. This is not only a contribution to Albanian and Balkan history it also engages with many broader issues, including religious conversion, methods of enslavement within the Ottoman Empire, and the nature of modern myth-making about national identity.

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