Guide to the Internet. The world wide web.

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals.     

Laboratory protocols on the internet

Summary The World Wide Web (WWW) is of major significance to the Biotechnologist. One of the fastest growing and most useful areas of the internet, the WWW contains information sites, genome and sequence databases, newsgroups and forums, search and comparison tools, and electronic journals. To many scientists, the WWW has become an indispensable research tool. This paper lists some of the sites providing a wide range of relevant protocols and techniques and describes how to access this information.     

Introducing the Internet.

The benefits to medical practitioners of using the Internet are growing rapidly as the Internet becomes easier to use and ever more biomedical resources become available on line. The Internet is the largest computer network in the world; it is also a virtual community, larger than many nation states, with its own rules of behaviour or "netiquette." There are several types of Internet connection and various ways of acquiring a connection. Once connected, you can obtain, free of charge, programs that allow easy use of the Internet''s resources and help on how to use these resources; you can access many of these resources through the hypertext references in the on line version of this series (go to http:@www.bmj.com/bmj/ to reach the electronic version). You can then explore the various methods for accessing, manipulating, or disseminating data on the Internet, such as electronic mail, telnet, file transfer protocol, and the world wide web. Results from a search of the world wide web for information on the rare condition of Recklinghausen''s neurofibromatosis illustrate the breadth of medical information available on the Internet.     

MADGE: scalable distributed data management software for cDNA microarrays

MOTIVATION: The human genome project and the development of new high-throughput technologies have created unparalleled opportunities to study the mechanism of diseases, monitor the disease progression and evaluate effective therapies. Gene expression profiling is a critical tool to accomplish these goals. The use of nucleic acid microarrays to assess the gene expression of thousands of genes simultaneously has seen phenomenal growth over the past five years. Although commercial sources of microarrays exist, investigators wanting more flexibility in the genes represented on the array will turn to in-house production. The creation and use of cDNA microarrays is a complicated process that generates an enormous amount of information. Effective data management of this information is essential to efficiently access, analyze, troubleshoot and evaluate the microarray experiments. RESULTS: We have developed a distributable software package designed to track and store the various pieces of data generated by a cDNA microarray facility. This includes the clone collection storage data, annotation data, workflow queues, microarray data, data repositories, sample submission information, and project/investigator information. This application was designed using a 3-tier client server model. The data access layer (1st tier) contains the relational database system tuned to support a large number of transactions. The data services layer (2nd tier) is a distributed COM server with full database transaction support. The application layer (3rd tier) is an internet based user interface that contains both client and server side code for dynamic interactions with the user. AVAILABILITY: This software is freely available to academic institutions and non-profit organizations at http://www.genomics.mcg.edu/niddkbtc.     

ASAP: analysis of peptide composition

SUMMARY: ASAP is a web tool designed to search for specific dipeptides, tripeptides and tetrapeptides in a protein sequence database. The server allows for: (a) identification of frequent and infrequent peptides and the creation of peptide probability tables for a given database of sequences (GenerNet program), (b) determination of the compatibility of an amino-acid sequence to the given peptide probability tables (ClonErrNet program); and (c) comparison of different protein databases based on peptide composition (CompNet program). ASAP server can be useful in protein engineering and/or protein classification studies.     

Social circulation and consumption of breast cancer health information among Yamatji in Western Australia

Breast cancer is one of the most common cancers in Australia, and other parts of the world, especially for women. Over the last few decades, more and more information has become available to the public about breast cancer. Throughout Yamatji country various formats for the dissemination of this information have been implemented, with varying degrees of success. Data collected as part of a doctoral research project on Yamatji breast cancer experiences shows that for information to be considered trustworthy and valid, it needs to be passed along social pathways that allow information ‘consumers’ to evaluate the information ‘provider’. Through this social circulation of health information, Yamatji actively engage and shape health information provision, as well as distribution. Likewise, by rejecting certain health information as untrustworthy, Yamatji assert agency in their self‐health management.     

Healthcare narratives from diverse communities--a self-assessment tool for healthcare providers

Research examining cultural diversity in the healthcare context has produced general themes about particular patient populations, and tools based on this research vary in their approach to improving cultural sensitivity and competency. Some tools pose questions that providers may ask patients to help them become better informed about their culture; others name areas of sensitivity that providers ought to be aware of in caring for culturally diverse patients. This tool is different. It focuses on the provider and its goal is to raise the provider's consciousness through self-reflection and examination. It consists of three parts: stories from interviews with actual patients followed by thought-provoking questions; commentaries on four of the narratives to help you measure your assessment of the ethical issues contained in each one; and a decision-making analysis grid to help you use the tool more effectively. It concludes with a bibliography for additional reading.     

Integrated databanks access and sequence/structure analysis services at the PBIL

The World Wide Web server of the PBIL (P?le Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.     

Efficient public key encryption with revocable keyword search in cloud computing

Public key encryption with keyword search plays very important role in the outsourced data management. In most of public key encryption schemes with keyword search, the server can unlimitedly execute keyword search ability after obtaining a trapdoor information of a keyword. To restrict the ability of the server’s unlimited search, we propose a novel public key encryption with revocable keyword search by combining hash chain and anonymous multi-receiver encryption scheme in this paper. The scheme can not only achieve security property of the indistinguishability of ciphertexts against an adaptive chosen keywords attack, but also resist off-line keyword guess attack. By comparison with Yu et al.’s scheme, our scheme is more efficient in terms of computational cost and communication overhead for the whole system.     

Medical professionalism videos on YouTube: Content exploration and appraisal of user engagement

BackgroundSocial media has become the fastest growing platform for sharing and retrieving information and knowledge, and YouTube is one of the most popular and growing sources of health and educational information video-sharing website. But, videos on this open platform are not peer-assessed, therefore, the accessible data should be adequately assessed. Till date, no exploration and analysis for assessing the credibility and usefulness of Medical professionalism videos available on YouTube are conducted.ObjectiveTo analyze the video sources, contents and quality of YouTube videos about the topic of medical professionalism.MethodsA systematic search was accomplished on YouTube videos during the period between March 1, 2020 and March 27, 2020. The phrases as significant words used throughout YouTube web search were ‘Professionalism in Medical Education’, Professionalism in medicine’, ‘Professionalism of medical students’, ‘Professionalism in healthcare’. ‘Teaching professionalism’, ‘Attributes of professionalism’. The basic information collected for each video included author’s/publisher’s name, total number of watchers, likes, dislikes and positive and undesirable remarks. The videos were categorized into educationally useful and useless established on the content, correctness of the knowledge and the advices. Different variables were measured and correlated for the data analysis.YouTube website was searched the using keywords ‘Professionalism in Medical Education’, Professionalism in medicine’, ‘Professionalism of medical students’, ‘Professionalism in healthcare’. ‘Teaching professionalism’, and ‘Attributes of professionalism’.ResultsAfter 2 rounds of screening by the subject experts and critical analysis of all the 137 YouTube videos, only 41 (29.92%) were identified as pertinent to the subject matter, i.e., educational type. After on expert viewing these 41 videos established upon our pre-set inclusion/exclusion criteria, only 17 (41.46%) videos were found to be academically valuable in nature.ConclusionMedical professionalism multimedia videos uploaded by the healthcare specialists or organizations on YouTube provided reliable information for medical students, healthcare workers and other professional. We conclude that YouTube is a leading and free online source of videos meant for students or other healthcare workers yet the viewers need to be aware of the source prior to using it for training learning.     

Politics of Presence at the Urban Margins. Emplacement as a Performative Force Among Migrant-Settlers in Chile*

ABSTRACT

Drawing from fieldwork conducted in Arica, a northern Chilean city, this paper addresses the process of ‘emplacement from the margins’ as a performative force in which materialities, affective dimensions and claims are tied together. It analyses how migrants become settlers in unauthorised camps on the fringes of Arica. I argue that in this process a ‘politics of presence’ emerges, intimately imbricated in the material constitution of these settlements. I explore the potential of such politics to break the ‘sensible’ order and open the possibility for ignored actors to become present as legitimate urban interlocutors. I discuss aspects of what Kathleen Stewart describes as ‘ordinary things that matter’ because they shimmer precariously, such as the dynamic contingency derived from the building procedures commonly used in unauthorised camps.     

ORBIT: an integrated environment for user-customized bioinformatics tools

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.     

Towards a multi‐trophic extension of metacommunity ecology

Metacommunity theory provides an understanding of how spatial processes determine the structure and function of communities at local and regional scales. Although metacommunity theory has considered trophic dynamics in the past, it has been performed idiosyncratically with a wide selection of possible dynamics. Trophic metacommunity theory needs a synthesis of a few influential axis to simplify future predictions and tests. We propose an extension of metacommunity ecology that addresses these shortcomings by incorporating variability among trophic levels in ‘spatial use properties’. We define ‘spatial use properties’ as a set of traits (dispersal, migration, foraging and spatial information processing) that set the spatial and temporal scales of organismal movement, and thus scales of interspecific interactions. Progress towards a synthetic predictive framework can be made by (1) documenting patterns of spatial use properties in natural food webs and (2) using theory and experiments to test how trophic structure in spatial use properties affects metacommunity dynamics.     

人类和模式生物标准转录数据库Web服务系统"StdTransDb"的技术实现

以RefSeq数据库和已测序基因组序列为模板,通过大规模计算得到代表转录各层次信息的"标准转录数据库",并利用通用网关接口技术,建立了人类和模式生物标准转录数据集Web服务系统。用户提交RefSeq记录号或自由注释词,可检索获得序列的全部信息,实现对基因结构解析的在线计算。目前系统覆盖了人、拟南芥、水稻、大鼠、小鼠、斑马鱼等6个物种,拥有数据记录18万余条。为深入研究人类及其他物种转录组提供了重要工具,并为进一步分析真核基因的可变剪接方式提供了坚实的数据基础。     

The Age of Angels: spiritualism and evolutionary progressionism in a nineteenth-century geologic time chart

The term ‘Anthropocene’ often carries apocalyptic overtones of environmental devastation, but many nineteenth-century iterations of the ‘Age of Humans’ idea were explicitly optimistic. The current time period was framed as a ‘Psychozoic Era’ or ‘Age of Mind’ in which human beings took their predetermined place at the pinnacle of ‘creation’. Hiram Alvin Reid, an amateur scientist in the midwestern United States, took this line of thinking a step further. He drafted a geologic time chart in which the current ‘Age of Man’ was succeeded by a future ‘Age of Angels’, wherein humans will become higher beings. Reid was a Christian spiritualist who thought that evolution drove both physical and spiritual advancement, including the recent development of a ‘sixth sense’ that allowed humans to perceive ghosts and angels. Reid’s views, while idiosyncratic and coloured by his metaphysical beliefs, drew heavily on mainstream concepts in biology and geology. Prominent geologists like James Dana and Joseph Le Conte argued for an Age of Mind in terms that mixed scientific rigor with religious and progressionist ideas. The Psychozoic was also embraced by many progressive-minded individuals outside the natural sciences, paralleling widespread modern interest in the Anthropocene.     

Location,location, location? No. Catalog number

Once you start to read this Editor’s Corner, you might wonder why I have devoted an entire article, albeit a short one, to this topic. Let me assure you there are reasons. First, I want to announce a new policy for the journal that will affect all research papers. Starting with all papers that are not currently in press, we will no longer be asking for geographical locations of research companies that follow the listing of a reagent. In Materials and Methods the authors typically refer to a reagent and then list the company and its location parenthetically. For example, “…p-nitrophenyl phosphate (Sigma-Aldrich, St. Louis, MO).” Instead, we will require catalog numbers. The reason is that it is now quite easy to find a company using the internet, and in fact you rarely need to know the location because it is rare that you would send a written order. On the other hand, knowing the name of the reagent is not always sufficient to narrow down the precise item. For example, if you search for “p-nitrophenyl phosphate” at the Sigma-Aldrich site, you get seven primary choices and it is not at all obvious which one to choose. When my lab uses p-nitrophenyl phosphate for the Pho8?60 assay, we use item N9389, which narrows it down to a precise reagent. Thus, we will start requiring papers to write “…p-nitrophenyl phosphate (Sigma-Aldrich, N9389).

Second, I think this is actually a useful change, and one that many journals will start to institute once they see it being done here. The old style of listing the city and state is a relic that is no longer relevant. Furthermore, it is not even clear in the current global marketplace if this is particularly helpful. For example, if I am ordering an item from Roche Applied Science, why would anyone care where it is coming from? It is highly unlikely that a researcher in Germany or Japan is going to order from Roche Applied Science that happens to be based in Indianapolis, IN when there are much closer sites in Mannheim, Germany and Tokyo, Japan. So, do not be surprised when you start to see more and more journals adopting this approach, and remember that you saw it here first. Autophagy—the cutting edge.     

EvoDesign: Designing Protein–Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function

EvoDesign (https://zhanglab.ccmb.med.umich.edu/EvoDesign) is an online server system for protein design. The method uses evolutionary profiles to guide the sequence search simulation and demonstrated significant advantages over physics-based approaches in terms of more accurately designing proteins that adopt desired target folds. Despite the success, the previous EvoDesign program focused only on monomer protein design, which limited its ability and usefulness in terms of designing functional proteins. In this work, we propose a new EvoDesign server, which extends the principles of evolution-based design to design protein–protein interactions. Starting from a two-chain complex structure, structurally similar interfaces are identified from known protein–protein interaction databases. An interface evolutionary profile is then constructed from a multiple sequence alignment of the interface analogies, which is combined with a newly developed, atomic-level physical energy function to guide the replica-exchange Monte Carlo simulation search. The purpose of the server is to redesign the specified complex chain to increase its stability and binding affinity for the other chain in the complex. With the improved scope and accuracy of the methodology, the new EvoDesign pipeline should become a useful online tool for functional protein design and drug discovery studies.     

PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions

The pseudo-amino acid composition has been widely used to convert complicated protein sequences with various lengths to fixed length digital feature vectors while keeping considerable sequence order information. However, so far the only software available to the public is the web server PseAAC (http://www.csbio.sjtu.edu.cn/bioinf/PseAAC), which has some limitations in dealing with large-scale datasets. Here, we propose a new cross-platform stand-alone software program, called PseAAC-Builder (http://www.pseb.sf.net), which can be used to generate various modes of Chou's pseudo-amino acid composition in a much more efficient and flexible way. It is anticipated that PseAAC-Builder may become a useful tool for studying various protein attributes.     

Elite responsiveness or elite autonomy: British immigration policy reconsidered

In recent years, a wide variety of organizations (notably the UN and nongovernmental organizations) have used sport as an interventionist tool to nurture peacemaking across divided communities. This paper examines and theorizes these peacemaking initiatives across the expanding ‘sport, development and peace’ (SDP) sector. I begin by locating SDP projects within their historical contexts, and as significant elements within the emerging ‘global civil society’. I then set out three ideal-type models of SDP project; namely, the ‘technical’, ‘dialogical’, and ‘critical’. Each model is examined through a set of common social heuristics, such as its core objectives and paradigmatic methods. The models may be employed to analyse other peacemaking and development fields. The first two models are most influential among existing SDP projects; the potential benefits of the ‘critical’ model are also outlined.     

Ten simple rules for finding and selecting R packages

R is an increasingly preferred software environment for data analytics and statistical computing among scientists and practitioners. Packages markedly extend R’s utility and ameliorate inefficient solutions to data science problems. We outline 10 simple rules for finding relevant packages and determining which package is best for your desired use. We begin in Rule 1 with tips on how to consider your purpose, which will guide your search to follow, where, in Rule 2, you’ll learn best practices for finding and collecting options. Rules 3 and 4 will help you navigate packages’ profiles and explore the extent of their online resources, so that you can be confident in the quality of the package you choose and assured that you’ll be able to access support. In Rules 5 and 6, you’ll become familiar with how the R Community evaluates packages and learn how to assess the popularity and utility of packages for yourself. Rules 7 and 8 will teach you how to investigate and track package development processes, so you can further evaluate their merit. We end in Rules 9 and 10 with more hands-on approaches, which involve digging into package code.