Web Apollo: a web-based genomic annotation editing platform

Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.     

Confundiendo al confuso: reflexiones sobre el factor de impacto,el índice h(irsch), el valor Q y otros cofactores que influyen en la felicidad del investigador

BackgroundThe need to evaluate curricula for sponsorship for research projects or professional promotion, has led to the search for tools that allow an objective valuation. However, the total number papers published, or citations of articles of a particular author, or the impact factor of the Journal where they are published are inadequate indicators for the evaluation of the quality and productivity of researchers. The h index, proposed by Hirsch, categorises the papers according to the number of citations per article. This tool appears to lack the limitations of other bibliometric tools but is less useful for non English-speaking authors.AimsTo propose and debate the usefulness of the existing bibliometric indicators and tools for the evaluation and categorization of researchers and scientific journals.MethodsSearch for papers on bibliometric tools.ResultsThere are some hot spots in the debate on the national and international evaluation of researchers’ productivity and quality of scientific journals. Opinions on impact factors and h index have been discussed. The positive discrimination, using the Q value, is proposed as an alternative for the evaluation of Spanish and Iberoamerican researchers.ConclusionsIt is very important de-mystify the importance of bibliometric indicators. The impact factor is useful for evaluating journals from the same scientific area but not for the evaluation of researchers’ curricula. For the comparison of curricula from two or more researchers, we must use the h index or the proposed Q value. the latter allows positive discrimination of the task for Spanish and Iberoamerican researchers.     

If We Share Data,Will Anyone Use Them? Data Sharing and Reuse in the Long Tail of Science and Technology

Research on practices to share and reuse data will inform the design of infrastructure to support data collection, management, and discovery in the long tail of science and technology. These are research domains in which data tend to be local in character, minimally structured, and minimally documented. We report on a ten-year study of the Center for Embedded Network Sensing (CENS), a National Science Foundation Science and Technology Center. We found that CENS researchers are willing to share their data, but few are asked to do so, and in only a few domain areas do their funders or journals require them to deposit data. Few repositories exist to accept data in CENS research areas.. Data sharing tends to occur only through interpersonal exchanges. CENS researchers obtain data from repositories, and occasionally from registries and individuals, to provide context, calibration, or other forms of background for their studies. Neither CENS researchers nor those who request access to CENS data appear to use external data for primary research questions or for replication of studies. CENS researchers are willing to share data if they receive credit and retain first rights to publish their results. Practices of releasing, sharing, and reusing of data in CENS reaffirm the gift culture of scholarship, in which goods are bartered between trusted colleagues rather than treated as commodities.     

Bioterrorism and biodefence research: changing the focus of microbiology

Fear that terrorists can use biological agents as weapons of mass destruction is significantly impacting the conduct of microbiological research. Abundant new funds are available for biodefence research, and many researchers are racing to enter the field. There are some concerns, however, that a large emphasis on this issue could skew the microbiology research agenda. Furthermore, new responsibilities for safely conducting research with biothreat agents and concern that information might be misused could drive some researchers away from the field.     

Certificates of confidentiality in research: rationale and usage

Certificates of confidentiality (COCs) are a tool to protect researchers from being compelled to release identifying information about their subjects. Whereas institutional review board (IRB) review and informed consent procedures are mandatory tools to protect human subjects, COCs are voluntary. There are limited data about who procures COCs and why, and whether they are useful. Three Institutes of the National Institutes of Health (NIH) provided data on 114 research projects that had received COCs. Eighty-three researchers had procured a single COC and 11 researchers had procured 31 COCs. One hundred and four (91%) of the COCs were obtained by researchers at academic sites, and 17 institutions collectively accounted for 82 COCs. The most commonly cited sources of information about COCs came from colleagues (n = 18, 35%) and previous experience (n = 17, 33%). The most common reasons for procuring a COC were that the research involved genetics (n = 28, 54%), the research could lead to social stigmatization or discrimination (n = 22, 42%), or the research could damage an individual's financial standing, employability, or reputation (n = 21, 40%). These findings show that COCs are often congregated within institutions and by particular individuals. This may be because others are unaware of COCs or because others do not believe they are necessary or useful.     

LabVelocity: online tools for life science products, protocols, technical information, MEDLINE searches, and laboratory calculations.

As the pace of life science discovery increases, so do the demands on researchers. To remain competitive in the life science industry, researchers must use every tool at their disposal to keep up with new products, protocols, news, and literature in their field. While there are now myriad Web sites that assist researchers with this problem, many suffer from confusing user interfaces, poorly designed search engines, and a narrow information focus. Here, we present LabVelocity, a user-friendly Web site that provides a free multidisciplinary information-gathering service for the life science research community. Using LabVelocity, a researcher can quickly find the products, protocols, technical references, news, MEDLINE abstracts, and interactive software tools necessary for an experiment. This aggregation of information can streamline experimental planning and is especially useful when researchers want to set up a new laboratory or to venture outside their field of expertise.     

How Can the Operating Environment for Nutrition Research Be Improved in Sub-Saharan Africa? The Views of African Researchers

Optimal nutrition is critical for human development and economic growth. Sub-Saharan Africa is facing high levels of food insecurity and only few sub-Saharan African countries are on track to eradicate extreme poverty and hunger by 2015. Effective research capacity is crucial for addressing emerging challenges and designing appropriate mitigation strategies in sub-Saharan Africa. A clear understanding of the operating environment for nutrition research in sub-Saharan Africa is a much needed prerequisite. We collected data on the barriers and requirements for conducting nutrition research in sub-Saharan Africa through semi-structured interviews with 144 participants involved in nutrition research in 35 countries in sub-Saharan Africa. A total of 133 interviews were retained for coding. The main barriers identified for effective nutrition research were the lack of funding due to poor recognition by policymakers of the importance of nutrition research and under-utilisation of research findings for developing policy, as well as an absence of research priority setting from within Africa. Current research topics were perceived to be mainly determined by funding bodies from outside Africa. Nutrition researchers argued for more commitment from policymakers at national level. The low capacity for nutrition research was mainly seen as a consequence of insufficient numbers of nutrition researchers, limited skills and a poor research infrastructure. In conclusion, African nutrition researchers argued how research priorities need to be identified by African stakeholders, accompanied by consensus building to enable creating a problem-driven national research agenda. In addition, it was considered necessary to promote interactions among researchers, and between researchers and policymakers. Multidisciplinary research and international and cross-African collaboration were seen as crucial to build capacity in sub-Saharan nutrition research.     

Guest research facilities at the Biologische Anstalt Helgoland: Past and present

The Biologische Anstalt Helgoland (BAH) offers unique possibilities for research and education in marine sciences in the southern part of the North Sea. Besides its own research duties, the Institute provides research facilities and technical assistance for guest scientists, assists in the teaching and education of university student groups, and conducts its own courses. The Institute further supplies universities and research institutions on the mainland with marine organisms. The marine station on Helgoland has 14 laboratories, with a total of 32 working places available for guest scientists. The Wadden Sea Institute in List on the island of Sylt offers 6 laboratories with a total of 18 working places. Furthermore, laboratory classrooms are located on Helgoland and in List for 50 and 20 participants, respectively. For the convenience of the guest researchers staying at the BAH, guest-houses are run on Helgoland (Arthur-Hagmeier-Haus, Wilhelm-Mielk-Haus) und in List (Adolf-Bückmann-Haus). Guest researchers have been welcome since the founding of the Institute in 1892. Heincke gave a brief report on the activities of the first visitors from 1892 to 1897. Only sporadic reports are available for the first 60 years of this century. Guest scientists and their activities have only been recorded in detail in the annual reports of the BAH since 1962. The number of researchers and the length of their visits have increased continuously since 1962. The research facilities on Helgoland, in List and Hamburg have been modernized during the last 20 years. In 1971, four modern laboratories for guest researchers could be opened on Helgoland with financial support of the German Research Foundation (DFG). The number, of guest researchers in List and Hamburg increased after the completion of new buildings in 1979 and 1982. The recent increase in research activities by guest scientists is due to numerous students, from many different universities, using the superb research facilities to do their Masters thesis, or Ph.D. Guest researchers and students either perform their own research or cooperate with scientists of the BAH.     

Human Research Ethics Committees: Examining their Roles and Practices

considerable time and resources are invested in the ethics review process. We present qualitative data on how human research ethics committee members and health researchers perceive the role and function of the committee. The findings are based on interviews with 34 Australian ethics committee members and 54 health researchers. Although all participants agreed that the primary role of the ethics committee was to protect participants, there was disagreement regarding the additional roles undertaken by committees. Of particular concern were the perceptions from some ethics committee members and researchers that ethics committees were working to protect the institution's interests, as well as being overprotective toward research participants. This has the potential to lead to poor relations and mistrust between ethics committees and researchers.     

The replicability crisis in science and protected area research: Poor practices and potential solutions

The reliability of some published research from well-funded disciplines of medicine and psychology has been brought into question. This is because some researchers failed to achieve consistent results after replicating published studies using the same methodology. Researchers have referred to this as the ‘replicability in science crisis’ and have identified several practices contributing to unreliable science. Protected area and other conservation researchers are unlikely to be immune from these poor practices given they use the same scientific approaches as other disciplines. Fortunately, there are solutions to the poor practices contributing to unreliable science. In this paper I identify those poor practices and describe solutions as identified by researchers from a range of disciplines. These solutions are transferable to protected area science and related conservation disciplines. Most solutions are not costly or demanding to implement. Adopting these solutions can improve the reliability of both published and unpublished research.     

A collaborative approach to bridging the gap between wildlife managers and researchers

Although most wildlife professionals agree that science should inform wildlife management decisions, disconnect still exists between researchers and managers. If researchers are not striving to incorporate their findings into management decisions, support for research programs by managers can wane. If managers are not using research findings to inform management decisions, those decisions may be less effective or more vulnerable to legal challenges. Both of these situations can have negative consequences for wildlife conservation. We outline a collaborative research-management approach to bridging the gap between wildlife managers and researchers. We describe differences in perspectives, perceptions, and priorities between managers and researchers; outline how and why the divide between researchers and managers has likely occurred and continues to grow; and present specific strategies and recommendations to foster stronger collaborations between managers and researchers. We advocate increased synergy between managers and researchers based on a shared vision of conservation and a collaborative structure that rewards researchers and managers. Most importantly, we suggest that relationships and communication between managers and researchers must be established early in research development and decision-making processes, fostering the trust needed for collaboration. Institutions and agencies can facilitate these relationships by creating opportunities and incentives for integrating collaborative research into management decisions. We suggest this approach will strengthen ties between researchers and managers, increase relevance of research to management decisions, promote effectiveness of management decisions, reduce legal challenges, and ultimately produce positive, tangible, and lasting effects on wildlife conservation. © 2019 The Wildlife Society.     

Data Sharing in Medical Research: An Empirical Investigation

Background:
Scientific research entails systematic investigation. Publishing the findings of research in peer reviewed journals implies a high level of confidence by the authors in the veracity of their interpretation. Therefore it stands to reason that researchers should be prepared to share their raw data with other researchers, so that others may enjoy the same level of confidence in the findings.
Method:
In a prospective study, 29 corresponding authors of original research articles in a medical journal (the British Medical Journal ) were contacted to ascertain their preparedness to share the data from their research. The email contact was in one of two forms, a general request and a specific request. The type of request a researcher received was randomly allocated.
Findings:
Researchers receiving specific requests for data were less likely, and slower, to respond than researchers receiving general requests. Only one researcher released data. Most researchers were reluctant to release their data. Some required further information, clarification, or authorship.
Interpretation:
The general reluctance of researchers to consider requests for their data is of concern. It raises questions about the level of confidence that should be placed on their interpretations of the data. It also highlights an unfortunate situation where researchers are more concerned with losing an advantage than advancing science.     

Challenges for proteomics core facilities

Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities.     

The MDCK variety pack: choosing the right strain

The MDCK cell line provides a tractable model for studying protein trafficking, polarity and junctions (tight, adherens, desmosome and gap) in epithelial cells. However, there are many different strains of MDCK cells available, including the parental line, MDCK I, MDCK II, MDCK.1, MDCK.2, superdome and supertube, making it difficult for new researchers to decide which strain to use. Furthermore, there is often inadequate reporting of strain types and where cells were obtained from in the literature. This review aims to provide new researchers with a guide to the different MDCK strains and a directory of where they can be obtained. We also hope to encourage experienced researchers to report the stain and origin of their MDCK cells.     

Protein micro- and macroarrays: digitizing the proteome

The early applications of microarrays and detection technologies have been centered on DNA-based applications. The application of array technologies to proteomics is now occurring at a rapid rate. Numerous researchers have begun to develop technologies for the creation of microarrays of protein-based screening tools. The stability of antibody molecules when bound to surfaces has made antibody arrays a starting point for proteomic microarray technology. To minimize disadvantages due to size and availability, some researchers have instead opted for antibody fragments, antibody mimics or phage display technology to create libraries for protein chips. Even further removed from antibodies are libraries of aptamers, which are single-stranded oligonucleotides that express high affinity for protein molecules. A variation on the theme of protein chips arrayed with antibody mimics or other protein capture ligand is that of affinity MS where the protein chips are directly placed in a mass spectrometer for detection. Other approaches include the creation of intact protein microarrays directly on glass slides or chips. Although many of the proteins may likely be denatured, successful screening has been demonstrated. The investigation of protein-protein interactions has formed the basis of a technique called yeast two-hybrid. In this method, yeast "bait" proteins can be probed with other yeast "prey" proteins fused to DNA binding domains. Although the current interpretation of protein arrays emphasizes microarray grids of proteins or ligands on glass slides or chips, 2-D gels are technically macroarrays of authentic proteins. In an innovative departure from the traditional concept of protein chips, some researchers are implementing microfluidic printing of arrayed chemistries on individual protein spots blotted onto membranes. Other researchers are using in-jet printing technology to create protein microarrays on chips. The rapid growth of proteomics and the active climate for new technology is driving a new generation of companies and academic efforts that are developing novel protein microarray techniques for the future.     

Neurotree: A Collaborative,Graphical Database of the Academic Genealogy of Neuroscience

Neurotree is an online database that documents the lineage of academic mentorship in neuroscience. Modeled on the tree format typically used to describe biological genealogies, the Neurotree web site provides a concise summary of the intellectual history of neuroscience and relationships between individuals in the current neuroscience community. The contents of the database are entirely crowd-sourced: any internet user can add information about researchers and the connections between them. As of July 2012, Neurotree has collected information from 10,000 users about 35,000 researchers and 50,000 mentor relationships, and continues to grow. The present report serves to highlight the utility of Neurotree as a resource for academic research and to summarize some basic analysis of its data. The tree structure of the database permits a variety of graphical analyses. We find that the connectivity and graphical distance between researchers entered into Neurotree early has stabilized and thus appears to be mostly complete. The connectivity of more recent entries continues to mature. A ranking of researcher fecundity based on their mentorship reveals a sustained period of influential researchers from 1850–1950, with the most influential individuals active at the later end of that period. Finally, a clustering analysis reveals that some subfields of neuroscience are reflected in tightly interconnected mentor-trainee groups.     

基于深度学习的蛋白质建模与设计

随着蛋白质序列及结构数据的大量累积,在获得了大量描述性信息之后如何有效利用海量数据,从已有数据中高效提取信息并且应用到下游任务当中就成为了研究者亟待解决的问题。蛋白质的设计可使新蛋白的研发不再受限于实验条件,这对药物靶点预测、新药研发和材料设计等领域具有重要意义。深度学习作为一种高效的数据特征提取方法,可以通过它对蛋白质数据进行建模,进而加入先验信息对蛋白质进行设计。故此基于深度学习的蛋白质设计就成为一个具有广阔前景的研究领域。文中主要阐述基于深度学习的蛋白质序列与结构数据的建模和设计方法。详述该方法的策略、原理、适用范围、应用实例。讨论了深度学习方法在本领域的应用前景及局限性,以期为相关研究提供参考。     

Identifying Trustworthy Experts: How Do Policymakers Find and Assess Public Health Researchers Worth Consulting or Collaborating With?

This paper reports data from semi-structured interviews on how 26 Australian civil servants, ministers and ministerial advisors find and evaluate researchers with whom they wish to consult or collaborate. Policymakers valued researchers who had credibility across the three attributes seen as contributing to trustworthiness: competence (an exemplary academic reputation complemented by pragmatism, understanding of government processes, and effective collaboration and communication skills); integrity (independence, "authenticity", and faithful reporting of research); and benevolence (commitment to the policy reform agenda). The emphases given to these assessment criteria appeared to be shaped in part by policymakers' roles and the type and phase of policy development in which they were engaged. Policymakers are encouraged to reassess their methods for engaging researchers and to maximise information flow and support in these relationships. Researchers who wish to influence policy are advised to develop relationships across the policy community, but also to engage in other complementary strategies for promoting research-informed policy, including the strategic use of mass media.