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ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTWater as an Active Constituent in Cell BiologyPhilip BallView Author Information Nature, 4-6 Crinan Street, London N1 9XW, U.K. Cite this: Chem. Rev. 2008, 108, 1, 74–108Publication Date (Web):December 21, 2007Publication History Received28 December 2006Published online21 December 2007Published inissue 1 January 2008https://pubs.acs.org/doi/10.1021/cr068037ahttps://doi.org/10.1021/cr068037aresearch-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views15708Altmetric-Citations1751LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Hydration,Hydrophobicity,Ions,Molecules,Noncovalent interactions Get e-Alerts

As information and communication technology has become pervasive in our society, we are increasingly dependent on both digital data and repositories that provide access to and enable the use of such resources. Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold.

The quantitative rescattering theory (QRS) for high-order harmonic generation (HHG) by intense laser pulses is presented. According to the QRS, HHG spectra can be expressed as a product of a returning electron wave packet and the photorecombination differential cross section of the laser-free continuum electron back to the initial bound state. We show that the shape of the returning electron wave packet is determined mostly by the laser. The returning electron wave packets can be obtained from the strong-field approximation or from the solution of the time-dependent Schr\"odinger equation (TDSE) for a reference atom. The validity of the QRS is carefully examined by checking against accurate results for both harmonic magnitude and phase from the solution of the TDSE for atomic targets within the single active electron approximation. Combining with accurate transition dipoles obtained from state-of-the-art molecular photoionization calculations, we further show that available experimental measurements for HHG from partially aligned molecules can be explained by the QRS. Our results show that quantitative description of the HHG from aligned molecules has become possible. Since infrared lasers of pulse durations of a few femtoseconds are easily available in the laboratory, they may be used for dynamic imaging of a transient molecule with femtosecond temporal resolutions.

Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements. As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing such links. We consider 531, 889 journal articles published by PLOS and BMC, develop an automatic system for labelling their data availability statements according to four categories based on their content and the type of data availability they display, and finally analyze the citation advantage of different statement categories via regression. We find that, following mandated publisher policies, data availability statements become very common. In 2018 93.7% of 21,793 PLOS articles and 88.2% of 31,956 BMC articles had data availability statements. Data availability statements containing a link to data in a repository-rather than being available on request or included as supporting information files-are a fraction of the total. In 2017 and 2018, 20.8% of PLOS publications and 12.2% of BMC publications provided DAS containing a link to data in a repository. We also find an association between articles that include statements that link to data in a repository and up to 25.36% (± 1.07%) higher citation impact on average, using a citation prediction model. We discuss the potential implications of these results for authors (researchers) and journal publishers who make the effort of sharing their data in repositories. All our data and code are made available in order to reproduce and extend our results.

P‐wave and S‐wave delay times from the broadband data of the southern Africa seismic experiment have been inverted to obtain three‐dimensional images of velocity perturbations in the mantle beneath southern Africa. High velocity mantle roots appear to extend to depths of at least 250 km, and locally to depths of 300 km beneath the Kaapvaal and Zimbabwe cratons. Thick roots are confined to the Archean cratons, with no evidence for similar structures beneath the adjacent Proterozoic mobile belts. The Kaapvaal craton was modified ca. 2.05 Ga by the Bushveld magmatic event, which affected a broad swath of cratonic mantle beneath and to the west of the exposed Bushveld Complex. The mantle beneath the extended Bushveld province is characterized by seismic velocities lower than those observed in regions of undisturbed cratonic mantle. The mantle beneath the Limpopo Belt, an Archean collisional zone sandwiched between the Kaapvaal and Zimbabwe cratons, exhibits a cratonic signature.

Following our call to join in the discussion over the suitability of implementing a reporting checklist for bio–nano papers, the community responds.

The idea of nature as engineer is an old one, but the realization that this metaphor can be extended (should we say retracted?) to the molecular scale has become common currency only over the past two decades or so. Two reasons for this are perhaps paramount. First, the picture of the cell has been transformed from that of a 'wet chemical' melange—'a vessel, filled with a homogeneous solution, in which all chemical processes take place', as Franz Hofmeister put it in 1901—into an image of a sort of fluid factory, a production plant in which molecular machinery works in near-fantastic orchestration to generate complex products from raw materials. This mechanism is self-assembling, self-repairing and self-replicating. The concept of proteins and nucleic acids as 'molecular machines' is now a mainstream one in cell biology. Second, technological advances have made us accustomed to the idea that engineering can be conducted at scales too small to see with the naked eye, yet employing principles—mechanical, electrical, hydraulic, optical, tribological—familiar from the macroscopic world. Molecular electronics and computing, microelectromechanical devices and nanotechnology, are now mainstream concepts, and are validated by at least some degree of physical realization.

We present a consensus-based checklist to improve and document the transparency of research reports in social and behavioural research. An accompanying online application allows users to complete the form and generate a report that they can submit with their manuscript or post to a public repository.

ESEP Ethics in Science and Environmental Politics Contact the journal RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections ESEP 8:5-7 (2008) - DOI: https://doi.org/10.3354/esep00078 Escape from the impact factor Philip Campbell* Nature, 4 Crinan Street, London N1 9XW, UK *Email: nature@nature.com ABSTRACT: As Editor-in-Chief of the journal Nature, I am concerned by the tendency within academic administrations to focus on a journal's impact factor when judging the worth of scientific contributions by researchers, affecting promotions, recruitment and, in some countries, financial bonuses for each paper. Our own internal research demonstrates how a high journal impact factor can be the skewed result of many citations of a few papers rather than the average level of the majority, reducing its value as an objective measure of an individual paper. Proposed alternative indices have their own drawbacks. Many researchers say that their important work has been published in low-impact journals. Focusing on the citations of individual papers is a more reliable indicator of an individual's impact. A positive development is the increasing ability to track the contributions of individuals by means of author-contribution statements and perhaps, in the future, citability of components of papers rather than the whole. There are attempts to escape the hierarchy of high-impact-factor journals by means of undifferentiated databases of peer-reviewed papers such as PLoS One. It remains to be seen whether that model will help outstanding work to rise to due recognition regardless of editorial selectivity. Although the current system may be effective at measuring merit on national and institutional scales, the most effective and fair analysis of a person's contribution derives from a direct assessment of individual papers, regardless of where they were published. KEY WORDS: Bibliometrics · Impact factor · Academic merit Full text in pdf format PreviousNextCite this article as: Campbell P (2008) Escape from the impact factor. Ethics Sci Environ Polit 8:5-7. https://doi.org/10.3354/esep00078 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in ESEP Vol. 8, No. 1. Online publication date: June 03, 2008 Print ISSN: 1863-5415; Online ISSN: ISSN Copyright © 2008 Inter-Research.

This article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP), a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH BioCADDIE program. The structure of the roadmap presented here follows the "life of a paper" workflow and includes the categories Pre-submission, Submission, Production, and Publication. The roadmap is intended to be publisher-agnostic so that all publishers can use this as a starting point when implementing JDDCP-compliant data citation. Authors reading this roadmap will also better know what to expect from publishers and how to enable their own data citations to gain maximum impact, as well as complying with what will become increasingly common funder mandates on data transparency.

Without careful dissection of the ways in which biases can be encoded into artificial intelligence (AI) health technologies, there is a risk of perpetuating existing health inequalities at scale. One major source of bias is the data that underpins such technologies. The STANDING Together recommendations aim to encourage transparency regarding limitations of health datasets and proactive evaluation of their effect across population groups. Draft recommendation items were informed by a systematic review and stakeholder survey. The recommendations were developed using a Delphi approach, supplemented by a public consultation and international interview study. Overall, more than 350 representatives from 58 countries provided input into this initiative. 194 Delphi participants from 25 countries voted and provided comments on 32 candidate items across three electronic survey rounds and one in-person consensus meeting. The 29 STANDING Together consensus recommendations are presented here in two parts. Recommendations for Documentation of Health Datasets provide guidance for dataset curators to enable transparency around data composition and limitations. Recommendations for Use of Health Datasets aim to enable identification and mitigation of algorithmic biases that might exacerbate health inequalities. These recommendations are intended to prompt proactive inquiry rather than acting as a checklist. We hope to raise awareness that no dataset is free of limitations, so transparent communication of data limitations should be perceived as valuable, and absence of this information as a limitation. We hope that adoption of the STANDING Together recommendations by stakeholders across the AI health technology lifecycle will enable everyone in society to benefit from technologies which are safe and effective.

Busy busy busy: Water is not a passive solvent in biology, but plays an active role in many biomolecular and cell processes. It can be regarded as a kind of biomolecule in its own right, adapting its structure and dynamics to the biological macromolecules and other cell solutes that it accommodates. In particular, water may hold the key to the way some proteins interact, fold and bind their substrates.

A large extraterrestrial body hit the Yucatán Peninsula at the end of the Cretaceous period. Models suggest that a substantial amount of thermal radiation was delivered to the Earth’s surface by the impact, leading to the suggestion that it was capable of igniting extensive wildfires and contributed to the end-Cretaceous extinctions. We have reproduced in the laboratory the most intense impact-induced heat fluxes estimated to have reached different points on the Earth’s surface using a fire propagation apparatus and investigated the ignition potential of forest fuels. The experiments indicate that dry litter can ignite, but live fuels typically do not, suggesting that any ignition caused by impact-induced thermal radiation would have been strongly regional dependent. The intense, but short-lived, pulse downrange and at proximal and intermediate distances from the impact is insufficient to ignite live fuel. However, the less intense but longer-lasting thermal pulse at distal locations may have ignited areas of live fuels. Because plants and ecosystems are generally resistant to single localized fire events, we conclude that any fires ignited by impact-induced thermal radiation cannot be directly responsible for plant extinctions, implying that heat stress is only part of the end-Cretaceous story.

OBJECTIVE: ) became the first journals to routinely include patients and the public in the peer review process of journal articles. This survey explores the perspectives and early experiences of these reviewers. DESIGN: A cross-sectional survey. SETTING AND PARTICIPANTS: who have been invited to review. RESULTS: The response rate was 69% (157/227) for those who had previously reviewed and 31% (67/217) for those who had not yet reviewed. Reviewers described being motivated to review by the opportunity to include the patient voice in the research process, influence the quality of the biomedical literature and ensure it meets the needs of patients. Of the 157 who had reviewed, 127 (81%) would recommend being a reviewer to other patients and carers. 144 (92%) thought more journals should adopt patient and public review. Few reviewers (16/224, 7%) reported concerns about doing open review. Annual acknowledgement on the journals' websites was welcomed as was free access to journal information. Participants were keen to have access to more online resources and training to improve their reviewing skills. Suggestions on how to improve the reviewing experience included: allowing more time to review; better and more frequent communication; a more user-friendly process; improving guidance on how to review including videos; improving the matching of papers to reviewers' experience; providing more varied sample reviews and brief feedback on the usefulness of reviews; developing a sense of community among reviewers; and publicising of the contribution that patient and public review brings. CONCLUSIONS: Patient and public reviewers shared practical ideas to improve the reviewing experience and these will be reviewed to enhance the guidance and support given to them.

An output of the Data policy standardisation and implementation Interest Group (IG) of the Research Data Alliance (RDA) More journals and publishers – and funding agencies and institutions – are introducing research data policies. But as the prevalence of policies increases, there is potential to confuse researchers and support staff with numerous or conflicting policy requirements. We define and describe 14 features of journal research data policies and arrange these into a set of six standard policy types or tiers, which can be adopted by journals and publishers to promote data sharing in a way that encourages good practice and is appropriate for their audience’s perceived needs. Policy features include coverage of topics such as data citation, data repositories, data availability statements, data standards and formats, and peer review of research data. These policy features and types have been created by reviewing the policies of multiple scholarly publishers, which collectively publish more than 10,000 journals, and through discussions and consensus building with multiple stakeholders in research data policy via the Data Policy Standardisation and Implementation Interest Group of the Research Data Alliance. Implementation guidelines for the standard research data policies for journals and publishers are also provided, along with template policy texts which can be implemented by journals in their Information for Authors and publishing workflows. We conclude with a call for collaboration across the scholarly publishing and wider research community to drive further implementation and adoption of consistent research data policies. <strong>Publisher's Note:</strong> a correction article relating to this publication has been published and can be found at <a href="http://doi.org/10.5334/dsj-2020-017">http://doi.org/10.5334/dsj-2020-017</a>

OBJECTIVES: To assess whether reports from reviewers recommended by authors show a bias in quality and recommendation for editorial decision, compared with reviewers suggested by other parties, and whether reviewer reports for journals operating on open or single-blind peer review models differ with regard to report quality and reviewer recommendations. DESIGN: Retrospective analysis of the quality of reviewer reports using an established Review Quality Instrument, and analysis of reviewer recommendations and author satisfaction surveys. SETTING: BioMed Central biology and medical journals. BMC Infectious Diseases and BMC Microbiology are similar in size, rejection rates, impact factors and editorial processes, but the former uses open peer review while the latter uses single-blind peer review. The Journal of Inflammation has operated under both peer review models. SAMPLE: Two hundred reviewer reports submitted to BMC Infectious Diseases, 200 reviewer reports submitted to BMC Microbiology and 400 reviewer reports submitted to the Journal of Inflammation. RESULTS: For each journal, author-suggested reviewers provided reports of comparable quality to non-author-suggested reviewers, but were significantly more likely to recommend acceptance, irrespective of the peer review model (p<0.0001 for BMC Infectious Diseases, BMC Microbiology and the Journal of Inflammation). For BMC Infectious Diseases, the overall quality of reviewer reports measured by the Review Quality Instrument was 5% higher than for BMC Microbiology (p=0.042). For the Journal of Inflammation, the quality of reports was the same irrespective of the peer review model used. CONCLUSIONS: Reviewers suggested by authors provide reports of comparable quality to non-author-suggested reviewers, but are significantly more likely to recommend acceptance. Open peer review reports for BMC Infectious Diseases were of higher quality than single-blind reports for BMC Microbiology. There was no difference in quality of peer review in the Journal of Inflammation under open peer review compared with single blind.

Abstract The discovery of large amounts of soot in clays deposited at the Cretaceous‐Paleogene (K‐Pg) boundary and linked to the ~65 Ma Chicxulub impact crater led to the hypothesis that major wildfires were a consequence of the asteroid impact. Subsequently, several lines of evidence, including the lack of charcoal in North American sites, were used to argue against global wildfires. Close to the impact site fires are likely to be directly ignited by the impact fireball, whereas globally they could be ignited by radiation from the reentry of hypervelocity ejecta. To‐date, models of the latter have yet to take into account that ejection—and thus the emission of thermal radiation—is asymmetric and dependent on impact angle. Here, we model: (1) the impact and ejection of material, (2) the ballistic continuation of ejecta around a spherical Earth, and (3) the thermal pulse delivered to the Earth's surface when ejecta reenters the atmosphere. We find that thermal pulses in the downrange direction are sufficient to ignite flora several thousand kilometers from Chicxulub, whereas pulses at most sites in the uprange direction are too low to ignite even the most susceptible plant matter. Our analyses and models suggest some fires were ignited by the impact fireball and ejecta reentry, but that the nonuniform distribution of thermal radiation across the surface of the Earth is inconsistent with the ignition of fires globally as a direct and immediate result of the Chicxulub impact. Instead, we propose that the desiccation of flora by ejecta reentry, as well as the effects of postimpact global cooling/darkness, left much of the terrestrial flora prone to fires, and that the volume of soot in the global K‐Pg layer is explained by a combination of syn‐ and postimpact wildfires.

In recent years, many questions have been raised about whether public confidence in science is changing. To clarify recent trends in the public's confidence and factors that are associated with these feelings, an effort initiated by the National Academies' Strategic Council for Research Excellence, Integrity, and Trust (the Strategic Council) analyzed findings from multiple survey research organizations. The Strategic Council's effort, which began in 2022, found that U.S. public confidence in science, the scientific community, and leaders of scientific communities is high relative to other civic, cultural, and governmental institutions for which researchers regularly collect such data. However, confidence in these institutions has fallen during the previous 5 years. Science's decline, while real, is similar to or less than that in the other groups. A recent study goes into greater detail by exploring public views of science. From these data, we observe that many of the surveyed U.S. public question the extent to which scientists share their values or overcome personal biases when presenting conclusions. At the same time, large majorities agree on certain types of actions that they want scientists to take. For example, 84% respond that it is "somewhat important" or "very important" for scientists to disclose their funders. Ninety-two percent (92%) offer the same responses to scientists "being open to changing their minds based on new evidence." Collectively, these data clarify how the U.S. public views science and scientists. They also suggest actions that can affect public confidence in science and scientists in the years to come.

Unconventional prefoldin RPB5 interactor (URI), an evolutionary conserved member of the prefoldin family of molecular chaperones, plays a central role in the regulation of nutrient-sensitive, TOR (target-of-rapamycin)-dependent gene expression programs in yeast. Mammalian URI has been shown to associate with key components of the transcriptional machinery, including RPB5, a shared subunit of all three RNA polymerases, the ATPases TIP48 and TIP49, which are present in various chromatin remodeling complexes, and human PAF1 and parafibromin, which are components of a transcription elongation complex. Here, we provide the first functional characterization of a URI-1 homolog in a multicellular organism and show that the C. elegans gene uri-1 is essential for germ cell proliferation. URI-1-deficient cells exhibit cell cycle arrest and display DNA breaks as evidenced by TUNEL staining and the appearance of HUS-1::GFP foci formation. In addition, uri-1(lf) mutants and uri-1(RNAi) worms show a p53-dependent increase in germline apoptosis. Our findings indicate that URI-1 has an important function in the mitotic and meiotic cell cycles. Furthermore, they imply that URI-1 participates in a pathway(s) that is associated with the suppression of endogenous genotoxic DNA damage and highlight a role for URI-1 in the control of genome integrity.

Synthetic biology—the redesign of biological molecules, structures and organisms—is potentially one of the most powerful emerging technologies today. The modification of biological structures has already been pursued for a variety of nanotechnological objectives; but synthetic biology could provide the tools and understanding needed both to develop 'nanobiotechnology' in a more systematic manner and to expand the scope of what it might achieve. In this article I shall review what has been attained so far in this field, and look at some of the nanoscale possibilities that an engineering approach to cell biology might herald.