Peer Review Of Proposals Research Articles

Elevating the Fitness of Use of GBIF Occurrence Datasets: A proposal for peer review

Biodiversity data plays a pivotal role in understanding and conserving our natural world. As the largest occurrence data aggregator, the Global Biodiversity Information Facility (GBIF) serves as a valuable platform for researchers and practitioners to access and analyze biodiversity information from across the globe (Ball-Damerow et al. 2019). However, ensuring the quality of GBIF datasets remains a critical challenge (Chapman 2005). The community emphasizes the importance of data quality and its direct impact on the fitness of use for biodiversity research and conservation efforts (Chapman et al. 2020). While GBIF continues to grow in terms of the quantity of data it provides, the quality of these datasets varies significantly (Zizka et al. 2020). The biodiversity informatics community has been working diligently to ensure data quality at every step of data creation, curation, publication (Waller et al. 2021), and end-use (Gueta et al. 2019) by employing automated tools and flagging systems to identify and address issues. However, there is still more work to be done to effectively address data quality problems and enhance the fitness of use for GBIF-mediated data. I highlight a missing component in GBIF's data publication process: the absence of formal peer reviews. Despite GBIF encompassing the essential elements of a data paper, including detailed metadata, data accessibility, and robust data citation mechanisms, the lack of peer review hinders the credibility and reliability of the datasets mobilized through GBIF. To bridge this gap, I propose the implementation of a comprehensive peer review system within GBIF. Peer reviews would involve subjecting GBIF datasets to rigorous evaluation by domain experts and data scientists, ensuring the accuracy, completeness, and consistency of the data. This process would enhance the trustworthiness and usability of datasets, enabling researchers and policymakers to make informed decisions based on reliable biodiversity information. Furthermore, the establishment of a peer review system within GBIF would foster collaboration and knowledge exchange among the biodiversity community, as experts provide constructive feedback to dataset authors. This iterative process would not only improve data quality but also encourage data contributors to adhere to best practices, thereby elevating the overall standards of biodiversity data mobilization through GBIF.

How to Embed SRL in Online Learning Settings? Design Through Learning Analytics and Personalized Learning Design in Moodle

One of the main generic competencies in Higher Education is “Learning to Learn”. The key component of this competence is the capacity for self-regulated learning (SRL). For this competence to be developed, peer feedback seems useful because it fosters evaluative judgement. Following the principles of peer feedback processes, an online peer feedback proposal was created in the context of complex tasks in several degree courses (n = 448 students) at the University of Barcelona. A specific didactic sequence supported by digital technologies through Moodle was designed and validated after a deep analysis of the theoretical underpinnings of SRL models. A peer review proposal was ratified by the students, who pointed out the benefits of both receiving and, especially, giving feedback. The integration of Moodle tools with external tools such as Personalized Learning Design was highly valued by reviewers (n = 3 expert judges) and the possibilities for students to monitor their own progress through task completion was revealed as a positive aspect. Furthermore, the creation of personalized alerts to support learning processes also received a very high rating. The final model includes the changes derived from the validation process and suggests a reliable technology-supported intervention in an LMS, which is transferable to a larger scale.

Characterization and Speciation of Marine Materials Using Synchrotron Probes: Guidelines for New Users

Synchrotron instruments are useful for marine studies because they make nondestructive measurements of chemical composition and speciation on small sample volumes and at low concentrations. Synchrotron beamtime is available without cost using a peer-reviewed proposal system. New users do not have to be synchrotron radiation experts to design a good experiment, but some guidance is needed to design and propose appropriate experiments. Here we present some of that guidance to encourage and increase access to synchrotron facilities for marine science. We provide advice and examples from experts on how to access these instruments, choose the optimal sample preparation, and avoid common pitfalls. We then present some examples of successful marine studies that use these techniques.

Twin High-Resolution, High-Speed Imagers for the Gemini Telescopes: Instrument Description and Science Verification Results

Two new imaging instruments, ‘Alopeke and Zorro, were designed, built, and commissioned at the Gemini-North and Gemini-South telescopes in 2018 and 2019, respectively. Here we describe them and present the results from over a year of operation. The two identical instruments are based on the legacy of the DSSI (Differential Speckle Survey Instrument) instrument, successfully used for years at the WIYN and the Gemini telescopes in Hawaii and Chile. ‘Alopeke and Zorro are dual-channel imagers having both speckle (6.7″) and “wide-field” (∼1 arcminute) field-of-view options. They were built to primarily perform speckle interferometry providing diffraction-limited imagery at optical wavebands, yielding pixel scale uncertainties of ±0.21 mas, position angle uncertainties of ±0.7◦, and photometric uncertainties of Δm ± 0.02–0.04 magnitudes (for the blue and red channels, respectively) when run through the standard data reduction pipeline. One of their main scientific roles is the validation and characterization of exoplanets and their host stars as discovered by transit surveys such as the NASA Kepler, K2, and TESS missions. The limiting magnitude for speckle observations at Gemini can be quite faint (r ∼18 in good observing conditions) but typically the observed targets are brighter. The instruments can also function as conventional CCD imagers providing a 1 arc-minute field of view and allowing simultaneous two-color, high-speed time-series operation. These resident visitor instruments are remotely operable and are available for use by the community via the peer-reviewed proposal process.

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source.

In fragment-based drug discovery, hundreds or often thousands of compounds smaller than ~300 Da are tested against the protein of interest to identify chemical entities that can be developed into potent drug candidates. Since the compounds are small, interactions are weak, and the screening method must therefore be highly sensitive; moreover, structural information tends to be crucial for elaborating these hits into lead-like compounds. Therefore, protein crystallography has always been a gold-standard technique, yet historically too challenging to find widespread use as a primary screen. Initial XChem experiments were demonstrated in 2014 and then trialed with academic and industrial collaborators to validate the process. Since then, a large research effort and significant beamtime have streamlined sample preparation, developed a fragment library with rapid follow-up possibilities, automated and improved the capability of I04-1 beamline for unattended data collection, and implemented new tools for data management, analysis and hit identification. XChem is now a facility for large-scale crystallographic fragment screening, supporting the entire crystals-to-deposition process, and accessible to academic and industrial users worldwide. The peer-reviewed academic user program has been actively developed since 2016, to accommodate projects from as broad a scientific scope as possible, including well-validated as well as exploratory projects. Academic access is allocated through biannual calls for peer-reviewed proposals, and proprietary work is arranged by Diamond's Industrial Liaison group. This workflow has already been routinely applied to over a hundred targets from diverse therapeutic areas, and effectively identifies weak binders (1%-30% hit rate), which both serve as high-quality starting points for compound design and provide extensive structural information on binding sites. The resilience of the process was demonstrated by continued screening of SARS-CoV-2 targets during the COVID-19 pandemic, including a 3-week turn-around for the main protease.

High-pressure small-angle X-ray scattering cell for biological solutions and soft materials.

Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.

An alternate Proposal for Peer Review

An alternate Proposal for Peer Review

The XFP (17-BM) beamline for X-ray footprinting at NSLS-II.

Hydroxyl-radical mediated synchrotron X-ray footprinting (XF) is a powerful solution-state technique in structural biology for the study of macromolecular structure and dynamics of proteins and nucleic acids, with several synchrotron resources available to serve the XF community worldwide. The XFP (Biological X-ray Footprinting) beamline at the NSLS-II was constructed on a three-pole wiggler source at 17-BM to serve as the premier beamline for performing this technique, providing an unparalleled combination of high flux density broadband beam, flexibility in beam morphology, and sample handling capabilities specifically designed for XF experiments. The details of beamline design, beam measurements, and science commissioning results for a standard protein using the two distinct XFP endstations are presented here. XFP took first light in 2016 and is now available for general user operations through peer-reviewed proposals. Currently, beam sizes from 450 µm × 120 µm to 2.7 mm × 2.7 mm (FWHM) are available, with a flux of 1.6 × 1016 photons s-1 (measured at 325 mA ring current) in a broadband (∼5-16 keV) beam. This flux is expected to rise to 2.5 × 1016 photons s-1 at the full NSLS-II design current of 500 mA, providing an incident power density of >500 W mm-2 at full focus.

Multidisciplinary Science at the Molecular Foundry

Multidisciplinary Science at the Molecular Foundry

The file drawer is full. Should we worry?

Social Science Experiments that produce null results face a higher barrier to publication than those that yield statistically significant differences. Whether this is a problem depends on how many null but otherwise valid results might be trapped in the file drawer. Franco et al. use a Time-sharing Experiments in the Social Sciences archive of nearly 250 peer-reviewed proposals of social science experiments conducted on nationally representative samples. They find that only 10 out of 48 null results were published, whereas 56 out of 91 studies with strongly significant results made it into a journal. Science , this issue p. [1502][1] [1]: /lookup/doi/10.1126/science.1255484

Social science. Publication bias in the social sciences: unlocking the file drawer.

We studied publication bias in the social sciences by analyzing a known population of conducted studies--221 in total--in which there is a full accounting of what is published and unpublished. We leveraged Time-sharing Experiments in the Social Sciences (TESS), a National Science Foundation-sponsored program in which researchers propose survey-based experiments to be run on representative samples of American adults. Because TESS proposals undergo rigorous peer review, the studies in the sample all exceed a substantial quality threshold. Strong results are 40 percentage points more likely to be published than are null results and 60 percentage points more likely to be written up. We provide direct evidence of publication bias and identify the stage of research production at which publication bias occurs: Authors do not write up and submit null findings.

Blind Dates in Sciences

Every researcher remembers the moment when he or she sends in a manuscript or proposal for peer review. It is truly like going out on a blind date. Without knowing the identities of the peers, we often wait in the dark for an answer as to whether our best ideas will receive precious funding or years of hard labor will be recognized by a prestigious journal. Because our academic success and sometimes even viability depend on such an outcome, the wait can be excruciating. Unfortunately, as any seasoned member of the scientific community will warn you, the outcome of scientific peer reviews is dominated by rejection. Current funding levels at the National Institutes of Health imply that ≈90% of applications will be rejected and some top tier journals see even higher rejection rates among submitted manuscripts. Learning the odds-improving skills to navigate through various peer review processes has become a required course of scientific training and teaching curriculum for junior investigators.1 However, no matter how much you think you are prepared, the reality is, as long as we choose to pursue a scientific career, rejection from peer review will always be a constant in this occupation. Therefore, it is useful to discuss how to make the peer review experience constructive rather than destructive. In this article, we will focus our discussion on the peer review process for manuscripts, with particular insights provided by the editors of several leading scientific journals. With overwhelmingly negative verdicts and being blinded from much of the process, an author’s perception of peer review is expectedly dark and suspicious. Based on an online survey reported by Ho et al,2 less than half of authors think that biomedical journal review systems are fair and only a quarter of them think that the outcome is scientifically …

Beamline 08ID-1, the prime beamline of the Canadian Macromolecular Crystallography Facility

Beamline 08ID-1 is the prime macromolecular crystallography beamline at the Canadian Light Source. Based on a small-gap in-vacuum undulator, it is designed for challenging projects like small crystals and crystals with large cell dimensions. Beamline 08ID-1, together with a second bending-magnet beamline, constitute the Canadian Macromolecular Crystallography Facility (CMCF). This paper presents an overall description of the 08ID-1 beamline, including its specifications, beamline software and recent scientific highlights. The end-station of the beamline is equipped with a CCD X-ray detector, on-axis crystal visualization system, a single-axis goniometer and a sample automounter allowing remote access to the beamline. The general user program is guaranteed up to 55% of the useful beam time and is run under a peer-review proposal system. The CMCF staff provide `Mail-in' crystallography service to the users with the highest-scored proposals.

Status of CHESS facility and research programs: 2010

Abstract CHESS is a hard X-ray synchrotron radiation national facility located at Cornell University and funded by the National Science Foundation. It is open to all scientists by peer-reviewed proposal and serves 500–1000 visitors each year. The CHESS scientific and technical staff develops forefront research tools and X-ray instrumentation and methods and supports 12 experimental stations delivering high intensity X-ray beams produced at 5.3 GeV and 250 mA. The facility consists of a mix of dedicated and flexible experimental stations that are easily configured for general X-ray diffraction (wide- and small-angle), spectroscopy, imaging applications, etc. Dedicated stations support high-pressure powder X-ray diffraction, pulsed-laser deposition for layer-by-layer growth of surfaces, and three dedicated stations for protein crystallography. Specialized resource groups at the laboratory include: an X-ray detector group; MacCHESS, an NIH-supported research resource for protein crystallography; the G-line division, which primarily organizes graduate students and Cornell faculty members around three X-ray stations; a high-pressure diamond-anvil cell support laboratory; and a monocapillary drawing facility for making microbeam X-ray optics. Research is also ongoing to upgrade CHESS to a first-ever 5 GeV, 100 mA Energy Recovery Linac (ERL) hard X-ray source. This source will provide ultra-high spectral-brightness and

Business Boost Thwarted

A congressional Democrat with clout and a Republican with conviction have teamed up to block a plan to give small businesses a bigger slice of the federal research pie. Last week's vote by the House of Representatives came on a bill to reauthorize two research programs that fund peer-reviewed proposals from startup companies through a tax on 11 science agencies. Of greatest concern to science lobbyists was language raising the share going to the SBIR (Small Business Innovation Research) and STTR (technology transfer research) programs from a combined 2.8% to 3.6%, an increase that would have siphoned off an additional $650 million a year. But representatives David Obey (D-WI), chair of the powerful appropriations committee, and Vernon Ehlers (R-MI), a former physics professor who had failed to derail the increase during an earlier committee vote, argued successfully on the House floor that this was the wrong time to tap already stressed science budgets.

SALSA: Advances in Residual Stress Measurement at ILL

SALSA (Strain Analyser for Large Scale engineering Applications) is a novel instrument for strain imaging at the high flux neutron reactor of the Institut Max von Laue – Paul Langevin (ILL) in Grenoble, France. It is the first of its kind that uses a precise robotic sample stage for sample manipulation. In addition to standard xyz-translation it provides tilts up to ±30° about any horizontal axis. Its load capacity is more than 500 kg and samples up to 1.5 m in length can be scanned with high accuracy. Thanks to a double focusing monochromator and supermirror guide count times are very short. A broad wavelength range, variable beam optics, including radial focusing collimators for high lateral resolution, make it a very flexible instrument for a large variety of strain imaging applications in small and large specimens. The instrument has been commissioned in 2005 and is open for access by a peer review proposal system and as well by industry. The paper describes the important aspects of the instrument and results from the first experiments.

The James Webb Space Telescope

The James Webb Space Telescope (JWST) is a large (6.6 m), cold (<50 K), infrared (IR)-optimized space observatory that will be launched early in the next decade into orbit around the second Earth–Sun Lagrange point. The observatory will have four instruments: a near-IR camera, a near-IR multiobject spectrograph, and a tunable filter imager will cover the wavelength range, 0.6 < ; < 5.0 μ m, while the mid-IR instrument will do both imaging and spectroscopy from 5.0 < ; < 29 μ m. The JWST science goals are divided into four themes. The key objective of The End of the Dark Ages: First Light and Reionization theme is to identify the first luminous sources to form and to determine the ionization history of the early universe. The key objective of The Assembly of Galaxies theme is to determine how galaxies and the dark matter, gas, stars, metals, morphological structures, and active nuclei within them evolved from the epoch of reionization to the present day. The key objective of The Birth of Stars and Protoplanetary Systems theme is to unravel the birth and early evolution of stars, from infall on to dust-enshrouded protostars to the genesis of planetary systems. The key objective of the Planetary Systems and the Origins of Life theme is to determine the physical and chemical properties of planetary systems including our own, and investigate the potential for the origins of life in those systems. Within these themes and objectives, we have derived representative astronomical observations. To enable these observations, JWST consists of a telescope, an instrument package, a spacecraft, and a sunshield. The telescope consists of 18 beryllium segments, some of which are deployed. The segments will be brought into optical alignment on-orbit through a process of periodic wavefront sensing and control. The instrument package contains the four science instruments and a fine guidance sensor. The spacecraft provides pointing, orbit maintenance, and communications. The sunshield provides passive thermal control. The JWST operations plan is based on that used for previous space observatories, and the majority of JWST observing time will be allocated to the international astronomical community through annual peer-reviewed proposal opportunities.

The Scholarship of Teaching and Learning

The origins and conceptual foundations for the scholarship of teaching and learning (SOTL) are described. National programs aimed at building understanding and acceptance of SOTL are reviewed. To illustrate campus activity, NC State's faculty-led teaching initiatives over the past six years are recounted. Finally, with the goal of providing for teaching what peer-reviewed journals provide for research, a proposal for national peer-review of teaching is offered.

The National High Magnetic Field Laboratory

We describe two of the main user facilities of the National High Magnetic Field Laboratory (NHMFL): (a) the General Purpose DC Field Facility with nine resistive and hybrid magnet stations with continuous fields between 20 and 45 T, and (b) the CIMAR Facilities with 17 spectrometers for the NMR Spectroscopy and Imaging Program, the Fourier Transform ICR Mass Spectrometry Program and the Electron Magnetic Resonance Spectroscopy Program. The facilities are located in Tallahassee, and Gainesville, FL. Members of the worldwide science and engineering communities can access NHMFL facilities, generally without cost, through a peer-reviewed proposal process.

Expanding your laboratory by accessing collaboratory resources.

The Environmental Molecular Sciences Laboratory (EMSL) in Richland, Washington, is the home of a research facility setup by the United States Department of Energy (DOE). The facility is atypical because it houses over 100 cutting-edge research systems for the use of researchers all over the United States and the world. Access to the lab is requested through a peer-review proposal process and the scientists who use the facility are generally referred to as ‘users’. There are six main research facilities housed in EMSL, all of which host visiting researchers. Several of these facilities also participate in the EMSL Collaboratory, a remote access capability supported by EMSL operations funds. Of these, the High-Field Magnetic Resonance Facility (HFMRF) and Molecular Science Computing Facility (MSCF) have a significant number of their users performing remote work. The HFMRF in EMSL currently houses 12 NMR spectrometers that range in magnet field strength from 7.05T to 21.1T. Staff associated with the NMR facility offers scientific expertise in the areas of structural biology, solid-state materials/catalyst characterization, and magnetic resonance imaging (MRI) techniques. The way in which the HFMRF operates, with a high level of dedication to remote operation across the full suite of High-Field NMR spectrometers, hasmore » earned it the name “Virtual NMR Facility”. This review will focus on the operational aspects of remote research done in the High-Field Magnetic Resonance Facility and the computer tools that make remote experiments possible.« less