The role of community-based Hubs in reef restoration: Collaborative monitoring at Moore Reef

The Cairns-Port Douglas region is home to multiple coral rehabilitation and stewardship projects supported by scientists, Traditional Owners, and a range of local stakeholders. The Cairns-Port Douglas Reef Hub has been a platform for collaboration across Traditional Owners, tourism operators, not-for-profits and scientists from the Reef Restoration and Adaptation Program (AIMS and CSIRO) to design and deliver a project at Moore Reef that assesses how new techniques for assisted coral recovery can be applied in rubble habitats. The collaborative project evaluates the viability of newly engineered coral seeding devices developed by AIMS, for deploying coral recruits that were spawned in the National Sea Simulator in December 2022 to sites at Moore Reef close to tourist pontoons. This project provides important data to inform future scaling up of restoration activities and provides a model for active involvement of a range of partners. Through this work, the project builds understanding around key ingredients for best-practice, place-based engagement opportunities for Reef communities and the general public

Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in Kenya with a Markov transition model.

BACKGROUND: There are more than 90 serotypes of Streptococcus pneumoniae, with varying biologic and epidemiologic properties. Animal studies suggest that carriage induces an acquired immune response that reduces duration of colonization in a nonserotype-specific fashion. METHODS: We studied pneumococcal nasopharyngeal carriage longitudinally in Kenyan children 3-59 months of age, following up positive swabs at days 2, 4, 8, 16, and 32 and then monthly thereafter until 2 swabs were negative for the original serotype. As previously reported, 1868/2840 (66%) of children swabbed at baseline were positive. We estimated acquisition, clearance, and competition parameters for 27 serotypes using a Markov transition model. RESULTS: Point estimates of type-specific acquisition rates ranged from 0.00025/d (type 1) to 0.0031/d (type 19F). Point estimates of time to clearance (inverse of type-specific immune clearance rate) ranged from 28 days (type 20) to 124 days (type 6A). For the serotype most resistant to competition (type 19F), acquisition of other serotypes was 52% less likely (95% confidence interval = 37%-63%) than in an uncolonized host. Fitness components (carriage duration, acquisition rate, lack of susceptibility to competition) were positively correlated with each other and with baseline prevalence, and were associated with biologic properties previously shown to associate with serotype. Duration of carriage declined with age for most serotypes. CONCLUSIONS: Common S. pneumoniae serotypes appear superior in many dimensions of fitness. Differences in rate of immune clearance are attenuated as children age and become capable of more rapid clearance of the longest-lived serotypes. These findings provide information for comparison after introduction of pneumococcal conjugate vaccine

Author Correction: A consensus-based transparency checklist.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase

Little is known about quality control of proteins that aberrantly or persistently engage the endoplasmic reticulum (ER)-localized translocon en route to membrane localization or the secretory pathway. Hrd1 and Doa10, the primary ubiquitin ligases that function in ER-associated degradation (ERAD) in yeast, target distinct subsets of misfolded or otherwise abnormal proteins based primarily on degradation signal (degron) location. We report the surprising observation that fusing Deg1, a cytoplasmic degron normally recognized by Doa10, to the Sec62 membrane protein rendered the protein a Hrd1 substrate. Hrd1-dependent degradation occurred when Deg1-Sec62 aberrantly engaged the Sec61 translocon channel and underwent topological rearrangement. Mutations that prevent translocon engagement caused a reversion to Doa10-dependent degradation. Similarly, a variant of apolipoprotein B, a protein known to be cotranslocationally targeted for proteasomal degradation, was also a Hrd1 substrate. Hrd1 therefore likely plays a general role in targeting proteins that persistently associate with and potentially obstruct the translocon

Platform trial design for neurofibromatosis type 1, NF2-related schwannomatosis and non-NF2-related schwannomatosis:A potential model for rare diseases

Background Neurofibromatosis type 1, NF2-related schwannomatosis and non-NF2-related schwannomatosis (grouped under the abbreviation "NF") are rare hereditary tumor predisposition syndromes. Due to the low prevalence, variability in the range, and severity of manifestations, as well as limited treatment options, these conditions require innovative trial designs to accelerate the development of new treatments.Methods Within European Patient-Centric Clinical Trial Platforms (EU-PEARL), we designed 2 platform-basket trials in NF. The trials were designed by a team of multidisciplinary NF experts and trial methodology experts.Results The trial will consist of an observational and a treatment period. The observational period will serve as a longitudinal natural history study. The platform trial design and randomization to a sequence of available interventions allow for the addition of interventions during the trial. If a drug does not meet the predetermined efficacy endpoint or reveals unacceptable toxicities, participants may stop treatment on that arm and re-enter the observational period, where they can be re-randomized to a different treatment arm if eligible. Intervention-specific eligibility criteria and endpoints are listed in intervention-specific-appendices, allowing the flexibility and adaptability needed for highly variable and rare conditions like NF.Conclusions These innovative platform-basket trials for NF may serve as a model for other rare diseases, as they will enhance the chance of identifying beneficial treatments through optimal learning from a small number of patients. The goal of these trials is to identify beneficial treatments for NF more rapidly and at a lower cost than traditional, single-agent clinical trials

Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine

Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a “long tail” of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. In one patient, previously undetected findings guided clinical trial enrollment leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Kant, race, and natural history

This article presents a new argument concerning the relation between Kant’s theory of race and aspects of the critical philosophy. It argues that Kant’s treatment of the problem of the systematic unity of nature and knowledge in the Critique of Pure Reason and the Critique of the Power of Judgment can be traced back a methodological problem in the natural history of the period – that of the possibility of a natural system of nature. Kant’s transformation of the methodological problem from natural history into a set of philosophical (and specifically epistemological) problems proceeds by way of the working out of his own problem in natural history – the problem of the natural history of the human races – and specifically the problem of the unity in diversity of the human species, in response to which he develops a theory of race. This theory of race is, further, the first developed model of the use of teleological judgment in Kant’s work. The article thus argues that Kant’s philosophical position on the systematic unity of nature and of knowledge in the first and third Critiques, and his account and defense of teleological judgment, are developed out of problems first articulated in his solution to the problem of the unity in diversity of the human species – that is, in his theory of race. The article does not seek to establish that these aspects of the critical philosophy are therefore racialised. But it does demonstrate, against those who deny its salience to his philosophy, how the problem of the unity in diversity of the human species and Kant’s theory of race is significant for the development of aspects of the critical philosophy and thus contributes to their philosophical problematics

SN 2013ai: a link between Hydrogen-rich and Hydrogen-poor Core-collapse Supernovae

We present a study of the optical and near-infrared (NIR) spectra of SN 2013ai along with its light curves. These data range from discovery until 380 days after explosion. SN 2013ai is a fast declining Type II supernova (SN II) with an unusually long rise time, 18.9 2.7 days in the V-band, and a bright V-band peak absolute magnitude of -18.7 0.06 mag. The spectra are dominated by hydrogen features in the optical and NIR. The spectral features of SN 2013ai are unique in their expansion velocities, which, when compared to large samples of SNe II, are more than 1,000 km s-1 faster at 50 days past explosion. In addition, the long rise time of the light curve more closely resembles SNe IIb rather than SNe II. If SN 2013ai is coeval with a nearby compact cluster, we infer a progenitor zero-age main-sequence mass of ∼17 M o˙. After performing light-curve modeling, we find that SN 2013ai could be the result of the explosion of a star with little hydrogen mass, a large amount of synthesized 56Ni, 0.3-0.4 M o˙, and an explosion energy of 2.5-3.0 1051 erg. The density structure and expansion velocities of SN 2013ai are similar to those of the prototypical SN IIb, SN 1993J. However, SN 2013ai shows no strong helium features in the optical, likely due to the presence of a dense core that prevents the majority of γ-rays from escaping to excite helium. Our analysis suggests that SN 2013ai could be a link between SNe II and stripped-envelope SNe.Fil: Davis, Scott. University of California; Estados UnidosFil: Pessi, Priscila Jael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Fraser, M.. University College Dublin; IrlandaFil: Ertini, Keila Yael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Martinez, Veronica Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Hoeflich, Peter. Florida State University; Estados UnidosFil: Hsiao, Eric. Florida State University; Estados UnidosFil: Folatelli, Gaston. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Ashall, Chris. University of Hawaii at Manoa; Estados UnidosFil: Phillips, Mark. Carnegie Observatories. Las Campanas Observatory; ChileFil: Anderson, J. P.. European Southern Observatory Chile; ChileFil: Bersten, Melina Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Astrofísica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas. Instituto de Astrofísica La Plata; ArgentinaFil: Englert, B.. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; ArgentinaFil: Fisher, A.. Florida State University; Estados UnidosFil: Benetti, S.. Osservatorio Astronomico di Padova; ItaliaFil: Simaz Bunzel, Adolfo. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Burns, Christopher R.. Observatories of the Carnegie Institution for Science; Estados UnidosFil: Chen, T. W.. Stockholm University; SueciaFil: Contreras, Carlos. 9Carnegie Observatories. Las Campanas Observatory; ChileFil: Elias Rosa, N.. Osservatorio Astronomico di Padova; ItaliaFil: Falco, E.. Harvard-Smithsonian Center for Astrophysics; Estados UnidosFil: Galbany, Lluís. Harvard-Smithsonian Center for Astrophysics; Estados UnidosFil: Kirshner, Robert. Harvard-Smithsonian Center for Astrophysics; Estados UnidosFil: Kumar, S.. Florida State University; Estados UnidosFil: Lu, J.. Florida State University; Estados UnidosFil: Lyman, D.. University of Warwick; Reino UnidoFil: Marion, G. H.. University of Warwick; Reino UnidoFil: Mattila, S.. University of Turku; FinlandiaFil: Maund, J.. University of Sheffield; Reino UnidoFil: Morrell, Nidia Irene. Carnegie Observatories. Las Campanas Observatory; ChileFil: Serón, J.. University of Sheffield; Reino UnidoFil: Stritzinger, Maximilian. Aarhus University; DinamarcaFil: Shahbandeh, Melissa. Florida State University; Estados UnidosFil: Sullivan, Mark. Aarhus University; DinamarcaFil: Suntzeff, N. B.. Texas A&M University; Estados UnidosFil: Young, D. R.. Texas A&M University; Estados Unido