Consensus nomenclature for dyneins and associated assembly factors.

Dyneins are highly complex, multicomponent, microtubule-based molecular motors. These enzymes are responsible for numerous motile behaviors in cytoplasm, mediate retrograde intraflagellar transport (IFT), and power ciliary and flagellar motility. Variants in multiple genes encoding dyneins, outer dynein arm (ODA) docking complex subunits, and cytoplasmic factors involved in axonemal dynein preassembly (DNAAFs) are associated with human ciliopathies and are of clinical interest. Therefore, clear communication within this field is particularly important. Standardizing gene nomenclature, and basing it on orthology where possible, facilitates discussion and genetic comparison across species. Here, we discuss how the human gene nomenclature for dyneins, ODA docking complex subunits, and DNAAFs has been updated to be more functionally informative and consistent with that of the unicellular green alga Chlamydomonas reinhardtii, a key model organism for studying dyneins and ciliary function. We also detail additional nomenclature updates for vertebrate-specific genes that encode dynein chains and other proteins involved in dynein complex assembly

Cytoplasmic dynein nomenclature

A variety of names has been used in the literature for the subunits of cytoplasmic dynein complexes. Thus, there is a strong need for a more definitive consensus statement on nomenclature. This is especially important for mammalian cytoplasmic dyneins, many subunits of which are encoded by multiple genes. We propose names for the mammalian cytoplasmic dynein subunit genes and proteins that reflect the phylogenetic relationships of the genes and the published studies clarifying the functions of the polypeptides. This nomenclature recognizes the two distinct cytoplasmic dynein complexes and has the flexibility to accommodate the discovery of new subunits and isoforms

International Study of Chaplains’ Attitudes About Research

An online survey was conducted by twelve professional chaplain organizations to assess chaplains’ attitudes about and involvement in research. A total of 2,092 chaplains from 23 countries responded to the survey. Over 80% thought research was definitely important and nearly 70% thought chaplains should definitely be research literate. Just over 40% said they regularly read research articles and almost 60% said they occasionally did. The respondents rated their own research literacy as 6.5 on a 0–10 scale. Significant positive inter-correlations were found among all four measures: importance of (a) research and (b) research literacy; (c) frequency of reading articles; and (d) research literacy rating. Approximately 35% were never involved, 37% had been involved, 17% were currently involved, and 11% expected to be involved in research. The last three groups were significantly more likely to think research and research literacy were important and to read research articles than chaplains who were never involved in research. Given chaplains’ interest in research, actions should be undertaken to facilitate further research engagement

Improved efficacy of pembrolizumab combined with soluble EphB4-albumin in HPV-negative EphrinB2 positive head neck squamous cell carcinoma

ObjectivePatients with relapsed or metastatic head and neck squamous cell carcinoma (HNSCC) after primary local therapy have low response rates with cetuximab, systemic chemotherapy or check point inhibitor therapy. Novel combination therapies with the potential to improve outcomes for patients with HNSCC is an area of high unmet need.MethodsThis is a phase II single-arm clinical trial of locally advanced or metastatic HNSCC patients treated with a combination of soluble EphB4-human serum albumin (sEphB4-HSA) fusion protein and pembrolizumab after platinum-based chemotherapy with up to 2 prior lines of treatment. The primary endpoints were safety and tolerability and the primary efficacy endpoint was overall response rate (ORR). Secondary endpoints included progression free survival (PFS) and overall survival (OS). HPV status and EphrinB2 expression were evaluated for outcome.ResultsTwenty-five patients were enrolled. Median follow up was 40.4 months (range 9.8 - 40.4). There were 6 responders (ORR 24%). There were 5 responders in the 11 HPV-negative and EphrinB2 positive patients, (ORR 45%) with 2 of these patients achieving a complete response (CR). The median PFS in HPV-negative/EphrinB2 positive patients was 3.2 months (95% CI 1.1, 7.3). Median OS in HPV-negative/EphrinB2 positive patients was 10.9 months (95% CI 2.0, 13.7). Hypertension, transaminitis and fatigue were the most common toxicities.DiscussionThe combination of sEphB4-HSA and pembrolizumab has a favorable toxicity profile and favorable activity particularly among HPV-negative EphrinB2 positive patients with HNSCC

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

The K2-3 system revisited: testing photoevaporation and core-powered mass loss with three small planets spanning the radius valley

Multi-planet systems orbiting M dwarfs provide valuable tests of theories of small planet formation and evolution. K2-3 is an early M dwarf hosting three small exoplanets (1.5-2.0 Earth radii) at distances of 0.07-0.20 AU. We measure the high-energy spectrum of K2-3 with HST/COS and XMM-Newton, and use empirically-driven estimates of Ly-alpha and extreme ultraviolet flux. We use EXOFASTv2 to jointly fit radial velocity, transit, and SED data. This constrains the K2-3 planet radii to 4% uncertainty and the masses of K2-3b and c to 13% and 30%, respectively; K2-3d is not detected in RV measurements. K2-3b and c are consistent with rocky cores surrounded by solar composition envelopes (mass fractions of 0.36% and 0.07%), H2O envelopes (55% and 16%), or a mixture of both. However, based on the high-energy output and estimated age of K2-3, it is unlikely that K2-3b and c retain solar composition atmospheres. We pass the planet parameters and high-energy stellar spectrum to atmospheric models. Dialing the high-energy spectrum up and down by a factor of 10 produces significant changes in trace molecule abundances, but not at a level detectable with transmission spectroscopy. Though the K2-3 planets span the small planet radius valley, the observed system architecture cannot be readily explained by photoevaporation or core-powered mass loss. We instead propose 1) the K2-3 planets are all volatile-rich, with K2-3d having a lower density than typical of super-Earths, and/or 2) the K2-3 planet architecture results from more stochastic processes such as planet formation, planet migration, and impact erosion.Comment: 15 pages, 7 figure, published in AJ, HLSPs at https://archive.stsci.edu/hlsp/mstarpanspe

ACCESS, LRG-BEASTS, & MOPSS: Featureless Optical Transmission Spectra of WASP-25b and WASP-124b

We present new optical transmission spectra for two hot Jupiters: WASP-25b (M = 0.56~M$_J$; R = 1.23 R$_J$; P =~3.76 days) and WASP-124b (M = 0.58~M$_J$; R = 1.34 R$_J$; P = 3.37 days), with wavelength coverages of 4200 - 9100\AA\ and 4570 - 9940\AA, respectively. These spectra are from the ESO Faint Object Spectrograph and Camera (v.2) mounted on the New Technology Telescope (NTT) and Inamori-Magellan Areal Camera & Spectrograph on Magellan Baade. No strong spectral features were found in either spectra, with the data probing 4 and 6 scale heights, respectively. \texttt{Exoretrievals} and \texttt{PLATON} retrievals favor stellar activity for WASP-25b, while the data for WASP-124b did not favor one model over another. For both planets the retrievals found a wide range in the depths where the atmosphere could be optically thick ($\sim0.4\mu$ - 0.2 bars for WASP-25b and 1.6 $\mu$ -- 32 bars for WASP-124b) and recovered a temperature that is consistent with the planets' equilibrium temperatures, but with wide uncertainties (up to $\pm$430$^\circ$K). For WASP-25b, the models also favor stellar spots that are $\sim$500-3000$^\circ$K cooler than the surrounding photosphere. The fairly weak constraints on parameters are owing to the relatively low precision of the data, with an average precision of 840 and 1240 ppm per bin for WASP-25b and WASP-124b, respectively. However, some contribution might still be due to an inherent absence of absorption or scattering in the planets' upper atmospheres, possibly because of aerosols. We attempt to fit the strength of the sodium signals to the aerosol-metallicity trend proposed by McGruder et al. 2023, and find WASP-25b and WASP-124b are consistent with the prediction, though their uncertainties are too large to confidently confirm the trend.Comment: Accepted in AJ July 202

Pion production in the 40Ar+40Ca reaction at 1.05 GeV/nucleon

Pion-production cross sections have been measured for the reaction 40Ar+40Ca--> pi ++X at a laboratory energy of 1.05 GeV/nucleon. A maximum in the pi + cross section occurs at mid-rapidity, which is anomalous relative to p+p and p+nucleus reactions and compared to many other heavy-ion reactions. Calculations based on cascade and thermal models fail to fit the data

Emission patterns in central and peripheral relativistic heavy-ion collisions

Proton emission in relativistic nuclear collisions is examined for events of low and high multiplicity, corresponding to large and small impact parameters. Peripheral reactions exhibit distributions of protons in agreement with spectator-participant decay modes. Central collisions of equal-size nuclei are dominated by the formation and decay of a fireball system. Central collisions of light projectiles with heavy targets exhibit an enhancement in sideward emission which is predicted by recent hydrodynamical calculations

Pion production and charged-particle multiplicity selection in relativistic nuclear collisions

Spectra of positive pions with energies of 15-95 MeV were measured for high energy proton, 4He, 20Ne, and 40Ar bombardments of targets of 27Al, 40Ca, 107,109Ag, 197Au, and 238U. A Si-Ge telescope was used to identify charged pions by dE / dx-E and, in addition, stopped pi + were tagged by the subsequent muon decay. In all, results for 14 target-projectile combinations are presented to study the dependence of pion emission patterns on the bombarding energy (from E / A=0.25 to 2.1 GeV) and on the target and the projectile masses. In addition, associated charged-particle multiplicities were measured in an 80-paddle array of plastic scintillators, and used to make impact parameter selections on the pion-inclusive data. NUCLEAR REACTIONS U(20Ne, pi +), E / A=250 MeV; U(40Ar, pi +), Ca(40Ar, pi +), U(20Ne, pi +), Au(20Ne, pi +), Ag(20Ne, pi +), Al(20Ne, pi +), U(4He, pi +), Al(4He, pi +). E / A=400 MeV; Ca(40Ar, pi +), U(20Ne, pi +), U(4He, pi +), U(p, pi +), E / A=1.05), GeV; U(20Ne, pi +), E / A=2.1 GeV; measured sigma (E, theta ), inclusive and selected on associated charged-particle multiplicity