Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination

Some microbial public goods can provide both individual and community‐wide benefits, and are open to exploitation by non‐producing species. One such example is the production of metal‐detoxifying siderophores. Here, we investigate whether conflicting selection pressures on siderophore production by heavy metals – a detoxifying effect of siderophores, and exploitation of this detoxifying effect – result in a net increase or decrease. We show that the proportion of siderophore‐producing taxa increases along a natural heavy metal gradient. A causal link between metal contamination and siderophore production was subsequently demonstrated in a microcosm experiment in compost, in which we observed changes in community composition towards taxa that produce relatively more siderophores following copper contamination. We confirmed the selective benefit of siderophores by showing that taxa producing large amounts of siderophore suffered less growth inhibition in toxic copper. Our results suggest that ecological selection will favour siderophore‐mediated decontamination, with important consequences for potential remediation strategies

RadAdapt: Radiology Report Summarization via Lightweight Domain Adaptation of Large Language Models

We systematically investigate lightweight strategies to adapt large language models (LLMs) for the task of radiology report summarization (RRS). Specifically, we focus on domain adaptation via pretraining (on natural language, biomedical text, and clinical text) and via prompting (zero-shot, in-context learning) or parameter-efficient fine-tuning (prefix tuning, LoRA). Our results on the MIMIC-III dataset consistently demonstrate best performance by maximally adapting to the task via pretraining on clinical text and parameter-efficient fine-tuning on RRS examples. Importantly, this method fine-tunes a mere 0.32% of parameters throughout the model, in contrast to end-to-end fine-tuning (100% of parameters). Additionally, we study the effect of in-context examples and out-of-distribution (OOD) training before concluding with a radiologist reader study and qualitative analysis. Our findings highlight the importance of domain adaptation in RRS and provide valuable insights toward developing effective natural language processing solutions for clinical tasks.Comment: 12 pages, 9 figure

Clinical Text Summarization: Adapting Large Language Models Can Outperform Human Experts

Sifting through vast textual data and summarizing key information imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown immense promise in natural language processing (NLP) tasks, their efficacy across diverse clinical summarization tasks has not yet been rigorously examined. In this work, we employ domain adaptation methods on eight LLMs, spanning six datasets and four distinct summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Our thorough quantitative assessment reveals trade-offs between models and adaptation methods in addition to instances where recent advances in LLMs may not lead to improved results. Further, in a clinical reader study with six physicians, we depict that summaries from the best adapted LLM are preferable to human summaries in terms of completeness and correctness. Our ensuing qualitative analysis delineates mutual challenges faced by both LLMs and human experts. Lastly, we correlate traditional quantitative NLP metrics with reader study scores to enhance our understanding of how these metrics align with physician preferences. Our research marks the first evidence of LLMs outperforming human experts in clinical text summarization across multiple tasks. This implies that integrating LLMs into clinical workflows could alleviate documentation burden, empowering clinicians to focus more on personalized patient care and other irreplaceable human aspects of medicine.Comment: 23 pages, 22 figure

New contributions of measurements in Europe to the global inventory of the stable isotopic composition of methane

Recent climate change mitigation strategies rely on the reduction of methane (CH4) emissions. Carbon and hydrogen isotope ratio (δ13CCH4 and δ2HCH4) measurements can be used to distinguish sources and thus to understand the CH4 budget better. The CH4 emission estimates by models are sensitive to the isotopic signatures assigned to each source category, so it is important to provide representative estimates of the different CH4 source isotopic signatures worldwide. We present new measurements of isotope signatures of various, mainly anthropogenic, CH4 sources in Europe, which represent a substantial contribution to the global dataset of source isotopic measurements from the literature, especially for δ2HCH4. They improve the definition of δ13CCH4 from waste sources, and demonstrate the use of δ2HCH4 for fossil fuel source attribution. We combined our new measurements with the last published database of CH4 isotopic signatures and with additional literature, and present a new global database. We found that microbial sources are generally well characterised. The large variability in fossil fuel isotopic compositions requires particular care in the choice of weighting criteria for the calculation of a representative global value. The global dataset could be further improved by measurements from African, South American, and Asian countries, and more measurements from pyrogenic sources. We improved the source characterisation of CH4 emissions using stable isotopes and associated uncertainty, to be used in top-down studies. We emphasise that an appropriate use of the database requires the analysis of specific parameters in relation to source type and the region of interest. The final version of the European CH4 isotope database coupled with a global inventory of fossil and non-fossil δ13CCH4 and δ2HCH4 source signature measurements is available at 10.24416/UU01-YP43IN

Gonadotrophins versus clomifene citrate with or without intrauterine insemination in women with normogonadotropic anovulation and clomifene failure (M-OVIN):A randomised, two-by-two factorial trial

Background: In many countries, clomifene citrate is the treatment of first choice in women with normogonadotropic anovulation (ie, absent or irregular ovulation). If these women ovulate but do not conceive after several cycles with clomifene citrate, medication is usually switched to gonadotrophins, with or without intrauterine insemination. We aimed to assess whether switching to gonadotrophins is more effective than continuing clomifene citrate, and whether intrauterine insemination is more effective than intercourse. Methods: In this two-by-two factorial multicentre randomised clinical trial, we recruited women aged 18 years and older with normogonadotropic anovulation not pregnant after six ovulatory cycles of clomifene citrate (maximum of 150 mg daily for 5 days) from 48 Dutch hospitals. Women were randomly assigned using a central password-protected internet-based randomisation programme to receive six cycles with gonadotrophins plus intrauterine insemination, six cycles with gonadotrophins plus intercourse, six cycles with clomifene citrate plus intrauterine insemination, or six cycles with clomifene citrate plus intercourse. Clomifene citrate dosages varied from 50 to 150 mg daily orally and gonadotrophin starting dose was 50 or 75 IU daily subcutaneously. The primary outcome was conception leading to livebirth within 8 months after randomisation defined as any baby born alive after a gestational age beyond 24 weeks. Primary analysis was by intention to treat. We made two comparisons, one in which gonadotrophins were compared with clomifene citrate and one in which intrauterine insemination was compared with intercourse. This completed study is registered with the Netherlands Trial Register, number NTR1449. Findings: Between Dec 8, 2008, and Dec 16, 2015, we randomly assigned 666 women to gonadotrophins and intrauterine insemination (n=166), gonadotrophins and intercourse (n=165), clomifene citrate and intrauterine insemination (n=163), or clomifene citrate and intercourse (n=172). Women allocated to gonadotrophins had more livebirths than those allocated to clomifene citrate (167 [52%] of 327 women vs 138 [41%] of 334 women, relative risk [RR] 1·24 [95% CI 1·05–1·46]; p=0·0124). Addition of intrauterine insemination did not increase livebirths compared with intercourse (161 [49%] vs 144 [43%], RR 1·14 [95% CI 0·97–1·35]; p=0·1152). Multiple pregnancy rates for the two comparisons were low and not different. There were three adverse events: one child with congenital abnormalities and one stillbirth in two women treated with clomifene citrate, and one immature delivery due to cervical insufficiency in a woman treated with gonadotrophins. Interpretation: In women with normogonadotropic anovulation and clomifene citrate failure, a switch of treatment to gonadotrophins increased the chance of livebirth over treatment with clomifene citrate; there was no evidence that addition of intrauterine insemination does so. Funding: The Netherlands Organization for Health Research and Development

Illumination of Parainfluenza Virus Infection and Transmission in Living Animals Reveals a Tissue-Specific Dichotomy

The parainfluenza viruses (PIVs) are highly contagious respiratory paramyxoviruses and a leading cause of lower respiratory tract (LRT) disease. Since no vaccines or antivirals exist, non-pharmaceutical interventions are the only means of control for these pathogens. Here we used bioluminescence imaging to visualize the spatial and temporal progression of murine PIV1 (Sendai virus) infection in living mice after intranasal inoculation or exposure by contact. A non-attenuated luciferase reporter virus (rSeV-luc(M-F*)) that expressed high levels of luciferase yet was phenotypically similar to wild-type Sendai virus in vitro and in vivo was generated to allow visualization. After direct intranasal inoculation, we unexpectedly observed that the upper respiratory tract (URT) and trachea supported robust infection under conditions that result in little infection or pathology in the lungs including a low inoculum of virus, an attenuated virus, and strains of mice genetically resistant to lung infection. The high permissivity of the URT and trachea to infection resulted in 100% transmission to naïve contact recipients, even after low-dose (70 PFU) inoculation of genetically resistant BALB/c donor mice. The timing of transmission was consistent with the timing of high viral titers in the URT and trachea of donor animals but was independent of the levels of infection in the lungs of donors. The data therefore reveals a disconnect between transmissibility, which is associated with infection in the URT, and pathogenesis, which arises from infection in the lungs and the immune response. Natural infection after transmission was universally robust in the URT and trachea yet limited in the lungs, inducing protective immunity without weight loss even in genetically susceptible 129/SvJ mice. Overall, these results reveal a dichotomy between PIV infection in the URT and trachea versus the lungs and define a new model for studies of pathogenesis, development of live virus vaccines, and testing of antiviral therapies

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Interspecific social interactions shape public goods production in natural microbial communities

The R code (Hesse_etal.R) descibes step by step how metal polution affects the ecology and evolution of a community-wide public good – the production of metal-detoxifying siderophores. This code accompanies the manuscript "Interspecific interactions shape public goods production in natural microbial communities" (https://www.biorxiv.org/content/10.1101/710715v1)Fil: Hesse, Elze. University Exeter; United Kingdom.Fil: O'Brien, Siobhan. University of Liverpool; United Kingdom.Fil: Luján, Adela. Universidad Católica de Córdoba; Argentina.Fil: Luján, Adela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sánchez Labrador S.J.; Argentina.Fil: Bayer, Florian. University Exeter; United Kingdom.Fil: van Veen, Eleanor. University Exeter; United Kingdom.Fil: Hodgson, Dave. University Exeter; United Kingdom.Fil: Buckling, Angus. University Exeter; United Kingdom