Contact tracing for SARS-CoV-2: what can be learned from other conditions?

Contact tracing is central to the public health response to COVID-19, but the approach taken has received criticism for failing to make enough of an impact on disease transmission. We discuss what can be learned from contact tracing in other infections, and how the natural history of COVID-19 should shape the strategies used

An Optical Counterpart to the Anomalous X-ray Pulsar 4U 0142+61

The energy source of the anomalous X-ray pulsars is not well understood, hence their designation as anomalous. Unlike binary X-ray pulsars, no companions are seen, so the energy cannot be supplied by accretion of matter from a companion star. The loss of rotational energy, which powers radio pulsars, is insufficient to power AXPs. Two models are generally considered: accretion from a large disk left over from the birth process, or decay of a very strong magnetic field (10^15 G) associated with a 'magnetar'. The lack of counterparts at other wavelengths has hampered progress in our understanding of these objects. Here, we present deep optical observations of the field around 4U 0142+61, which is the brightest AXP in X-rays. We find an object with peculiar optical colours at the position of the X-ray source, and argue that it is the optical counterpart. The optical emission is too faint to admit the presence of a large accretion disk, but may be consistent with magnetospheric emission from a magnetar.Comment: 16 pages, 3 figures, accepted by Nature. Press embargo until 1900 hrs London time (GMT) on 6 December 200

Seasonal and spatial variability in rates of primary production and detritus release by intertidal stands of Laminaria digitata and Saccharina latissima on wave-exposed shores in the northeast Atlantic

Coastal habitats are increasingly recognized as fundamentally important components of global carbon cycles, but the rates of carbon flow associated with marine macrophytes are not well resolved for many species in many regions. We quantified density, rates of primary productivity, and detritus production of intertidal stands of two common intertidal kelp species—Laminaria digitata (oarweed) and Saccharina latissima (sugar kelp)—on four NE Atlantic rocky shores over 22 months. The density of L. digitata was greater at exposed compared to moderately exposed shores but remained consistently low for S. latissima throughout the survey period. Individual productivity and erosion rates of L. digitata did not differ between exposed and moderately exposed shores but differed across exposure levels throughout the year at moderately exposed sites only. Productivity and erosion of S. latissima remained low on moderately exposed shores and showed no clear seasonal pattern. Patterns of productivity and total detrital production (erosion and dislodgement) per m2 of both L. digitata and S. latissima followed closely that of densities per m2, peaking in May during both survey years. Temperature and light were key factors affecting the productivity rates of L. digitata and S. latissima. Erosion rates of L. digitata were affected by wave exposure, temperature, light, grazing, and epiphyte cover, but only temperature-affected erosion of S. latissima. Production of biomass and detritus was greater in L. digitata than in S. latissima and exceeded previous estimates for subtidal and warmer-water affinity kelp populations (e.g., Laminaria ochroleuca). These biogenic habitats are clearly important contributors to the coastal carbon cycle that have been overlooked previously and should be included in future ecosystem models. Further work is required to determine the areal extent of kelp stands in intertidal and shallow subtidal habitats, which is needed to scale up local production estimates to entire coastlines

Hospital admissions for vitamin D related conditions and subsequent immune-mediated disease: record-linkage studies

PMCID: PMC3729414The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7015/11/171. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

The two-hour orbit of a binary millisecond X-ray pulsar

Typical radio pulsars are magnetized neutron stars that are born rapidly rotating and slow down as they age on time scales of 10 to 100 million years. However, millisecond radio pulsars spin very rapidly even though many are billions of years old. The most compelling explanation is that they have been "spun up" by the transfer of angular momentum during accretion of material from a companion star in so-called low-mass X-ray binary systems, LMXBs. (LMXBs consist of a neutron star or black hole accreting from a companion less than one solar mass.) The recent detection of coherent X-ray pulsations with a millisecond period from a suspected LMXB system appears to confirm this link. Here we report observations showing that the orbital period of this binary system is two hours, which establishes it as an LMXB. We also find an apparent modulation of the X-ray flux at the orbital period (at the two per cent level), with a broad minimum when the pulsar is behind this low-mass companion star. This system seems closely related to the "black widow" millisecond radio pulsars, which are evaporating their companions through irradiation. It may appear as an eclipsing radio pulsar during periods of X-ray quiescence.Comment: 4 pages with 1 figure. Style files included. Fig. 2 deleted and text revised. To appear in Nature. Press embargo until 18:00 GMT on 1998 July 2

Plasmodium vivax and Plasmodium falciparum infection dynamics: re-infections, recrudescences and relapses

Background: In malaria endemic populations, complex patterns of Plasmodium vivax and Plasmodium falciparum blood-stage infection dynamics may be observed. Genotyping samples from longitudinal cohort studies for merozoite surface protein (msp) variants increases the information available in the data, allowing multiple infecting parasite clones in a single individual to be identified. msp genotyped samples from two longitudinal cohorts in Papua New Guinea (PNG) and Thailand were analysed using a statistical model where the times of acquisition and clearance of each clone in every individual were estimated using a process of data augmentation. Results: For the populations analysed, the duration of blood-stage P. falciparum infection was estimated as 36 (95% Credible Interval (CrI): 29, 44) days in PNG, and 135 (95% CrI 94, 191) days in Thailand. Experiments on simulated data indicated that it was not possible to accurately estimate the duration of blood-stage P. vivax infections due to the lack of identifiability between a single blood-stage infection and multiple, sequential blood-stage infections caused by relapses. Despite this limitation, the method and data point towards short duration of blood-stage P. vivax infection with a lower bound of 24 days in PNG, and 29 days in Thailand. On an individual level, P. vivax recurrences cannot be definitively classified into re-infections, recrudescences or relapses, but a probabilistic relapse phenotype can be assigned to each P. vivax sample, allowing investigation of the association between epidemiological covariates and the incidence of relapses. Conclusion: The statistical model developed here provides a useful new tool for in-depth analysis of malaria data from longitudinal cohort studies, and future application to data sets with multi-locus genotyping will allow more detailed investigation of infection dynamics

Continuous heating of a giant X-ray flare on Algol

Giant flares can release large amounts of energy within a few days: X-ray emission alone can be up to ten percent of the star's bolometric luminosity. These flares exceed the luminosities of the largest solar flares by many orders of magnitude, which suggests that the underlying physical mechanisms supplying the energy are different from those on the Sun. Magnetic coupling between the components in a binary system or between a young star and an accretion disk has been proposed as a prerequisite for giant flares. Here we report X-ray observations of a giant flare on Algol B, a giant star in an eclipsing binary system. We observed a total X-ray eclipse of the flare, which demonstrates that the plasma was confined to Algol B, and reached a maximum height of 0.6 stellar radii above its surface. The flare occurred around the south pole of Algol B, and energy must have been released continously throughout its life. We conclude that a specific extrastellar environment is not required for the presence of a flare, and that the processes at work are therefore similar to those on the Sun.Comment: Nature, Sept. 2 199

Prescribing hand strengthening exercise for patients with rheumatoid arthritis; clinical cues influencing occupational therapists' and physiotherapists' judgements

Acknowledgements: The authors acknowledge the therapists who took part in both phases of this study. This work was supported by Brunel University London and the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care Oxford at Oxford Health NHS Foundation Trust, and supported by the NIHR Biomedical Research Centre, Oxford.Data Availability Statement: The data that support the findings for phase 2 of this study are openly available in figshare at https://doi.org/10.6084/m9.figshare.24681309 .Supporting Information is available online at: https://onlinelibrary.wiley.com/doi/full/10.1002/msc.1849#support-information-section .Copyright © 2023 The Authors. Objective: To explore the clinical judgements of therapists in prescribing the intensity of hand strengthening exercise in rheumatoid arthritis (RA). Methods: Phase I: Eleven therapists knowledgeable in treating patients with RA subjectively identified seven clinical cues. These were incorporated into 54 hypothetical patient case scenarios. Phase II: Therapists with ≥2 years post-registration experience and current or recent experience in treating patients with RA were asked to assess 69 case scenarios in total (54 + 15 repeats) and judge what intensity of hand strengthening exercise they would prescribe using the OMNI-Resistance Exercise Scale of perceived exertion. Using responses to the repeated cases, the Cochran-Weiss-Shanteau index of expertise was used to identify therapists who prescribed more consistently. Multiple regression was used to determine which clinical cues were most strongly associated with the intensity of exercise prescribed. A sub-group analysis explored differences between consistent and inconsistent prescribers. Results: Fifty-three therapists took part. Thirty completed all 69 case scenarios. Across all therapists, the three most important clinical cues associated with lower intensity of exercise prescribed were (1) Patient's reported pain intensity whilst practising the exercise (β = −1.150, p < 0.001), (2) Disease activity (β = −0.425, p < 0.001) and (3) average hand pain over the last week (β = −0.353 p < 0.001). Twelve therapists were categorised as consistent prescribers. This group relied on fewer clinical cues (three vs. seven) when judging what intensity of exercise to prescribe. Conclusion: This study provides insights into how therapists prescribe hand exercises. Intensity of hand strengthening exercise was influenced by three key clinical cues, including pain intensity and disease activity.Brunel University London; National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care Oxford at Oxford Health NHS Foundation Trust; NIHR Biomedical Research Centre, Oxford

Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation.

Recent studies suggest that cells make stochastic choices with respect to differentiation or division. However, the molecular mechanism underlying such stochasticity is unknown. We previously proposed that the timing of vertebrate neuronal differentiation is regulated by molecular oscillations of a transcriptional repressor, HES1, tuned by a post-transcriptional repressor, miR-9. Here, we computationally model the effects of intrinsic noise on the Hes1/miR-9 oscillator as a consequence of low molecular numbers of interacting species, determined experimentally. We report that increased stochasticity spreads the timing of differentiation in a population, such that initially equivalent cells differentiate over a period of time. Surprisingly, inherent stochasticity also increases the robustness of the progenitor state and lessens the impact of unequal, random distribution of molecules at cell division on the temporal spread of differentiation at the population level. This advantageous use of biological noise contrasts with the view that noise needs to be counteracted

Genome Diversity of Epstein-Barr Virus from Multiple Tumor Types and Normal Infection

Epstein-Barr virus (EBV) infects most of the world’s population and is causally associated with several human cancers, but little is known about how EBV genetic variation might influence infection or EBV-associated disease. There are currently no published wild-type EBV genome sequences from a healthy individual and very few genomes from EBV-associated diseases. We have sequenced 71 geographically distinct EBV strains from cell lines, multiple types of primary tumor, and blood samples and the first EBV genome from the saliva of a healthy carrier. We show that the established genome map of EBV accurately represents all strains sequenced, but novel deletions are present in a few isolates. We have increased the number of type 2 EBV genomes sequenced from one to 12 and establish that the type 1/type 2 classification is a major feature of EBV genome variation, defined almost exclusively by variation of EBNA2 and EBNA3 genes, but geographic variation is also present. Single nucleotide polymorphism (SNP) density varies substantially across all known open reading frames and is highest in latency-associated genes. Some T-cell epitope sequences in EBNA3 genes show extensive variation across strains, and we identify codons under positive selection, both important considerations for the development of vaccines and T-cell therapy. We also provide new evidence for recombination between strains, which provides a further mechanism for the generation of diversity. Our results provide the first global view of EBV sequence variation and demonstrate an effective method for sequencing large numbers of genomes to further understand the genetics of EBV infection