Compressively sampling the optical transmission matrix of a multimode fibre (article)

This is the final version. Available on open access from Springer Nature via the DOI in this recordThe dataset associated with this article is available in ORE at : https://doi.org/10.24378/exe.3204The measurement of the optical transmission matrix (TM) of an opaque material is an advanced form of space-variant aberration correction. Beyond imaging, TM-based methods are emerging in a range of fields, including optical communications, micro-manipulation, and computing. In many cases, the TM is very sensitive to perturbations in the configuration of the scattering medium it represents. Therefore, applications often require an up-to-the-minute characterisation of the fragile TM, typically entailing hundreds to thousands of probe measurements. Here, we explore how these measurement requirements can be relaxed using the framework of compressive sensing, in which the incorporation of prior information enables accurate estimation from fewer measurements than the dimensionality of the TM we aim to reconstruct. Examples of such priors include knowledge of a memory effect linking the input and output fields, an approximate model of the optical system, or a recent but degraded TM measurement. We demonstrate this concept by reconstructing the full-size TM of a multimode fibre supporting 754 modes at compression ratios down to ∼5% with good fidelity. We show that in this case, imaging is still possible using TMs reconstructed at compression ratios down to ∼1% (eight probe measurements). This compressive TM sampling strategy is quite general and may be applied to a variety of other scattering samples, including diffusers, thin layers of tissue, fibre optics of any refractive profile, and reflections from opaque walls. These approaches offer a route towards the measurement of high-dimensional TMs either quickly or with access to limited numbers of measurements.National Natural Science Foundation of ChinaNational Science Foundation (NSF)European Regional Development Fund (ERDF)European Research Council (ERC)Royal Academy of Engineering (RAE

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

Carbon budgets of Scotia Sea mesopelagic zooplankton and micronekton communities during austral spring

This is the final version. Available on open access from Elsevier via the DOI in this recordData availability: Macrozooplankton and nekton vertical distribution and abundance at the sustained observation location P3 in the northern Scotia Sea (Southern Ocean) during November and December 2017 https://doi.org/10.5285/e184e81a-e43c-424e-abec-122036ee2cfd. Micronekton and zooplankton respiration rates on COMICS Cruises DY086 and DY090 https://doi.org/10.5285/b9f5c5ec-100a-7ff0-e053-6c86abc0f494. All other data is available on request.Zooplankton form an integral component of epi- and mesopelagic ecosystems, and there is a need to better understand their role in ocean biogeochemistry. The export and remineralisation of particulate organic matter at depth plays an important role in controlling atmospheric CO2 concentrations. Pelagic mesozooplankton and micronekton communities may influence the fate of organic matter in a number of ways, including: the consumption of primary producers and export of this material as fast-sinking faecal pellets, and the active flux of carbon by animals undertaking diel vertical migration (DVM) into the mesopelagic. We present day and night vertical biomass profiles of mesozooplankton and micronekton communities in the upper 500 m during three visits to an ocean observatory station (P3) to the NW of South Georgia (Scotia Sea, South Atlantic) in austral spring, alongside estimates of their daily rates of ingestion and respiration throughout the water column. Day and night community biomass estimates were dominated by copepods >330 μm, including the lipid-rich species, Calanoides acutus and Rhincalanus gigas. We found little evidence of synchronised DVM, with only Metridia spp. and Salpa thompsoni showing patterns consistent with migratory behaviour. At depths below 250 m, estimated community carbon ingestion rates exceeded those of metabolic costs, supporting the understanding that food quality in the mesopelagic is relatively poor, and organisms have to consume a large amount of food in order to fulfil their nutritional requirements. By contrast, estimated community rates of ingestion and metabolic costs at shallower depths were approximately balanced, but only when we assumed that the animals were predominantly catabolising lipids (i.e. respiratory quotient = 0.7) and had relatively high absorption efficiencies. Our work demonstrates that it is possible to balance the metabolic budgets of mesopelagic animals to within observational uncertainties, but highlights the need for a better understanding of the physiology of lipid-storing animals and how it influences carbon budgeting in the pelagic.Natural Environment Research Council (NERC

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

APOLO-Bari, an internet-based program for longitudinal support of bariatric surgery patients: study protocol for a randomized controlled trial

Background: Despite evidence of successful weight loss for bariatric surgery patients, some patients experience considerable weight regain over the long term. Given the strong association between post-surgery health behaviors and outcomes, aftercare intervention to address key behaviors appears to be a reasonable relapse-prevention strategy. As the burden of obesity rates increases in healthcare centers, an internet-based program appears to be a reasonable strategy for supporting bariatric surgery patients in the long term. The primary purpose of the current project is to develop and test the efficacy and perceived utility of APOLO-Bari.Methods/design: This study is a randomized control trial, which will be conducted in two hospital centers in the North of Portugal; it includes a control group receiving treatment as usual and an intervention group receiving the APOLO-Bari program for one year in addition to treatment as usual. A total of 180 male and female participants who underwent bariatric surgery (gastric sleeve or gastric bypass surgery) for 12 to 20 months will be recruited. Both groups will complete a similar set of questionnaires at baseline, every 4 months until the end of the intervention, and at 6 and 12 months follow-up. Assessment includes anthropometric variables and psychological self-report measures. The primary outcome measure will be weight regain measured at the end of treatment, and at 6 and 12 months follow-up. The secondary aims are to test the cost-effectiveness of the intervention and to investigate psychological predictors and trajectories of weight regain. APOLO-Bari was developed to address the weight regain problem in the bariatric population by offering additional guidance to bariatric patients during the postoperative period. The program includes: (a) a psychoeducational cognitive-behavioral-based self-help manual, (b) a weekly feedback messaging system that sends a feedback statement related to information reported by the participant, and (c) interactive chat sessions scheduled witThis research was partially supported by the Fundacao para a Ciencia e a Tecnologia through a European Union COMPETE program grant to Eva Conceicao (IF/01219/2014 and PTDC/MHC-PCL/4974/2012), a doctoral scholarship to Ana Pinto-Bastos (SFRH/BD/104159/2014), a doctoral scholarship to Sofia Ramalho (SFRH/BD/104182/2014), and a postdoctoral scholarship to Ana Rita Vaz (SFRH/BPD/94490/2013), co-financed by FEDER under the PT2020 Partnership Agreement (UID/PSI/01662/2013).info:eu-repo/semantics/publishedVersio

Usefulness and acceptability of a standardised orientation and mobility training for partially-sighted older adults using an identification cane

<p>Abstract</p> <p>Background</p> <p>Orientation and mobility (O&M) training in using an identification (ID) cane is provided to partially-sighted older adults to facilitate independent functioning and participation in the community. Recently, a protocolised standardised O&M-training in the use of the ID cane was developed in The Netherlands. The purpose of this study is to assess the usefulness and acceptability of both the standardised training and the regular training for participants and O&M-trainers in a randomised controlled trial (NCT00946062).</p> <p>Methods</p> <p>The standardised O&M-training consists of two structured face-to-face sessions and one telephone follow-up, in which, in addition to the regular training, self-management and behavioural change techniques are applied. Questionnaires and interviews were used to collect data on the training’s usefulness, e.g. the population reached, self-reported benefits or achievements, and acceptability, e.g. the performance of the intervention according to protocol and participants’ exposure to and engagement in the training.</p> <p>Results</p> <p>Data was collected from 29 O&M-trainers and 68 participants. Regarding the self-reported benefits, outcomes were comparable for the standardised training and the regular training according the trainers and participants e.g., about 85% of the participants in both groups experienced benefits of the cane and about 70% gained confidence in their capabilities. Participants were actively involved in the standardised training. Nearly 40% of the participants in the standardised training group was not exposed to the training according to protocol regarding the number of sessions scheduled and several intervention elements, such as action planning and contracting.</p> <p>Conclusions</p> <p>The standardised and regular O&M-training showed to be useful and mostly acceptable for the partially-sighted older adults and trainers. Yet, a concern is the deviation from the protocol of the standardised O&M-training by the O&M-trainers regarding distinguishing elements such as action planning. Overall, participants appreciated both trainings and reported benefit.</p

The evolution of the student as a customer in Australian higher education: a policy perspective

In 2014, the Australian Federal Government attempted to de-regulate higher education fees so as to allow universities to set their own tuition fees. The associated public debate offer critical insights into how the identity of a student as a ‘customer’ of higher education is understood and deployed when developing higher education policy. This paper uses the 2014 Australian higher education reforms as a lens through which to further scholarly research into the student-as-customer metaphor and to see how it is influenced by the perceptions and understandings of policy actors external to the higher education sector. These include politicians, special interest groups, the students and their parents and prospective employers. This study reveals that the public/private nexus—both of funding and benefit— problematizes traditional conceptualisations of students and others as higher education customers. In turn, this restricts the ability or desire of policy actors to describe how the student functions as a customer as a consequence of market reform. This inability compromises the development of effective and sustainable higher education polic

Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability.

Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies