Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

Background: Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Results: Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination, with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus.Work was funded by a grant from the Sustainable Crop Production Research for International Development programme funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) with co-funding from the UK Department for International Development, the Bill & Melinda Gates Foundation, the Department of Biotechnology of India’s Ministry of Science and Technology, and the Indian Council of Agricultural Research (BB/J011762/1) and a Global Challenges Research Fund Foundation Award (BB/P023223/1). LAB was funded by a Cambridge BBSRC doctoral training programme studentship

Retrovirus Integration Database (RID): A public database for retroviral insertion sites into host genomes

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. Availability: https://rid.ncifcrf.gov; or http://home.ncifcrf.gov/hivdrp/resources.htm

Estimation of optimal birth weights and gestational ages for twin births in Japan

BACKGROUND: As multiple pregnancies show a higher incidence of complications than singletons and carry a higher perinatal risk, the calculation of birth weight – and gestational age (GA)-specific perinatal mortality rates (PMR) for multiple births is necessary in order to estimate the lowest PMR for these groups. METHODS: Details of all reported twins (192,987 live births, 5,539 stillbirths and 1,830 early neonatal deaths) in Japan between 1990 and 1999 were analyzed and compared with singletons (10,021,275 live births, 63,972 fetal deaths and 16,862 early neonatal deaths) in the annual report of vital statistics of Japan. The fetal death rate (FDR) and PMR were calculated for each category of birth weight at 500-gram intervals and GA at four-week intervals. The FDR according to birth weight and GA category was calculated as fetal deaths/(fetal deaths + live births) × 1000. The perinatal mortality rate (PMR) according to birth weight and GA category, was calculated as (fetal deaths + early neonatal deaths)/(fetal deaths + live births) × 1000. Within each category, the lowest FDR and PMR were assigned with a relative risk (RR) of 1.0 as a reference and all other rates within each category were compared to this lowest rate. RESULTS: The overall PMR per 1,000 births for singletons was 6.9, and the lowest PMR was 1.1 for birth weight (3.5–4.0 kg) and GA (40- weeks). For twins, the overall PMR per 1,000 births was 36.8, and the lowest PMR was 3.9 for birth weight (2.5–3.0 kg) and GA (36–39 weeks). At optimal birth weight and GA, the PMR was reduced to 15.9 percent for singletons, and 10.6 percent for twins, compared to the overall PMR. The risk of perinatal mortality was greater in twins than in singletons at the same deviation from the ideal category of each plurality. CONCLUSION: PMRs are potentially reduced by attaining the ideal birth weight and GA. More than 90 percent of mortality could be reduced by attaining the optimal GA and birth weight in twins by taking particular care to ensure appropriate pregnancy weight gain, as well as adequate control for obstetric complications

Synaesthesia: a distinct entity that is an emergent feature of adaptive neurocognitive differences

In this article, I argue that synaesthesia is not on a continuum with neurotypical cognition. Synaesthesia is special: its phenomenology is different; it has distinct causal mechanisms; and is likely to be associated with a distinct neurocognitive profile. However, not all synaesthetes are the same, and there are quantifiable differences between them. In particular, the number of types of synaesthesia that a person possesses is a hitherto underappreciated variable that predicts cognitive differences along a number of dimensions (mental imagery, sensory sensitivity, attention to detail). Together with enhanced memory, this may constitute a common core of abilities that may go some way to explaining why synaesthesia might have evolved. I argue that the direct benefits of synaesthesia are generally limited (i.e. the synaesthetic associations do not convey novel information about the world) but, nevertheless, synaesthesia may develop due to other adaptive functions (e.g. perceptual ability, memory) that necessitate changes to design features of the brain. The article concludes by suggesting that synaesthesia forces us to reconsider what we mean by a ‘normal’ mind/brain. There may be multiple ‘normal’ neurodevelopmental trajectories that can sculpt very different ways of experiencing the world, of which synaesthesia is but one. This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’

Aspiration of parenteral nutrition – a previously unreported complication of central venous access in an infant: a case report

Introduction: The insertion of percutaneous central venous catheters is a common procedure in neonatal intensive care nurseries. Placement of the catheter tip in a large central vein is most desirable. Occasionally, due to difficult venous access, catheter tips are left in places that are less than ideal. Case presentation: A female infant with a complicated gastroschisis developed signs of short bowel syndrome post surgery. She was treated with a combination of parenteral nutrition and enteral feeds. A central venous line was inserted through a scalp vein. The tip was noted to be in a vessel at the level of the mandible. She subsequently became unwell with large milky pharyngeal aspirates and episodes of bradycardia. Chest radiography revealed aspiration. The central venous line was removed because of presumed extravasation. This is the first reported case of parenteral nutrition extravasation into the pharynx causing aspiration in an infant. Conclusion: This complication may have been prevented by recognising that the tip of the catheter was not correctly placed. When catheters are in unusual positions it may be useful to obtain a second radiograph from a different angle or an ultrasound scan to confirm the positioning of the catheter tip

Aspiration of parenteral nutrition – a previously unreported complication of central venous access in an infant: a case report

Introduction: The insertion of percutaneous central venous catheters is a common procedure in neonatal intensive care nurseries. Placement of the catheter tip in a large central vein is most desirable. Occasionally, due to difficult venous access, catheter tips are left in places that are less than ideal. Case presentation: A female infant with a complicated gastroschisis developed signs of short bowel syndrome post surgery. She was treated with a combination of parenteral nutrition and enteral feeds. A central venous line was inserted through a scalp vein. The tip was noted to be in a vessel at the level of the mandible. She subsequently became unwell with large milky pharyngeal aspirates and episodes of bradycardia. Chest radiography revealed aspiration. The central venous line was removed because of presumed extravasation. This is the first reported case of parenteral nutrition extravasation into the pharynx causing aspiration in an infant. Conclusion: This complication may have been prevented by recognising that the tip of the catheter was not correctly placed. When catheters are in unusual positions it may be useful to obtain a second radiograph from a different angle or an ultrasound scan to confirm the positioning of the catheter tip

Problems and Pitfalls of Identifying Remyelination in Multiple Sclerosis.

Regenerative medicines that promote remyelination in multiple sclerosis (MS) are making the transition from laboratory to clinical trials. While animal models provide the experimental flexibility to analyze mechanisms of remyelination, here we discuss the challenges in understanding where and how remyelination occurs in MS.The authors acknowledge the following support: The UK Multiple Sclerosis Society (RTK, CZ, RJMF), The Adelson Medical Research Foundation (DSR, DEB, RJMF), Intramural Research Program of NINDS/NIH (DSR), European Research Council (ERC) under the European Union Horizon 2020 Re- search and Innovation Program (RTK), The Lister Institute (RTK), and a core support grant from the Wellcome and MRC to the Wellcome-Medical Research Council Cambridge Stem Cell Institute (RTK, RJMF)

The Rich Structure of Gauss-Bonnet Holographic Superconductors

We study fully backreacting, Gauss-Bonnet (GB) holographic superconductors in 5 bulk spacetime dimensions. We explore the system's dependence on the scalar mass for both positive and negative GB coupling, $\alpha$. We find that when the mass approaches the Breitenlohner-Freedman (BF) bound and $\alpha\rightarrow L^2/4$ the effect of backreaction is to increase the critical temperature, $T_c$, of the system: the opposite of its effect in the rest of parameter space. We also find that reducing $\alpha$ below zero increases $T_c$ and that the effect of backreaction is diminished. We study the zero temperature limit, proving that this system does not permit regular solutions for a non-trivial, tachyonic scalar field and constrain possible solutions for fields with positive masses. We investigate singular, zero temperature solutions in the Einstein limit but find them to be incompatible with the concept of GB gravity being a perturbative expansion of Einstein gravity. We study the conductivity of the system, finding that the inclusion of backreaction hinders the development of poles in the conductivity that are associated with quasi-normal modes approaching the real axis from elsewhere in the complex plane.Comment: 26 pages, 11 figures, V3, Added discussion of non-tachyonic scalars, alterations to figures and tex

Analysis of factors influencing the ultrasonic fetal weight estimation

Objective: The aim of our study was the evaluation of sonographic fetal weight estimation taking into consideration 9 of the most important factors of influence on the precision of the estimation. Methods: We analyzed 820 singleton pregnancies from 22 to 42 weeks of gestational age. We evaluated 9 different factors that potentially influence the precision of sonographic weight estimation ( time interval between estimation and delivery, experts vs. less experienced investigator, fetal gender, gestational age, fetal weight, maternal BMI, amniotic fluid index, presentation of the fetus, location of the placenta). Finally, we compared the results of the fetal weight estimation of the fetuses with poor scanning conditions to those presenting good scanning conditions. Results: Of the 9 evaluated factors that may influence accuracy of fetal weight estimation, only a short interval between sonographic weight estimation and delivery (0-7 vs. 8-14 days) had a statistically significant impact. Conclusion: Of all known factors of influence, only a time interval of more than 7 days between estimation and delivery had a negative impact on the estimation

Electron transport through 8-oxoG: NEGF/DFT study

We present a first-principles study of the conductance of Guanine and 8-Oxoguanine (8-oxoG) attached to Au(111) electrodes. Cellular levels of 8-oxoG have been found in larger concentrations in cancer patients. The current through the structure was calculated using a DFT–NEGF formalism. We have compared flat and pyramidal electrode geometries and show that there is a measurable difference between the I–V characteristics of the pristine molecule and the 8-oxoG. For a flat electrode geometry, 8-oxoG produces a 2.57 (18.3) times increase in current than the corresponding counterpart at 3 V with a bond separation of 1.2 Å (2.4 Å). This can be attributed to molecular orbital energies shifting at the junction. Overall the flat geometry produces larger currents. We have also investigated the sensitivity of the current to the electrode molecule separation. For the flat geometry, the current dropped approximately 80% (97%) for 8-oxoG (pristine Guanine) with the doubling of the electrode separation