Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species.

Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the Solanum section Petota, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of Solanum section Petota composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The Petota core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for Solanum section Petota.

Testing non-autonomous antimalarial gene drive effectors using self-eliminating drivers in the African mosquito vector Anopheles gambiae.

Gene drives for mosquito population modification are novel tools for malaria control. Strategies to safely test antimalarial effectors in the field are required. Here, we modified the Anopheles gambiae zpg locus to host a CRISPR/Cas9 integral gene drive allele (zpgD) and characterized its behaviour and resistance profile. We found that zpgD dominantly sterilizes females but can induce efficient drive at other loci when it itself encounters resistance. We combined zpgD with multiple previously characterized non-autonomous payload drives and found that, as zpgD self-eliminates, it leads to conversion of mosquito cage populations at these loci. Our results demonstrate how self-eliminating drivers could allow safe testing of non-autonomous effector-traits by local population modification. They also suggest that after engendering resistance, gene drives intended for population suppression could nevertheless serve to propagate subsequently released non-autonomous payload genes, allowing modification of vector populations initially targeted for suppression.

Understanding the causes of missingness in primary care: a realist review.

BACKGROUND: Although missed appointments in healthcare have been an area of concern for policy, practice and research, the primary focus has been on reducing single 'situational' missed appointments to the benefit of services. Little attention has been paid to the causes and consequences of more 'enduring' multiple missed appointments in primary care and the role this has in producing health inequalities. METHODS: We conducted a realist review of the literature on multiple missed appointments to identify the causes of 'missingness.' We searched multiple databases, carried out iterative citation-tracking on key papers on the topic of missed appointments and identified papers through searches of grey literature. We synthesised evidence from 197 papers, drawing on the theoretical frameworks of candidacy and fundamental causation. RESULTS: Missingness is caused by an overlapping set of complex factors, including patients not identifying a need for an appointment or feeling it is 'for them'; appointments as sites of poor communication, power imbalance and relational threat; patients being exposed to competing demands, priorities and urgencies; issues of travel and mobility; and an absence of choice or flexibility in when, where and with whom appointments take place. CONCLUSIONS: Interventions to address missingness at policy and practice levels should be theoretically informed, tailored to patients experiencing missingness and their identified needs and barriers; be cognisant of causal domains at multiple levels and address as many as practical; and be designed to increase safety for those seeking care.

The use of technology to address loneliness and social isolation among older adults: the role of social care providers.

BACKGROUND: Addressing loneliness and social isolation among older adults remains a public health priority. The restrictions enforced during the COVID-19 pandemic simultaneously heightened the need for services to overcome social isolation and reduce loneliness among older adults, while also limiting social care providers' ability to deliver these. The aim of this study was to explore the experiences of social care providers in using technology to address loneliness and social isolation among older adults during the pandemic. METHODS: This was a mixed methods study involving an online survey and interviews with providers of older adult social care in Wales, UK. Invitations to participate were sent to commissioners and providers of adult social care services, including those working in the voluntary and community sectors, across all local authorities in Wales. Data was collected between September 2021 and January 2022. RESULTS: Sixty-one service providers completed the survey, 19 of whom also took part in an interview. Addressing loneliness and isolation among older adults was reported as a key concern by nearly all survey respondents. While telephone calls were the most common means of facilitating social interaction, many service providers also tried to support older adults to make more use of devices that they already had (e.g., smartphones to hold video calls). Where funding was available, organisations purchased devices, such as tablets and smart speakers, for older adults. Analysis of interviews resulted in three themes: (1) The potential and limitations of technology; (2) Individuals' capabilities, confidence, motivations and values; and (3) The wider system. CONCLUSIONS: Technology was employed in a variety of ways during the pandemic to address loneliness and social isolation among older adults; many service providers continue to use technology in a hybrid system of care now that pandemic-related social restrictions have been lifted. Our findings emphasise a need for technology-assisted interventions to be designed and deployed in alignment with service users' values, motivations and capabilities. Further, there is a need to better support service providers to assess loneliness and social isolation among older adults, and to acknowledge the important role providers play in helping older adults to adopt technology-assisted interventions.

R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements.

Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a hallmark of ageing. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution of de novo rearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To characterize genome rearrangements during cellular ageing in non-dividing cells, we interrogated a single diagnostic measure, DNA breakpoint junctions, using Schizosaccharomyces pombe as a model system. Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints elsewhere in the genome, including the mitochondrial chromosome. Formation of breakpoint junctions at global hotspots was inhibited by the Sir2 histone deacetylase and might be triggered by an age-dependent de-repression of chromatin silencing. An unexpected mechanism of genomic instability may cause more local hotspots: age-associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and possible mechanisms of genome rearrangements in non-dividing cells, which can be promoted by ageing-related changes in gene-regulatory proteins.

Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model.

Designing implants for large and complex cranial defects is a challenging task, even for professional designers. Current efforts on automating the design process focused mainly on convolutional neural networks (CNN), which have produced state-of-the-art results on reconstructing synthetic defects. However, existing CNN-based methods have been difficult to translate to clinical practice in cranioplasty, as their performance on large and complex cranial defects remains unsatisfactory. In this paper, we present a statistical shape model (SSM) built directly on the segmentation masks of the skulls represented as binary voxel occupancy grids and evaluate it on several cranial implant design datasets. Results show that, while CNN-based approaches outperform the SSM on synthetic defects, they are inferior to SSM when it comes to large, complex and real-world defects. Experienced neurosurgeons evaluate the implants generated by the SSM to be feasible for clinical use after minor manual corrections. Datasets and the SSM model are publicly available at https://github.com/Jianningli/ssm .

Examining safety and efficacy of a fixed concentration heparin dosing strategy for anticoagulation in neonatal extracorporeal membrane oxygenation.

OBJECTIVES: The paediatric intensive care unit changed heparin infusion dosing from a variable weight-based concentration to a fixed concentration strategy, when smart pump-based drug library was introduced. This change meant significantly lower rates of infusion were needed for the same dose of heparin in the neonatal population. We performed a safety and efficacy assessment of this change. METHODS: We performed a retrospective single-centre evaluation based on data from respiratory VA-extracorporeal membrane oxygenation (ECMO) patients weighing ≤5 kg, pre and post the change to fixed strength heparin infusion. Efficacy was analysed by distribution of activated clotting times (ACT) and heparin dose requirements between the groups. Safety was analysed using thrombotic and haemorrhagic event rates. Continuous variables were reported as median, interquartile ranges, and non-parametric tests were used. Generalised estimating equations (GEE) were used to analyse associations of heparin dosing strategy with ACT and heparin dose requirements in the first 24 h of ECMO. Incidence rate ratios of circuit related thrombotic and haemorrhagic events between groups were analysed using Poisson regression with offset for run hours. RESULTS: 33 infants (20 variable weight-based, 13 fixed concentration) were analysed. Distribution of ACT ranges and heparin dose requirements were similar between the two groups during the ECMO run and this was confirmed by GEE. Incidence rate ratios of thrombotic (fixed v weight-based) (1.9 [0.5-8], p = .37), and haemorrhagic events (0.9 [0.1-4.9], p = .95) did not show statistically significant differences. CONCLUSIONS: Fixed concentration dosing of heparin was at least equally effective and safe compared to a weight-based dosing.

Leptospirosis in the Air: A Case Review Series During Air Medical Transport in Haiti.

Leptospirosis is an infectious illness encountered mostly in tropical climates and has been of particular concern in Haiti after natural disasters. Heavy rainfalls and natural disasters in combination with scarce resources to control and identify clusters of infections make certain populations and countries vulnerable. In some cases, patients who contract this disease may need air medical transport to hospitals that have a higher level of care. In this case report, a trio of cases is highlighted from an outbreak that required air transport to transfer patients to a facility with the availability of an intensive care unit. The goal of highlighting these cases is to increase the awareness of physicians and air transport providers to the manifestation and treatment of this disease and to provide pearls to stabilize patients during transport.

Extraction of mobile charge carrier photogeneration yield spectrum of ultrathin-film metal oxide photoanodes for solar water splitting.

Light absorption in strongly correlated electron materials can excite electrons and holes into a variety of different states. Some of these excitations yield mobile charge carriers, whereas others result in localized states that cannot contribute to photocurrent. The photogeneration yield spectrum, ξ(λ), represents the wavelength-dependent ratio between the contributing absorption that ultimately generates mobile charge carriers and the overall absorption. Despite being a vital material property, it is not trivial to characterize. Here, we present an empirical method to extract ξ(λ) through optical and external quantum efficiency measurements of ultrathin films. We applied this method to haematite photoanodes for water photo-oxidation, and observed that it is self-consistent for different illumination conditions and applied potentials. We found agreement between the extracted ξ(λ) spectrum and the photoconductivity spectrum measured by time-resolved microwave conductivity. These measurements revealed that mobile charge carrier generation increases with increasing energy across haematite's absorption spectrum. Low-energy non-contributing absorption fundamentally limits the photoconversion efficiency of haematite photoanodes and provides an upper limit to the achievable photocurrent that is substantially lower than that predicted based solely on absorption above the bandgap. We extended our analysis to TiO2 and BiVO4 photoanodes, demonstrating the broader utility of the method for determining ξ(λ).

Behavioral Consistency in the Digital Age.

Efforts to infer personality from digital footprints have focused on behavioral stability at the trait level without considering situational dependency. We repeated a classic study of intraindividual consistency with secondary data (five data sets) containing 28,692 days of smartphone usage from 780 people. Using per-app measures of pickup frequency and usage duration, we found that profiles of daily smartphone usage were significantly more consistent when taken from the same user than from different users (d > 1.46). Random-forest models trained on 6 days of behavior identified each of the 780 users in test data with 35.8% accuracy for pickup frequency and 38.5% accuracy for duration frequency. This increased to 73.5% and 75.3%, respectively, when success was taken as the user appearing in the top 10 predictions (i.e., top 1%). Thus, situation-dependent stability in behavior is present in our digital lives, and its uniqueness provides both opportunities and risks to privacy.

Monitoring a meat-free pledge with smartphones: An experimental study.

Pledges are a popular strategy to encourage meat reduction, though experimental studies of their efficacy are lacking. Three-hundred and twenty-five participants from three different countries (UK, Germany, Australia) were randomly assigned to pledge 28 days meat-free or not, and their behavior was tracked via smartphones. Participants answered daily surveys regarding their eating behavior, meat cravings, and shared photos of their meals. Baseline data was collected prior to the pledge, after the 28 days, and one-month post-intervention. Participants assigned to the pledge condition ate less meat across the 28 days, compared to control participants. Meat reductions, observed at outtake, did not endure one-month post-intervention. Overall, German participants ate the least amount of meat, and showed the sharpest decrease in consumption when pledging. Meat cravings tended to increase among pledgers, relative to control participants. Pledgers who reported high starting intentions and conflict about meat tended to eat less meat and reported fewer cravings. All participants reported reduced meat-eating justifications one-month post-intervention. These findings provide experimental evidence that pledges can encourage meat consumers to reduce their intake, though additional mechanisms are needed to sustain commitments.

Screening South American Potato Landraces and Potato Wild Relatives for Novel Sources of Late Blight Resistance.

Late blight (LB) caused by the oomycete Phytophthora infestans is one of the most important biotic constraints for potato production worldwide. This study assessed 508 accessions (79 wild potato species and 429 landraces from a cultivated core collection) held at the International Potato Center genebank for resistance to LB. One P. infestans isolate belonging to the EC-1 lineage, which is currently the predominant type of P. infestans in Peru, Ecuador, and Colombia, was used in whole plant assays under greenhouse conditions. Novel sources of resistance to LB were found in accessions of Solanum albornozii, S. andreanum, S. lesteri, S. longiconicum, S. morelliforme, S. stenophyllidium, S. mochiquense, S. cajamarquense, and S. huancabambense. All of these species are endemic to South America and thus could provide novel sources of resistance for potato breeding programs. We found that the level of resistance to LB in wild species and potato landraces cannot be predicted from altitude and bioclimatic variables of the locations where the accessions were collected. The high percentage (73%) of potato landraces susceptible to LB in our study suggests the importance of implementing disease control measures, including planting susceptible genotypes in less humid areas and seasons or switching to genotypes identified as resistant. In addition, this study points out a high risk of genetic erosion in potato biodiversity at high altitudes of the Andes due to susceptibility to LB in the native landraces, which has been exacerbated by climatic change that favors the development of LB in those regions.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Measurement practices exacerbate the generalizability crisis: Novel digital measures can help.

Psychology's tendency to focus on confirmatory analyses before ensuring constructs are clearly defined and accurately measured is exacerbating the generalizability crisis. Our growing use of digital behaviors as predictors has revealed the fragility of subjective measures and the latent constructs they scaffold. However, new technologies can provide opportunities to improve conceptualizations, theories, and measurement practices.

Open-source smartphone app and tools for measuring, quantifying, and visualizing technology use.

Psychological science has spent many years attempting to understand the impact of new technology on people and society. However, the frequent use of self-report methods to quantify patterns of usage struggle to capture subtle nuances of human-computer interaction. This has become particularly problematic for devices like smartphones that are used frequently and for a variety of purposes. While commercial apps can provide an element of objectivity, these are 'closed' and cannot be adapted to deliver a researcher-focused 'open' platform that allows for straightforward replication. Therefore, we have developed an Android app that provides accurate, highly detailed, and customizable accounts of smartphone usage without compromising participants' privacy. Further recommendations and code are provided to assist with data analysis. All source code, materials, and data are freely available (see links in supplementary materials section).

Educational associations with missed GP appointments for patients under 35 years old: administrative data linkage study.

BACKGROUND: There is an evidence gap about whether levels of engagement with public services such as schools and health care affect people across the lifespan. Data on missed patient appointments from a nationally representative sample of Scottish general practices (GP) (2013-2016) were probabilistically linked to secondary school pupil data. We tested whether school attendance, exclusions (2007-2011) or lower educational attainment (2007-2016) was associated with an increased risk of missing general practice appointments. METHODS: School attendance data were classified into quartiles of possible days attended for years we had data. School exclusions were derived as a categorical variable of 'ever excluded'. Attainment data were categorised via the Scottish Credit and Qualifications Framework (SCQF) level 3 or 6; a cumulative measure of attainment on leaving school. The associations between school attendance, exclusions and attainment and risk of missing medical appointments were investigated using negative binomial models, offset by number of GP appointments made and controlling for potential confounders. RESULTS: 112,534 patients (all aged under 35) had GP appointment and retrospective school attendance and exclusion data, and a subset of 66,967 also had attainment data available. Patients who had lower attendance, had been excluded from school or had lower educational attainment had an increased risk of missing GP appointments (all rate ratios > 1.40). CONCLUSIONS: This study provides the first evidence from a population-representative sample in a high-income country that increased numbers of missed appointments in health care are associated with reduced school attendance, higher levels of school exclusion and lower educational attainment. Insights into the epidemiology of missingness across public services can support future research, policy and practice that aim to improve healthcare, health outcomes and engagement in services.

Opening Pandora's Box: Peeking inside Psychology's data sharing practices, and seven recommendations for change.

Open data-sharing is a valuable practice that ought to enhance the impact, reach, and transparency of a research project. While widely advocated by many researchers and mandated by some journals and funding agencies, little is known about detailed practices across psychological science. In a pre-registered study, we show that overall, few research papers directly link to available data in many, though not all, journals. Most importantly, even where open data can be identified, the majority of these lacked completeness and reusability-conclusions that closely mirror those reported outside of Psychology. Exploring the reasons behind these findings, we offer seven specific recommendations for engineering and incentivizing improved practices, so that the potential of open data can be better realized across psychology and social science more generally.

Development of an Offline-Friend Addiction Questionnaire (O-FAQ): Are most people really social addicts?

A growing number of self-report measures aim to define interactions with social media in a pathological behavior framework, often using terminology focused on identifying those who are 'addicted' to engaging with others online. Specifically, measures of 'social media addiction' focus on motivations for online social information seeking, which could relate to motivations for offline social information seeking. However, it could be the case that these same measures could reveal a pattern of friend addiction in general. This study develops the Offline-Friend Addiction Questionnaire (O-FAQ) by re-wording items from highly cited pathological social media use scales to reflect "spending time with friends". Our methodology for validation follows the current literature precedent in the development of social media 'addiction' scales. The O-FAQ had a three-factor solution in an exploratory sample of N = 807 and these factors were stable in a 4-week retest (r = .72 to .86) and was validated against personality traits, and risk-taking behavior, in conceptually plausible directions. Using the same polythetic classification techniques as pathological social media use studies, we were able to classify 69% of our sample as addicted to spending time with their friends. The discussion of our satirical research is a critical reflection on the role of measurement and human sociality in social media research. We question the extent to which connecting with others can be considered an 'addiction' and discuss issues concerning the validation of new 'addiction' measures without relevant medical constructs. Readers should approach our measure with a level of skepticism that should be afforded to current social media addiction measures.

Comparability of Raman Spectroscopic Configurations: A Large Scale Cross-Laboratory Study.

The variable configuration of Raman spectroscopic platforms is one of the major obstacles in establishing Raman spectroscopy as a valuable physicochemical method within real-world scenarios such as clinical diagnostics. For such real world applications like diagnostic classification, the models should ideally be usable to predict data from different setups. Whether it is done by training a rugged model with data from many setups or by a primary-replica strategy where models are developed on a 'primary' setup and the test data are generated on 'replicate' setups, this is only possible if the Raman spectra from different setups are consistent, reproducible, and comparable. However, Raman spectra can be highly sensitive to the measurement conditions, and they change from setup to setup even if the same samples are measured. Although increasingly recognized as an issue, the dependence of the Raman spectra on the instrumental configuration is far from being fully understood and great effort is needed to address the resulting spectral variations and to correct for them. To make the severity of the situation clear, we present a round robin experiment investigating the comparability of 35 Raman spectroscopic devices with different configurations in 15 institutes within seven European countries from the COST (European Cooperation in Science and Technology) action Raman4clinics. The experiment was developed in a fashion that allows various instrumental configurations ranging from highly confocal setups to fibre-optic based systems with different excitation wavelengths. We illustrate the spectral variations caused by the instrumental configurations from the perspectives of peak shifts, intensity variations, peak widths, and noise levels. We conclude this contribution with recommendations that may help to improve the inter-laboratory studies.

Structural genome analysis in cultivated potato taxa.

KEY MESSAGE: Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X-5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

Operando X-ray Absorption Spectroscopy (XAS) Observation of Photoinduced Oxidation in FeNi (Oxy)hydroxide Overlayers on Hematite (α-Fe2O3) Photoanodes for Solar Water Splitting.

An FeNi (oxy)hydroxide cocatalyst overlayer was photoelectrochemically deposited on a thin-film hematite (α-Fe2O3) photoanode, leading to a cathodic shift of ∼100 mV in the photocurrent onset potential. Operando X-ray absorption spectroscopy (XAS) at the Fe and Ni K-edges was used to study the changes in the overlayer with potential in the dark and under illumination conditions. Potential or illumination only had a minor effect on the Fe oxidation state, suggesting that Fe atoms do not accumulate significant amount of charge over the whole potential range. In contrast, the Ni K-edge spectra showed pronounced dependence on potential in the dark and under illumination. The effect of illumination is to shift the onset for the Ni oxidation because of the generated photovoltage and suggests that holes that are photogenerated in hematite are transferred mainly to the Ni atoms in the overlayer. The increase in the oxidation state of Ni proceeds at potentials corresponding to the redox wave of Ni, which occurs immediately prior to the onset of the oxygen evolution reaction (OER). Linear combination fitting analysis of the obtained spectra suggests that the overlayer does not have to be fully oxidized to promote oxygen evolution. Cathodic discharge measurements show that the photogenerated charge is stored almost exclusively in the Ni atoms within the volume of the overlayer.