Global minimum estimates of children affected by COVID-19-associated orphanhood and deaths of caregivers: a modelling study.

BACKGROUND: The COVID-19 pandemic priorities have focused on prevention, detection, and response. Beyond morbidity and mortality, pandemics carry secondary impacts, such as children orphaned or bereft of their caregivers. Such children often face adverse consequences, including poverty, abuse, and institutionalisation. We provide estimates for the magnitude of this problem resulting from COVID-19 and describe the need for resource allocation. METHODS: We used mortality and fertility data to model minimum estimates and rates of COVID-19-associated deaths of primary or secondary caregivers for children younger than 18 years in 21 countries. We considered parents and custodial grandparents as primary caregivers, and co-residing grandparents or older kin (aged 60-84 years) as secondary caregivers. To avoid overcounting, we adjusted for possible clustering of deaths using an estimated secondary attack rate and age-specific infection-fatality ratios for SARS-CoV-2. We used these estimates to model global extrapolations for the number of children who have experienced COVID-19-associated deaths of primary and secondary caregivers. FINDINGS: Globally, from March 1, 2020, to April 30, 2021, we estimate 1 134 000 children (95% credible interval 884 000-1 185 000) experienced the death of primary caregivers, including at least one parent or custodial grandparent. 1 562 000 children (1 299 000-1 683 000) experienced the death of at least one primary or secondary caregiver. Countries in our study set with primary caregiver death rates of at least one per 1000 children included Peru (10·2 per 1000 children), South Africa (5·1), Mexico (3·5), Brazil (2·4), Colombia (2·3), Iran (1·7), the USA (1·5), Argentina (1·1), and Russia (1·0). Numbers of children orphaned exceeded numbers of deaths among those aged 15-50 years. Between two and five times more children had deceased fathers than deceased mothers. INTERPRETATION: Orphanhood and caregiver deaths are a hidden pandemic resulting from COVID-19-associated deaths. Accelerating equitable vaccine delivery is key to prevention. Psychosocial and economic support can help families to nurture children bereft of caregivers and help to ensure that institutionalisation is avoided. These data show the need for an additional pillar of our response: prevent, detect, respond, and care for children. FUNDING: UK Research and Innovation (Global Challenges Research Fund, Engineering and Physical Sciences Research Council, Medical Research Council), UK National Institute for Health Research, US National Institutes of Health, and Imperial College London.

Restoring speech following total removal of the larynx by a learned transformation from sensor data to acoustics.

Total removal of the larynx may be required to treat laryngeal cancer: speech is lost. This article shows that it may be possible to restore speech by sensing movement of the remaining speech articulators and use machine learning algorithms to derive a transformation to convert this sensor data into an acoustic signal. The resulting "silent speech," which may be delivered in real time, is intelligible and sounds natural. The identity of the speaker is recognisable. The sensing technique involves attaching small, unobtrusive magnets to the lips and tongue and monitoring changes in the magnetic field induced by their movement.

Characterizing coated paper surface for modeling apparent dot area of halftone prints.

A new model is proposed for predicting the apparent dot area of simulated halftone prints on coated paper surface without requiring printing. It is based on Hotelling's multivariate T(2) statistic which is shown to provide a measure of lateral light scattering. The T(2) statistic is computed from colorimetric coordinates obtained from of a knife shadow image response on the paper surface. The proposed method offers superior prediction of halftone dot area compared to current light scattering models. A method for characterising peaks on the coated paper surface is introduced in this work. The effect of the paper coating layer thickness and the surface peak height on lateral light scattering and printed dot size are shown.

Consistency and standardization of color in medical imaging: a consensus report.

This article summarizes the consensus reached at the Summit on Color in Medical Imaging held at the Food and Drug Administration (FDA) on May 8-9, 2013, co-sponsored by the FDA and ICC (International Color Consortium). The purpose of the meeting was to gather information on how color is currently handled by medical imaging systems to identify areas where there is a need for improvement, to define objective requirements, and to facilitate consensus development of best practices. Participants were asked to identify areas of concern and unmet needs. This summary documents the topics that were discussed at the meeting and recommendations that were made by the participants. Key areas identified where improvements in color would provide immediate tangible benefits were those of digital microscopy, telemedicine, medical photography (particularly ophthalmic and dental photography), and display calibration. Work in these and other related areas has been started within several professional groups, including the creation of the ICC Medical Imaging Working Group.

Consed: a graphical editor for next-generation sequencing.

SUMMARY: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added. AVAILABILITY: The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user's manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.html CONTACT: dgordon@uw.edu .

Characterisation of the n-colour printing process using the spot colour overprint model.

This paper is aimed at reproducing the solid spot colours using the n-colour separation. A simplified numerical method, called as the spot colour overprint (SCOP) model, was used for characterising the n-colour printing process. This model was originally developed for estimating the spot colour overprints. It was extended to be used as a generic forward characterisation model for the n-colour printing process. The inverse printer model based on the look-up table was implemented to obtain the colour separation for n-colour printing process. Finally the real-world spot colours were reproduced using 7-colour separation on lithographic offset printing process. The colours printed with 7 inks were compared against the original spot colours to evaluate the accuracy. The results show good accuracy with the mean CIEDE2000 value between the target colours and the printed colours of 2.06. The proposed method can be used successfully to reproduce the spot colours, which can potentially save significant time and cost in the printing and packaging industry.

The effectiveness of Hope Groups, a mental health, parenting support, and violence prevention program for families affected by the war in Ukraine: Findings from a pre-post study.

Background: Nearly one in six children lived in war zones in 2023. Evidence-based psychosocial and parenting support has potential to mitigate negative impacts for parents and children co-exposed to war and displacement, especially in relation to mental health and harsh parenting reactions. In the current war in Ukraine, local mental health experts co-created and evaluated, with global experts, the effectiveness of psychosocial and parenting support groups, called 'Hope Groups' on improvements in mental health, positive parenting, and violence against children. This paper aimed to assess the effectiveness of psychosocial and parenting support groups, called 'Hope Groups,' on improvements in caregiver mental health, positive parenting, and prevention of violence against children, for families affected by the war in Ukraine, using a pre/post study design. Methods: Participants (n = 577) included Ukrainian caregivers, 66% (381) of whom were parents and co-residing caregivers of children ages 0-17, while the remaining 34% were non-resident informal caregivers. Internally displaced, externally displaced, and those living at-home in war-torn regions were invited to groups by trained Ukrainian peer facilitators. Using a pre-post design, we compared individual level frequency measures at three time-points - baseline, midline, and endline, to assess changes in 4 mental health, and 9 parenting and child health outcomes. We analyzed these outcomes using paired t-tests to compare outcomes at baseline-to-midline (after 4-sessions) and baseline-to-endline (after 10-sessions), which estimated the mean changes in days per week and associated percent change, during the respective periods; we quantified uncertainties using bias-corrected and accelerated (BCa) bootstrapping with 95% uncertainty ranges for baseline-midline and baseline-endline estimates. We used this same approach for stratified analyses to assess potential effect modification by displacement status and facilitator type. We further used linear models to adjust for age and sex. Findings: Compared to baseline, every mental health, parenting, and child health outcome improved significantly at midline and endline. Mental health ratings showed endline reductions in depressive symptoms of 56.8% (95% CI: -59.0,-54.3; -1.8 days/week), and increases in hopefulness, coping with grief, and self-care, ranging from 62.0% (95% CI: 53.6,71.3; 2.2 days/week) to 77.0% (95% CI: 66.3,88.3; 2.2 days/week). Significant improvements in parenting and child health outcomes included monitoring children, reinforcing positive behavior, supporting child development, protecting child, nonviolent discipline, and child verbalizing emotions. By endline, emotional violence, physical violence, and child despondency had dropped by 57.7% (95% CI: -63.0%,-51.9; -1.3 days/week), 64.0% (95% CI: -79.0,-39.5; -0.22 days/week), and 51.9% (95% CI: -45.1,-57.9; -1.2 days/week), respectively. Outcomes stratified by displacement status remained significant across all groups, as did those according to facilitator type (lay versus professional). Interpretation: This study demonstrates preliminary evidence, using a brief survey and pre-post design as is appropriate for acute and early protracted emergency settings, of the feasibility and effectiveness of Hope Groups for war-affected Ukrainian caregivers, on improved mental health, positive parenting, and reduced violence against children.

Expression-based segmentation of the Drosophila genome.

BACKGROUND: It is generally accepted that gene order in eukaryotes is nonrandom, with adjacent genes often sharing expression patterns across tissues, and that this organization may be important for gene regulation. Here we describe a novel method, based on an explicit probability model instead of correlation analysis, for identifying coordinately expressed gene clusters ('coexpression segments'), apply it to Drosophila melanogaster, and look for epigenetic associations using publicly available data. RESULTS: We find that two-thirds of Drosophila genes fall into multigenic coexpression segments, and that such segments are of two main types, housekeeping and tissue-restricted. Consistent with correlation-based studies, we find that adjacent genes within the same segment tend to be physically closer to each other than to the adjacent genes in different segments, and that tissue-restricted segments are enriched for testis-expressed genes. Our segmentation pattern correlates with Hi-C based physical interaction domains, but segments are generally much smaller than domains. Intersegment regions (including those which do not correspond to physical domain boundaries) are enriched for insulator binding sites. CONCLUSIONS: We describe a novel approach for identifying coexpression clusters that does not require arbitrary cutoff values or heuristics, and find that coexpression of adjacent genes is widespread in the Drosophila genome. Coexpression segments appear to reflect a level of regulatory organization related to, but below that of physical interaction domains, and depending in part on insulator binding.

Genomic signatures of germline gene expression.

Transcribed regions in the human genome differ from adjacent intergenic regions in transposable element density, crossover rates, and asymmetric substitution and sequence composition patterns. We tested whether these differences reflect selection or are instead a byproduct of germline transcription, using publicly available gene expression data from a variety of germline and somatic tissues. Crossover rate shows a strong negative correlation with gene expression in meiotic tissues, suggesting that crossover is inhibited by transcription. Strand-biased composition (G+T content) and A → G versus T → C substitution asymmetry are both positively correlated with germline gene expression. We find no evidence for a strand bias in allele frequency data, implying that the substitution asymmetry reflects a mutation rather than a fixation bias. The density of transposable elements is positively correlated with germline expression, suggesting that such elements preferentially insert into regions that are actively transcribed. For each of the features examined, our analyses favor a nonselective explanation for the observed trends and point to the role of germline gene expression in shaping the mammalian genome.

Transcription-associated mutational asymmetry in mammalian evolution.

Although mutation is commonly thought of as a random process, evolutionary studies show that different types of nucleotide substitution occur with widely varying rates that presumably reflect biases intrinsic to mutation and repair mechanisms. A strand asymmetry, the occurrence of particular substitution types at higher rates than their complementary types, that is associated with DNA replication has been found in bacteria and mitochondria. A strand asymmetry that is associated with transcription and attributable to higher rates of cytosine deamination on the coding strand has been observed in enterobacteria. Here, we describe a qualitatively different transcription-associated strand asymmetry in mammals, which may be a byproduct of transcription-coupled repair in germline cells. This mutational asymmetry has acted over long periods of time to produce a compositional asymmetry, an excess of G+T over A+C on the coding strand, in most genes. The mutational and compositional asymmetries can be used to detect the orientations and approximate extents of transcribed regions.

Mutation patterns in cancer genomes.

Recent large-scale cancer sequencing studies have focused primarily on identifying cancer-associated genes, but as an important byproduct provide "passenger mutation" data that can potentially illuminate the mutational mechanisms at work in cancer cells. Here, we explore patterns of nucleotide substitution in several cancer types using published data. We first show that selection (negative or positive) has affected only a small fraction of mutations, allowing us to attribute observed trends to underlying mutational processes rather than selection. We then show that the increased CpG mutation frequency observed in some cancers primarily occurs outside of CpG islands and CpG island shores, thus rejecting the hypothesis that the increase is a byproduct of island or shore methylation followed by deamination. We observe an A-->G vs. T-->C mutational asymmetry in some cancers similar to one that has been observed in germline mutations in transcribed regions, suggesting that the mutation process may be influenced by gene expression. We also demonstrate that the relative frequency of mutations at dinucleotide "hotspots" can be used as a tool to detect likely technical artifacts in large-scale studies.

Widespread genomic signatures of natural selection in hominid evolution.

Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19-26% on the autosomes and 12-40% on the X chromosome. The overall trends are broadly consistent with "background selection" or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events.

Global, regional, and national minimum estimates of children affected by COVID-19-associated orphanhood and caregiver death, by age and family circumstance up to Oct 31, 2021: an updated modelling study.

BACKGROUND: In the 6 months following our estimates from March 1, 2020, to April 30, 2021, the proliferation of new coronavirus variants, updated mortality data, and disparities in vaccine access increased the amount of children experiencing COVID-19-associated orphanhood. To inform responses, we aimed to model the increases in numbers of children affected by COVID-19-associated orphanhood and caregiver death, as well as the cumulative orphanhood age-group distribution and circumstance (maternal or paternal orphanhood). METHODS: We used updated excess mortality and fertility data to model increases in minimum estimates of COVID-19-associated orphanhood and caregiver deaths from our original study period of March 1, 2020-April 30, 2021, to include the new period of May 1-Oct 31, 2021, for 21 countries. Orphanhood was defined as the death of one or both parents; primary caregiver loss included parental death or the death of one or both custodial grandparents; and secondary caregiver loss included co-residing grandparents or kin. We used logistic regression and further incorporated a fixed effect for western European countries into our previous model to avoid over-predicting caregiver loss in that region. For the entire 20-month period, we grouped children by age (0-4 years, 5-9 years, and 10-17 years) and maternal or paternal orphanhood, using fertility contributions, and we modelled global and regional extrapolations of numbers of orphans. 95% credible intervals (CrIs) are given for all estimates. FINDINGS: The number of children affected by COVID-19-associated orphanhood and caregiver death is estimated to have increased by 90·0% (95% CrI 89·7-90·4) from April 30 to Oct 31, 2021, from 2 737 300 (95% CrI 1 976 100-2 987 000) to 5 200 300 (3 619 400-5 731 400). Between March 1, 2020, and Oct 31, 2021, 491 300 (95% CrI 485 100-497 900) children aged 0-4 years, 736 800 (726 900-746 500) children aged 5-9 years, and 2 146 700 (2 120 900-2 174 200) children aged 10-17 years are estimated to have experienced COVID-19-associated orphanhood. Globally, 76·5% (95% CrI 76·3-76·7) of children were paternal orphans, whereas 23·5% (23·3-23·7) were maternal orphans. In each age group and region, the prevalence of paternal orphanhood exceeded that of maternal orphanhood. INTERPRETATION: Our findings show that numbers of children affected by COVID-19-associated orphanhood and caregiver death almost doubled in 6 months compared with the amount after the first 14 months of the pandemic. Over the entire 20-month period, 5·0 million COVID-19 deaths meant that 5·2 million children lost a parent or caregiver. Our data on children's ages and circumstances should support pandemic response planning for children globally. FUNDING: UK Research and Innovation (Global Challenges Research Fund, Engineering and Physical Sciences Research Council, and Medical Research Council), Oak Foundation, UK National Institute for Health Research, US National Institutes of Health, and Imperial College London.

Reconstructing the voice of an individual following laryngectomy.

This case study describes the generation of a synthetic voice resembling that of an individual before she underwent a laryngectomy. Recordings of this person (6-7 min) speaking prior to the operation were used to create the voice. Synthesis was based on statistical speech models and this method allows models pre-trained on many speakers to be adapted to resemble an individual voice. The results of a listening test in which participants were asked to judge the similarity of the synthetic voice to the pre-operation (target) voice are reported. Members of the patient's family were asked to make a similar judgment. These experiments show that, for most listeners, the voice is quite convincing despite the low quality and small quantity of adaptation data.

Novel percutaneous dual-lumen cannula-based right ventricular assist device provides effective support for refractory right ventricular failure after left ventricular assist device implantation.

OBJECTIVES: Right heart failure after left ventricular assist device (LVAD) implantation is associated with significant morbidity and mortality. A new generation of percutaneous right ventricular assist devices (RVADs) may mitigate the need for invasive surgical RVAD implantation. The purpose of this study was to evaluate the safety and efficacy of the Protek Duo (TandemLife, Pittsburgh, PA, USA) RVAD in patients who developed severe acute right heart failure in the intensive care unit after LVAD implantation. METHODS: This was a retrospective cohort study of 27 patients who received a Protek Duo after LVAD implantation from January 2016 to March 2019 at our centre. The primary outcome of interest was survival to hospital discharge. Secondary outcomes included procedural success, device-related complications and conversion to a surgical RVAD. RESULTS: The median age of patients was 63 years (interquartile range 58-71), 78% were men and 78% were Interagency Registry for Mechanically Assisted Circulatory Support (INTERMACS) profile 1 or 2. Patients were on a median of 2 inotropes and 2 pressors prior to Protek Duo insertion. The device successfully implanted on the first attempt in all patients a median of 1 day (interquartile range 1-2) after LVAD implantation and the median duration of support was 11 days (interquartile range 7-16). Device weaning occurred in 86% of patients, with 15% in-hospital mortality. Major complications related to the device included new moderate-to-severe tricuspid regurgitation (36%), haemolysis (14%) and cannula migration (7%). Three patients (11%) required conversion to surgical RVAD. Overall survival to 1 year was 81%. CONCLUSIONS: The use of the Protek Duo as a percutaneous RVAD is a safe and feasible treatment for patients who develop acute right heart failure after LVAD implantation.

A speech-controlled environmental control system for people with severe dysarthria.

Automatic speech recognition (ASR) can provide a rapid means of controlling electronic assistive technology. Off-the-shelf ASR systems function poorly for users with severe dysarthria because of the increased variability of their articulations. We have developed a limited vocabulary speaker dependent speech recognition application which has greater tolerance to variability of speech, coupled with a computerised training package which assists dysarthric speakers to improve the consistency of their vocalisations and provides more data for recogniser training. These applications, and their implementation as the interface for a speech-controlled environmental control system (ECS), are described. The results of field trials to evaluate the training program and the speech-controlled ECS are presented. The user-training phase increased the recognition rate from 88.5% to 95.4% (p<0.001). Recognition rates were good for people with even the most severe dysarthria in everyday usage in the home (mean word recognition rate 86.9%). Speech-controlled ECS were less accurate (mean task completion accuracy 78.6% versus 94.8%) but were faster to use than switch-scanning systems, even taking into account the need to repeat unsuccessful operations (mean task completion time 7.7s versus 16.9s, p<0.001). It is concluded that a speech-controlled ECS is a viable alternative to switch-scanning systems for some people with severe dysarthria and would lead, in many cases, to more efficient control of the home.

Cloud-Based Speech Technology for Assistive Technology Applications (CloudCAST).

The CloudCAST platform provides a series of speech recognition services that can be integrated into assistive technology applications. The platform and the services provided by the public API are described. Several exemplar applications have been developed to demonstrate the platform to potential developers and users.

An Innovative Speech-Based User Interface for Smarthomes and IoT Solutions to Help People with Speech and Motor Disabilities.

A better use of the increasing functional capabilities of home automation systems and Internet of Things (IoT) devices to support the needs of users with disability, is the subject of a research project currently conducted by Area Ausili (Assistive Technology Area), a department of Polo Tecnologico Regionale Corte Roncati of the Local Health Trust of Bologna (Italy), in collaboration with AIAS Ausilioteca Assistive Technology (AT) Team. The main aim of the project is to develop experimental low cost systems for environmental control through simplified and accessible user interfaces. Many of the activities are focused on automatic speech recognition and are developed in the framework of the CloudCAST project. In this paper we report on the first technical achievements of the project and discuss future possible developments and applications within and outside CloudCAST.

Restoring Speech Following Total Removal of the Larynx.

By speech articulator movement and training a transformation to audio we can restore the power of speech to someone who has lost their larynx. We sense changes in magnetic field caused by movements of small magnets attached to the lips and tongue. The sensor transformation uses recurrent neural networks.