Research Priorities of the Pediatric Spinal Cord Injury Population: An International Insight for Rehabilitation Care.

BACKGROUND: Although feedback from people with adult-onset spinal cord injury (SCI) has been considered for new rehabilitation programs, little is known about the priorities of the pediatric-onset SCI population. This study describes and compares health and life (H&L) domain research priorities of youth with pediatric-onset SCI and their parents/caregivers. METHODS: A cross-sectional survey, designed by the Pan-European Paediatric Spinal Cord Injury (PEPSCI) Collaboration, was performed at six European countries. Dyad data from 202 participants, youth with pediatric-onset SCI (n = 101) and their parents/caregivers (n = 101), were analyzed with the PEPSCI H&L domain surveys. RESULTS: The cohort was composed of 8 to 12-year-olds (30.7%), 13 to 17-year-olds (38.6%), and 18 to 25-year-olds (30.7%). The top three H&L domain research priorities reported by parents/caregivers of 8 to 12-year-olds were "walking/ability to move" (91%), "bladder" function (90%), and "general health/feel" (89%), compared with "physical function" (93%), "general health/feel" (90%), and "walking/ability to move" (89%) rated by parents/caregivers of 13 to 25-year-olds. "Bowel" function (85%), "leg/foot movement" (84%), and "bladder" function (84%) were reported as priorities by 13 to 25-year-olds, whereas "physical function" (84%), "experience at school" (83%), and "general mood" were highlighted by 8 to 12-year-olds. The top 10 priorities preferred by 13 to 25-year-olds when compared with the top 10 priorities reported by their parents/caregivers, included problems related to "bowel" and "pain." CONCLUSIONS: Health domain research priorities were highlighted by 13 to 25-year-olds, compared with their parents/caregivers who equally identified H&L domains. This survey will aid health care and clinical research organizations to engage stakeholders to implement a comprehensive research strategy for the pediatric SCI population.

Usefulness of the DN4, S-LANSS, and painDETECT screening questionnaires to detect the neuropathic pain components in people with acute whiplash-associated disorders: a cross-sectional study.

OBJECTIVE: Although the presence of neuropathic pain (NP) components has been reported in whiplash-associated disorders (WAD), no studies have analyzed the usefulness of NP screening questionnaires to detect NP components in WAD. This study aimed to assess the usefulness of 3 NP screening tools (Douleur Neuropathique 4 [DN4], self-administered Leeds Assessment of Neuropathic Symptoms and Signs [S-LANSS], and painDETECT questionnaire [PDQ]) to detect the presence of NP components in acute WAD. DESIGN: A cross-sectional study. SETTING: Hospital. SUBJECTS: Of 188 eligible individuals, 50 people (68% women, mean age = 40.3 ± 12.5 years) with acute WAD (52% Grade III) were included. METHODS: Specialized physicians initially screened participants for the presence of NP components according to clinical practice and international recommendations. After physician assessment, blinded investigators used NP screening questionnaires (DN4, S-LANSS, and PDQ) to assess participants within 2 weeks of their accident. The diagnostic accuracy of these tools was analyzed and compared with the reference standard (physicians' assessments). RESULTS: The 3 screening questionnaires showed excellent discriminant validity (area under the curve: ≥0.8), especially S-LANSS (area under the curve: 0.9; P < .001). DN4 demonstrated the highest sensitivity (87%), followed by S-LANSS (75%), while S-LANSS and PDQ showed the highest specificity (85% and 82%, respectively). These tools demonstrated a strong correlation with the reference standard (S-LANSS: rho = 0.7; PDQ: rho = 0.62; DN4: rho = 0.7; all, P < .001). CONCLUSIONS: The DN4, S-LANSS, and PDQ show excellent discriminant validity to detect the presence of NP components in acute WAD, especially S-LANSS. Initial screening with these tools might improve management of WAD.

CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes.

MOTIVATION: Whole genome alignment of eukaryote species remains an important method for the determination of sequence and structural variations and can also be used to ascertain the representative non-redundant core-genome sequence of a population. Many whole genome alignment tools were first developed for the more mature analysis of prokaryote species with few current tools containing the functionality to process larger genomes of eukaryotes as well as genomes of more divergent species. In addition, the functionality of these tools becomes computationally prohibitive due to the significant compute resources needed to handle larger genomes. RESULTS: In this research, we present CoreDetector, an easy-to-use general-purpose program that can align the core-genome sequences for a range of genome sizes and divergence levels. To illustrate the flexibility of CoreDetector, we conducted alignments of a large set of closely related fungal pathogen and hexaploid wheat cultivar genomes as well as more divergent fly and rodent species genomes. In all cases, compared to existing multiple genome alignment tools, CoreDetector exhibited improved flexibility, efficiency, and competitive accuracy in tested cases. AVAILABILITY AND IMPLEMENTATION: CoreDetector was developed in the cross platform, and easily deployable, Java language. A packaged pipeline is readily executable in a bash terminal without any external need for Perl or Python environments. Installation, example data, and usage instructions for CoreDetector are freely available from https://github.com/mfruzan/CoreDetector.

Improved genomic prediction using machine learning with Variational Bayesian sparsity.

BACKGROUND: Genomic prediction has become a powerful modelling tool for assessing line performance in plant and livestock breeding programmes. Among the genomic prediction modelling approaches, linear based models have proven to provide accurate predictions even when the number of genetic markers exceeds the number of data samples. However, breeding programmes are now compiling data from large numbers of lines and test environments for analyses, rendering these approaches computationally prohibitive. Machine learning (ML) now offers a solution to this problem through the construction of fully connected deep learning architectures and high parallelisation of the predictive task. However, the fully connected nature of these architectures immediately generates an over-parameterisation of the network that needs addressing for efficient and accurate predictions. RESULTS: In this research we explore the use of an ML architecture governed by variational Bayesian sparsity in its initial layers that we have called VBS-ML. The use of VBS-ML provides a mechanism for feature selection of important markers linked to the trait, immediately reducing the network over-parameterisation. Selected markers then propagate to the remaining fully connected feed-forward components of the ML network to form the final genomic prediction. We illustrated the approach with four large Australian wheat breeding data sets that range from 2665 lines to 10375 lines genotyped across a large set of markers. For all data sets, the use of the VBS-ML architecture improved genomic prediction accuracy over legacy linear based modelling approaches. CONCLUSIONS: An ML architecture governed under a variational Bayesian paradigm was shown to improve genomic prediction accuracy over legacy modelling approaches. This VBS-ML approach can be used to dramatically decrease the parameter burden on the network and provide a computationally feasible approach for improving genomic prediction conducted with large breeding population numbers and genetic markers.

Incorporating the pedigree information in multi-environment trial analyses for improving common vetch.

Common vetch is one of the most profitable forage legumes due to its versatility in end-use which includes grain, hay, green manure, and silage. Furthermore, common vetch is one of the best crops to rotate with cereals as it can increase soil fertility which results in higher yield in cereal crops. The National Vetch Breeding Program located in South Australia is focused on developing new vetch varieties with higher grain and dry matter yields, better resistance to major diseases, and wider adaptability to Australian cropping environments. As part of this program, a study was conducted with 35 field trials from 2015 to 2021 in South Australia, Western Australia, Victoria, and New South Wales with the objective of determining the best parents for future crosses and the vetch lines with highest commercial value in terms of grain yield production. A total of 392 varieties were evaluated. The individual field trials were combined in a multi-environment trial data, where each trial is identified as an environment. Multiplicative mixed models were used to analyze the data and a factor analytic approach to model the genetic by environment interaction effects. The pedigree of the lines was then assembled and incorporated into the analysis. This approach allowed to partition the total effects into additive and non-additive components. The total and additive genetic effects were inspected across and within environments for broad and specific selections of the lines with the best commercial value and the best parents. Summary measures of overall performance and stability were used to aid with selection of parents. To the best of our knowledge, this is the first study which used the pedigree information to breed common vetch. In this paper, the application of this statistical methodology has been successfully implemented with the inclusion of the pedigree improving the fit of the models to the data with most of the total genetic variation explained by the additive heritable component. The results of this study have shown the importance of including the pedigree information for common vetch breeding programs and have improved the ability of breeders to select superior commercial lines and parents.

The international spinal cord injury pain basic data set (version 3.0).

STUDY DESIGN: Expert opinion, feedback, revisions, and final consensus. OBJECTIVES: To update the International Spinal Cord Injury Pain Basic Data Set (ISCIPBDS version 2.0) and incorporate suggestions from the SCI pain clinical and research community with respect to overall utility. SETTING: International. METHODS: The ISCIPBDS working group evaluated these suggestions and made modifications. The revised ISCIPBDS (Version 3.0) was then reviewed by members of the International SCI Data Sets Committee, the American Spinal Injury Association (ASIA) Board, the International Spinal Cord Society (ISCoS) Executive and Scientific Committees, individual reviewers and societies, and posted on the ASIA and ISCoS websites for 1 month to elicit comments before final approval by ASIA and ISCoS. RESULTS: The ISCIPBDS (Version 3.0) was updated to make the dataset more flexible and useful: 1. The assessment can be based on the patient's perception of several of his/her "worst" pain(s) or based on the International SCI Pain (ISCIP) Classification-defined or other pain types, depending on the specific research questions or clinical needs. 2. Pain interference should usually be rated for overall pain but may also be used for specific pain problems if needed. 3. An optional pain drawing was added to complement the check box documentation of pain location. 4. Data categories consistent with the Extended Pain Dataset list of current treatments were added. 5. Several new training cases were added.

Wheat Oxylipins in Response to Aphids, CO2 and Nitrogen Regimes.

Wheat is critical for food security, and is challenged by biotic stresses, chiefly aphids and the viruses they transmit. The objective of this study was to determine whether aphids feeding on wheat could trigger a defensive plant reaction to oxidative stress that involved plant oxylipins. Plants were grown in chambers with a factorial combination of two nitrogen rates (100% N vs. 20% N in Hoagland solution), and two concentrations of CO2 (400 vs. 700 ppm). The seedlings were challenged with Rhopalosiphum padi or Sitobion avenae for 8 h. Wheat leaves produced phytoprostanes (PhytoPs) of the F1 series, and three types of phytofurans (PhytoFs): ent-16(RS)-13-epi-ST-Δ14-9-PhytoF, ent-16(RS)-9-epi-ST-Δ14-10-PhytoF and ent-9(RS)-12-epi-ST-Δ10-13-PhytoF. The oxylipin levels varied with aphids, but not with other experimental sources of variation. Both Rhopalosiphum padi and Sitobion avenae reduced the concentrations of ent-16(RS)-13-epi-ST-Δ14-9-PhytoF and ent-16(RS)-9-epi-ST-Δ14-10-PhytoF in relation to controls, but had little or no effect on PhytoPs. Our results are consistent with aphids affecting the levels of PUFAs (oxylipin precursors), which decreased the levels of PhytoFs in wheat leaves. Therefore, PhytoFs could be postulated as an early indicator of aphid hosting for this plant species. This is the first report on the quantification of non-enzymatic PhytoFs and PhytoPs in wheat leaves in response to aphids.

An international wheat diversity panel reveals novel sources of genetic resistance to tan spot in Australia.

KEY MESSAGE: Novel sources of genetic resistance to tan spot in Australia have been discovered using one-step GWAS and genomic prediction models that accounts for additive and non-additive genetic variation. Tan spot is a foliar disease in wheat caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr) and has been reported to generate up to 50% yield losses under favourable disease conditions. Although farming management practices are available to reduce disease, the most economically sustainable approach is establishing genetic resistance through plant breeding. To further understand the genetic basis for disease resistance, we conducted a phenotypic and genetic analysis study using an international diversity panel of 192 wheat lines from the Maize and Wheat Improvement Centre (CIMMYT), the International Centre for Agriculture in the Dry Areas (ICARDA) and Australian (AUS) wheat research programmes. The panel was evaluated using Australian Ptr isolates in 12 experiments conducted in three Australian locations over two years, with assessment for tan spot symptoms at various plant development stages. Phenotypic modelling indicated high heritability for nearly all tan spot traits with ICARDA lines displaying the greatest average resistance. We then conducted a one-step whole-genome analysis of each trait using a high-density SNP array, revealing a large number of highly significant QTL exhibiting a distinct lack of repeatability across the traits. To better summarise the genetic resistance of the lines, a one-step genomic prediction of each tan spot trait was conducted by combining the additive and non-additive predicted genetic effects of the lines. This revealed multiple CIMMYT lines with broad genetic resistance across the developmental stages of the plant which can be utilised in Australian wheat breeding programmes to improve tan spot disease resistance.

Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer.

Fibroblasts are poorly characterised cells that variably impact tumour progression. Here, we use single cell RNA-sequencing, multiplexed immunohistochemistry and digital cytometry (CIBERSORTx) to identify and characterise three major fibroblast subpopulations in human non-small cell lung cancer: adventitial, alveolar and myofibroblasts. Alveolar and adventitial fibroblasts (enriched in control tissue samples) localise to discrete spatial niches in histologically normal lung tissue and indicate improved overall survival rates when present in lung adenocarcinomas (LUAD). Trajectory inference identifies three phases of control tissue fibroblast activation, leading to myofibroblast enrichment in tumour samples: initial upregulation of inflammatory cytokines, followed by stress-response signalling and ultimately increased expression of fibrillar collagens. Myofibroblasts correlate with poor overall survival rates in LUAD, associated with loss of epithelial differentiation, TP53 mutations, proximal molecular subtypes and myeloid cell recruitment. In squamous carcinomas myofibroblasts were not prognostic despite being transcriptomically equivalent. These findings have important implications for developing fibroblast-targeting strategies for cancer therapy.

Long-term bilateral change in pain and sensitivity to high-frequency cutaneous electrical stimulation in healthy subjects depends on stimulus modality: a dermatomal examination.

Introduction: Contradictory changes in pain and sensitivity at long-term following cutaneous 100 Hz high frequency stimulation (HFS) have been previously observed. Thus, we aimed to document long-lasting changes in multimodal sensitivity following HFS, and factors influencing them. Methods: Long-lasting changes were assessed with mechanical [brush, von Frey filament (588.2 mN)] and thermal [heat (40°C)/cold (25°C)] bedside sensory testing, and electrical TS (0.2 ms single electrical stimuli), at the homotopic (ipsilateral C6 dermatome), adjacent heterotopic (ipsilateral C5 and C7 dermatomes) and contralateral (contralateral C6 dermatomes) dermatomal sites in a single testing session. TS were applied before and after application of 100 Hz HFS at the ipsilateral C6 dermatome. Subjects rated their sensation and pain intensity to TS, and completed questionnaires related to pain descriptors and quality of life. Results: Long-lasting changes in mechanical and cold sensitivity was detected up to 45 min after HFS at homotopic C6 dermatome, and a temporary increase in cold sensitivity at 20 min in the contralateral C6 dermatome (p < 0.05). A slow development of bilateral depotentiation to electrical pain TS was also detected from 40 min after HFS (p < 0.05). Higher HFS-induced mechanical and cold sensitivity was identified in women (p < 0.05). Age and quality of life were associated with pain intensity (p < 0.05). Conclusion: Long-term unilateral and bilateral changes in sensation and pain following electrical HFS have been found. These findings may suggest a new insight into the development of persistent pain mechanisms. Further studies are now needed.

Management of chickpea Ascochyta blight using fungicides and cultivar resistance improves grain yield, quality, and grower profitability.

International production of chickpea is under constant threat from the fungal disease Ascochyta blight (Ascochyta rabiei). In Australia, there is limited cultivar resistance, and disease management is reliant on foliar applied fungicides. Several recently registered fungicides in Australia that combine active ingredients with different modes of actions, have been shown to have curative properties. In this study, in the presence of Ascochyta blight, disease severity, grain yield and quality were measured and the subsequent gross margin for growers calculated in seven field experiments conducted in Victoria (Australia) across three seasons. These experiments investigated the effects of: two cultivars with differing disease resistance (PBA Striker and Genesis 090), and several fungicide strategies for the control of Ascochyta blight. Fungicides that combine different modes of actions (Tebuconazole + Azoxystrobin, Bixafen + Prothioconazole and Fludioxonil + Pydiflumetofen) were applied before a rainfall event (preventative) or after the first signs of disease (post-infection). Older, single active fungicides compared included Captan, Chlorothalonil, and Propiconazole, all applied preventatively. Maximum disease severities ranged from 87% at Horsham and 94% at Curyo across three seasons with Nhill recording 87% during 2020. Demonstrating the benefit of cultivar resistance for Ascochyta blight management, grain yield losses were substantially lower in the partially resistant cultivar Genesis 090 (64%) compared to the susceptible cultivar PBA Striker (96%), at Curyo in 2020. The preventative fungicide strategies reduced grain yield losses from 96 and 64% to 51 and 15% for PBA Striker and Genesis 090, respectively, demonstrating the benefit of fungicides in Ascochyta blight management. Across seasons and environments, a comparison between fungicides applied preventatively or post-infection highlighted both were both profitable ($23-$1,095/ha), except when dry conditions limited grain yield to less than 0.6 t/ha. The post infection timing had greater yield losses in sites/seasons with higher rainfall, but with dual active ingredient fungicides and partially resistant cultivars this timing could allow a reduction in the number of fungicide applications, thus improving profitability. These experiments highlighted the importance of controlling Ascochyta blight through cultivar resistance and fungicides to improve grain yields, grain quality, and grower profitability.

Pediatric health and life domain priorities: A national survey of people with spinal cord injury and their parents and caregivers.

CONTEXT/OBJECTIVE: No information is available regarding priorities for pediatric-onset spinal cord injury (SCI). This study described the Health and Life (H&L) domain priorities of youth with pediatric-onset SCI and their parents/caregivers living in Spain. DESIGN: A cross-sectional survey. SETTING: Two SCI rehabilitation centers. PARTICIPANTS: Sixty participants, youth with pediatric-onset SCI (n = 26) and parents/caregivers (n = 34). INTERVENTIONS: Not applicable. OUTCOME MEASURES: Median overall priorities calculated on the basis of importance, unhappiness, and research measured with a new survey of pediatric H&L domains and rated using a 5-point Likert Scale. RESULTS: A total of 60 surveys were received providing information on 35 individuals with SCI: 2-7-year-olds (25.7%), 8-12-year-olds (22.9%), 13-17-year-olds (31.4%), and 18-25-year-olds (20.0%). The top three overall H&L priorities reported by parents/caregivers of 2-12-year-olds were "parenthood expectations" (84%), "leg/foot movement" (83%), and "bladder" function (83%), compared to "dressing/undressing" (78%), "walking/ability to move" (77%) and "bladder" function (77%) rated for 13-25-year-olds. "Sit-to-stand" (79%), "leg/foot movement" (78%) and "arm/hand movement" (77%) were reported as priorities by 13-25-year-olds. The 13-25-year-olds highlighted "sit-to-stand" (100%), "eating/drinking" (54%), and "physical function" (94%) as their top unhappiness, importance, and research priorities, respectively. Significant differences between tetraplegia and paraplegia were found in "mobility in the community" (unhappiness item) for 13-25-years-old. CONCLUSION: Health domains were considered the top overall H&L priorities by parents/caregivers of 13-25-year-olds, compared to life domains reported for their 2-12-year-olds. This survey will aid rehabilitation professionals to engage stakeholders to implement a comprehensive SCI management program for the pediatric population.

The importance of self-efficacy and negative affect for neurofeedback success for central neuropathic pain after a spinal cord injury.

EEG-based neurofeedback uses mental behaviours (MB) to enable voluntary self-modulation of brain activity, and has potential to relieve central neuropathic pain (CNP) after a spinal cord injury (SCI). This study aimed to understand neurofeedback learning and the relationship between MB and neurofeedback success. Twenty-five non-CNP participants and ten CNP participants received neurofeedback training (reinforcing 9-12 Hz; suppressing 4-8 Hz and 20-30 Hz) on four visits. Participants were interviewed about the MB they used after each visit. Questionnaires examined the following factors: self-efficacy, locus of control, motivation, and workload of neurofeedback. MB were grouped into mental strategies (a goal-directed mental action) and affect (emotional experience during neurofeedback). Successful non-CNP participants significantly used more imagination-related MS and reported more negative affect compared to successful CNP participants. However, no mental strategy was clearly associated with neurofeedback success. There was some association between the lack of success and negative affect. Self-efficacy was moderately correlated with neurofeedback success (r = < 0.587, p = < 0.020), whereas locus of control, motivation, and workload had low, non-significant correlations (r < 0.300, p > 0.05). Affect may be more important than mental strategies for a successful neurofeedback performance. Self-efficacy was associated with neurofeedback success, suggesting that increasing confidence in one's neurofeedback abilities may improve neurofeedback performance.

Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea reproductive phenology.

Water deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model, and manipulate phenology. We define a new trait, drought effect on phenology (DEP), as the difference in flowering time between irrigated and rainfed crops, and use FST genome scanning to probe for genomic regions under selection for this trait in chickpea (Cicer arietinum). Owing to the negligible variation in daylength in our dataset, variation in phenology with sowing date was attributed to temperature and water; hence, genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects. Thermal-time to flowering was shortened with increasing water stress, as quantified with carbon isotope composition. Genomic regions on chromosomes 4-8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2, and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1, and ERF1. Modelling showed that DEP reduces the likelihood of drought and heat stress at the expense of increased likelihood of cold stress. Accounting for DEP would improve genetic and phenotypic models of phenology.

Health and LifeDomain ResearchPriorities in Children, Adolescents and Young Adults With Pediatric-Onset Spinal Cord Injury: A National Cross-Sectional Survey in England.

Background: Although feedback from people with adult-onset spinal cord injury (SCI) has been considered in developing research programs, little is known about pediatric-onset SCI priorities. Objectives: To describe the health and life (H&L) domain research priorities of youth with pediatric-onset SCI living in England. Methods: Youth with pediatric-onset SCI (≥6 months) were recruited from five English rehabilitation centers and invited with their parents/caregivers to complete the age-appropriate surveys designed by the Pan-European Paediatric Spinal Cord Injury (PEPSCI) collaboration. Results: A total of 73 surveys were received (32 from participants with SCI and 41 from their parents/caregivers), providing information on 47 individuals with SCI: 2- to 7-year-olds (29.8%), 8- to 12-year-olds (19.2%), 13- to 17-year-olds (17.0%), and 18 to 25-year-olds (34.0%). The top three research priorities reported by parents/caregivers of 2- to 12-year-old and 13- to 25-year-olds were pain (81%/89%), physical function (91%/83%) and health care access (78%/78%). Eighty-nine percent of 8- to 12-year-olds emphasized schooling, peer relationships, and general mood as their research priorities. The top three research priorities for Health or Life domains reported by 13- to 25-year-olds included spasms (95%), pain (91%), pressure injuries (91%), health care access (83%), physical function (78%), and daily personal needs (74%). Conclusion: Although there should be an emphasis on addressing important life domain issues for 8- to 12-year-olds with SCI, adolescents and young adults mostly prioritized health domain research priorities in addition to health care access. This survey will aid health care and clinical research organizations to engage stakeholders to implement a comprehensive SCI research strategy in England for the pediatric population.

HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences.

BACKGROUND: In diploid organisms, whole-genome haplotype assembly relies on the accurate identification and assignment of heterozygous single-nucleotide polymorphism alleles to the correct homologous chromosomes. This appropriate phasing of these alleles ensures that combinations of single-nucleotide polymorphisms on any chromosome, called haplotypes, can then be used in downstream genetic analysis approaches including determining their potential association with important phenotypic traits. A number of statistical algorithms and complementary computational software tools have been developed for whole-genome haplotype construction from genomic sequence data. However, many algorithms lack the ability to phase long haplotype blocks and simultaneously achieve a competitive accuracy. RESULTS: In this research we present HaploMaker, a novel reference-based haplotype assembly algorithm capable of accurately and efficiently phasing long haplotypes using paired-end short reads and longer Pacific Biosciences reads from diploid genomic sequences. To achieve this we frame the problem as a directed acyclic graph with edges weighted on read evidence and use efficient path traversal and minimization techniques to optimally phase haplotypes. We compared the HaploMaker algorithm with 3 other common reference-based haplotype assembly tools using public haplotype data of human individuals from the Platinum Genome project. With short-read sequences, the HaploMaker algorithm maintained a competitively low switch error rate across all haplotype lengths and was superior in phasing longer genomic regions. For longer Pacific Biosciences reads, the phasing accuracy of HaploMaker remained competitive for all block lengths and generated substantially longer block lengths than the competing algorithms. CONCLUSIONS: HaploMaker provides an improved haplotype assembly algorithm for diploid genomic sequences by accurately phasing longer haplotypes. The computationally efficient and portable nature of the Java implementation of the algorithm will ensure that it has maximal impact in reference-sequence-based haplotype assembly applications.

Needs and Research Priorities for Young People with Spinal Cord Lesion or Spina Bifida and Their Caregivers: A National Survey in Switzerland within the PEPSCI Collaboration.

The aim of this study was to describe the needs and research priorities of Swiss children/adolescents and young adults (from here, "young people") with spinal cord injury/disorder (SCI/D) or spina bifida (SB) and their parents in the health and life domains as part of the international Pan-European Pediatric Spinal Cord Injury (PEPSCI) collaboration. Surveys included queries about the satisfaction, importance, research priorities, quality of life (QoL), and characteristics of the young people. Fifty-three surveys with corresponding parent-proxy reports were collected between April and November 2019. The self-report QoL sum scores from young people with SCI/D and SB were 77% and 73%, respectively. Parent-proxy report QoL sum scores were lower, with 70% scores for parents of young people with SCI/D and 64% scores for parents of young people with SB. "Having fun", "relation to family members", and "physical functioning" were found to be highly important for all young people. "Physical functioning", "prevention of pressure injuries", "general health", and "bowel management" received the highest scores for research priority in at least one of the subgroups. As parents tend to underestimate the QoL of their children and young people prioritized research topics differently, both young peoples' and caregivers' perspectives should be included in the selection of research topics.

A multi-environment framework to evaluate the adaptation of wheat (Triticum aestivum) to heat stress.

KEY MESSAGE: Assessing adaptation to abiotic stresses such as high temperature conditions across multiple environments presents opportunities for breeders to target selection for broad adaptation and specific adaptation. Adaptation of wheat to heat stress is an important component of adaptation in variable climates such as the cereal producing areas of Australia. However, in variable climates stress conditions may not be present in every season or are present to varying degrees, at different times during the season. Such conditions complicate plant breeders' ability to select for adaptation to abiotic stress. This study presents a framework for the assessment of the genetic basis of adaptation to heat stress conditions with improved relevance to breeders' selection objectives. The framework was applied here with the evaluation of 1225 doubled haploid lines from five populations across six environments (three environments selected for contrasting temperature stress conditions during anthesis and grain fill periods, over two consecutive seasons), using regionally best practice planting times to evaluate the role of heat stress conditions in genotype adaptation. Temperature co-variates were determined for each genotype, in each environment, for the anthesis and grain fill periods. Genome-wide QTL analysis identified performance QTL for stable effects across all environments, and QTL that illustrated responsiveness to heat stress conditions across the sampled environments. A total of 199 QTL were identified, including 60 performance QTL, and 139 responsiveness QTL. Of the identified QTL, 99 occurred independent of the 21 anthesis date QTL identified. Assessing adaptation to heat stress conditions as the combination of performance and responsiveness offers breeders opportunities to select for grain yield stability across a range of environments, as well as genotypes with higher relative yield in stress conditions.

Transcutaneous spinal cord stimulation combined with locomotor training to improve walking ability in people with chronic spinal cord injury: study protocol for an international multi-centred double-blinded randomised sham-controlled trial (eWALK).

STUDY DESIGN: An international multi-centred, double-blinded, randomised sham-controlled trial (eWALK). OBJECTIVE: To determine the effect of 12 weeks of transcutaneous spinal stimulation (TSS) combined with locomotor training on walking ability in people with spinal cord injury (SCI). SETTING: Dedicated SCI research centres in Australia, Spain, USA and Scotland. METHODS: Fifty community-dwelling individuals with chronic SCI will be recruited. Participants will be eligible if they have bilateral motor levels between T1 and T11, a reproducible lower limb muscle contraction in at least one muscle group, and a Walking Index for SCI II (WISCI II) between 1 and 6. Eligible participants will be randomised to one of two groups, either the active stimulation group or the sham stimulation group. Participants allocated to the stimulation group will receive TSS combined with locomotor training for three 30-min sessions a week for 12 weeks. The locomotor sessions will include walking on a treadmill and overground. Participants allocated to the sham stimulation group will receive the same locomotor training combined with sham stimulation. The primary outcome will be walking ability with stimulation using the WISCI II. Secondary outcomes will record sensation, strength, spasticity, bowel function and quality of life. TRIAL REGISTRATION: ANZCTR.org.au identifier ACTRN12620001241921.

Analysis of Immune Landscape in Pancreatic and Ileal Neuroendocrine Tumours Demonstrates an Immune Cold Tumour Microenvironment.

INTRODUCTION: Neuroendocrine tumours (NETs) are rare tumours with an increasing incidence. While low- and intermediate-grade pancreatic NET (PanNET) and small intestinal NET (siNET) are slow growing, they have a relatively high rate of metastasizing to the liver, leading to substantially worse outcomes. In many solid tumours, the outcome is determined by the quality of the antitumour immune response. However, the quality and significance of antitumour responses in NETs are incompletely understood. This study provides clinico-pathological analyses of the tumour immune microenvironment in PanNET and siNETs. METHODS: Formalin-fixed paraffin-embedded tissue from consecutive resected PanNETs (61) and siNETs (131) was used to construct tissue microarrays (TMAs); 1-mm cores were taken from the tumour centre, stroma, tumour edge, and adjacent healthy tissue. TMAs were stained with antibodies against CD8, CD4, CD68, FoxP3, CD20, and NCR1. T-cell counts were compared with counts from lung cancers. RESULTS: For PanNET, median counts were CD8+ 35.4 cells/mm2, CD4+ 7.6 cells/mm2, and CD68+ macrophages 117.7 cells/mm2. For siNET, there were CD8+ 39.2 cells/mm2, CD4+ 24.1 cells/mm2, and CD68+ 139.2 cells/mm2. The CD8+ cell density in the tumour and liver metastases were significantly lower than in the adjacent normal tissues, without evidence of a cell-rich area at the tumour edge that might have suggested immune exclusion. T-cell counts in lung cancer were significantly higher than those in PanNET and siNETs: CD8+ 541 cells/mm2 and CD4+ 861 cells/mm2 (p ≤ 0.0001). CONCLUSION: PanNETs and siNETs are immune cold with no evidence of T cell exclusion; the low density of immune infiltrates indicates poor antitumour immune responses.