Array programming with NumPy.

Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis.

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.

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.

Multi-year field evaluation of nicotianamine biofortified bread wheat.

Conventional breeding efforts for iron (Fe) and zinc (Zn) biofortification of bread wheat (Triticum aestivum L.) have been hindered by a lack of genetic variation for these traits and a negative correlation between grain Fe and Zn concentrations and yield. We have employed genetic engineering to constitutively express (CE) the rice (Oryza sativa) nicotianamine synthase 2 (OsNAS2) gene and upregulate biosynthesis of two metal chelators - nicotianamine (NA) and 2'-deoxymugineic acid (DMA) - in bread wheat, resulting in increased Fe and Zn concentrations in wholemeal and white flour. Here we describe multi-location confined field trial (CFT) evaluation of a low-copy transgenic CE-OsNAS2 wheat event (CE-1) over 3 years and demonstrate higher concentrations of NA, DMA, Fe, and Zn in CE-1 wholemeal flour, white flour, and white bread and higher Fe bioavailability in CE-1 white flour relative to a null segregant (NS) control. Multi-environment models of agronomic and grain nutrition traits revealed a negative correlation between grain yield and grain Fe, Zn, and total protein concentrations, yet no correlation between grain yield and grain NA and DMA concentrations. White flour Fe bioavailability was positively correlated with white flour NA concentration, suggesting that NA-chelated Fe should be targeted in wheat Fe biofortification efforts.

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.

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.

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.

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.

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.

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.

Effect of posture and body weight loading on spinal posterior root reflex responses.

The posterior root muscle response (PRM) is a monosynaptic reflex that is evoked by single pulse transcutaneous spinal cord stimulation (tSCS). The main aim of this work was to analyse how body weight loading influences PRM reflex threshold measured from several lower limb muscles in healthy participants. PRM reflex responses were evoked with 1-ms rectangular monophasic pulses applied at an interval of 6 s via a self-adhesive electrode (9 × 5 cm) at the T11-T12 vertebral level. Surface electromyographic activity of lower limb muscles was recorded during four different conditions, one in decubitus supine (DS) and the other three involving standing at 100%, 50%, and 0% body weight loading (BW). PRM threshold intensity, peak-to-peak amplitude, and latency for each muscle were analysed in different conditions study. PRM reflex threshold increased with body weight unloading compared with DS, and the largest change was observed between DS and 0% BW for the proximal muscles and between DS and 50% BW for distal muscles. Peak-to-peak amplitude analysis showed only a significant mean decrease of 34.6% (SD 10.4, p = 0.028) in TA and 53.6% (SD 15.1, p = 0.019) in GM muscles between DS and 50% BW. No significant differences were observed for PRM latency. This study has shown that sensorimotor networks can be activated with tSCS in various conditions of body weight unloading. Higher stimulus intensities are necessary to evoke reflex response during standing at 50% body weight loading. These results have practical implications for gait rehabilitation training programmes that include body weight support.

Exploring the knowledge and attitudes of women of reproductive age from the general public towards egg donation and egg sharing: a UK-based study.

STUDY QUESTION: What are the knowledge and views of UK-based women towards egg donation (ED) and egg sharing (ES)? SUMMARY ANSWER: Lacking knowledge of the practices of ED and ES could be an influential factor in donor egg shortages, rather than negative perceptions or lack of donor anonymity and financial incentives. WHAT IS KNOWN ALREADY: The increasing age of women trying to conceive has led to donor egg shortages, with ED and ES failing to meet demand. Indeed, in recent years in the UK, ES numbers have fallen. This results in long waiting lists, forcing patients abroad for fertility treatment to take up cross border reproductive care. Previous research suggests a lack of knowledge of ED among members of the general public; however, no study has yet assessed knowledge or views of ES in the general public. STUDY DESIGN, SIZE, DURATION: Six hundred and thirty-five UK-based women over 18 years were voluntarily recruited from social media community groups by convenience sampling. The recruitment period was from February to April 2020. PARTICIPANTS/MATERIALS, SETTING, METHODS: Participants completed a previously validated questionnaire regarding female fertility, ED and ES, including knowledge, perceptions and approval of the practices and relevant legislation. This included ranking key benefits and issues regarding egg sharing. The questionnaire was completed using the online Qualtrics survey software. Statistical analysis was conducted using SPSS. MAIN RESULTS AND THE ROLE OF CHANCE: Regarding knowledge of ED and ES, 56.3% and 79.8%, respectively had little or no prior knowledge. Upon explanation, most approved of ED (85.8%) and ES (70.4%). A greater proportion of respondents would donate to a family member/friend (49.75%) than to an anonymous recipient (35.80%). Overall, ES was viewed less favourably than ED, with ethical and practical concerns highlighted. Women aged 18-30 years were significantly more likely to approve of egg donation practice compared to those aged >30 years (P < 0.0001). Those against ES found fears of financial coercion or negative psychological wellbeing the most concerning. About 35.8% and 49.7% would personally consider anonymous and known ED, respectively, whilst 56.7% would consider ES. Those answering in favour of egg sharing were significantly more likely to give higher benefit ratings compared to those against the practice (P < 0.001). Most agreed (55.8%) with and were not deterred to donate (60.1%) by the 'Disclosure of Donor Identity' legislation. Only 31.6% agreed with the compensatory cap; however, 52.7% would not be more motivated to donate by an increased cap. LIMITATIONS, REASONS FOR CAUTION: There were several limitations of the study, including the use of convenience sampling and the voluntary nature of participation opening the study up to sampling and participation bias. Finally, closed questions were predominantly used to allow the generation of quantitative data and statistical analysis. However, this approach prevented opinion justification and qualitative analysis, limiting the depth of conclusions drawn. WIDER IMPLICATIONS OF THE FINDINGS: To our knowledge, this is the first study to survey the general public's knowledge and views of ED/ES using a previously validated questionnaire. The conclusion that lack of knowledge could be contributing to the current donor shortfall in the UK demonstrates that campaigns to inform women of the practices are necessary to alleviate donor oocyte shortages. STUDY FUNDING/COMPETING INTEREST(S): No external funds were used for this study. The authors have no conflicts of interest. TRIAL REGISTRATION NUMBER: NA.

A QTL on the Ca7 chromosome of chickpea affects resistance to the root-lesion nematode Pratylenchus thornei.

The root-lesion nematode Pratylenchus thornei Sher & Allen, 1953 is a damaging parasite of many crop plants, including the grain legume chickpea (Cicer arietinum L.). Within cultivated chickpea, there are no known sources of strong resistance to P. thornei, but some cultivars have partial resistance. In the research reported here, the genetic basis for differences in P. thornei resistance was analysed using a population derived by accelerated single seed descent from a cross between a partially resistant cultivar, PBA HatTrick, and a very susceptible cultivar, Kyabra. A genetic linkage map was constructed from genotyping-by-sequencing data. Two quantitative trait loci were mapped, one on the Ca4 chromosome and one on the Ca7 chromosome. The Ca7 locus had a greater and more consistent effect than the Ca4 locus. Marker assays designed for single nucleotide polymorphisms on Ca7 were applied to a panel of chickpea accessions. Some of these markers should be useful for marker-assisted selection in chickpea breeding. Haplotype analysis confirmed the Iranian landrace ICC14903 to be the source of the resistance allele in PBA HatTrick and indicated that other Australian cultivars inherited the same allele from other Iranian landraces. A candidate region was defined on the Ca7 pseudomolecule. Within that region, 69 genes have been predicted with high confidence. Among these, two have annotations related to biotic stress response. Three others have previously been reported to be expressed in roots of PBA HatTrick and Kyabra, including one that is more highly expressed in PBA HatTrick than in Kyabra. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01271-8.

Efficacy of Anodal Suboccipital Direct Current Stimulation for Endogenous Pain Modulation and Tonic Thermal Pain Control in Healthy Participants: A Randomized Controlled Clinical Trial.

OBJECTIVE: The aim of this study was to assess whether anodal DCS applied to the suboccipital (SO) target area could potentiate antinociception assessed primarily with conditioned pain modulation of tonic thermal test stimuli. DESIGN: Randomized double-blinded control trial. SETTING: Rehabilitation hospital. SUBJECTS: Healthy participants. METHODS: Forty healthy participants were randomized to receive either SO-DCS or M1-DCS. The 20-minute 1.5 mA anodal or sham DCS intervention were applied to each participant in randomized order during two test sessions. The primary outcome measure included heterotopic cold-pressor conditioned pain modulation (CPM) of tonic heat pain. Secondary measures included pressure pain threshold and tonic thermal pain intensity. RESULTS: Heterotopic CPM of tonic heat pain intensity was unaffected by either SO-DCS or active M1, including the secondary measures of pressure pain threshold and tonic thermal pain intensity. Although low-power non-significant interactions were identified for DCS intervention (active versus sham) and time (before and after), a significant within-group inhibition of tonic cold pain was identified following SO-DCS (P = .011, mean [SD]: -0.76 ± 0.88 points) and M1-DCS (P < .002: -0.84 ± 0.82 points), without a significant change following sham DCS. CONCLUSIONS: Although heterotopic CPM was not facilitated with either SO-DCS or M1-DCS, a general significant inhibition of tonic cold pain intensity was demonstrated following both interventions. The general effects of active DCS compared to sham on tonic cold pain-irrespective of the M1 or SO target-need to be confirmed using standard quantitative sensory testing.

A systematic review exploring the patient decision-making factors and attitudes towards pre-implantation genetic testing for aneuploidy and gender selection.

INTRODUCTION: Pre-implantation genetic testing for aneuploidy (PGT-A) is in high demand worldwide, with ongoing debate among medical societies as to which patient groups it should be offered. The psychological aspects for patients regarding its use, lag behind the genomic technological advances, leaving couples with limited decision-making support. The development of this technology also leads to the possibility for its utilization in gender selection. Despite the controversy surrounding these issues, very few studies have investigated the psychological aspects of patients using PGT-A. MATERIAL AND METHODS: This systematic review provides an up-to-date analysis of the psychosocial aspects surrounding PGT for aneuploidy and sex selection, as well as decision-making factors. A systematic search of English peer-reviewed journals of three computerized databases were undertaken following PRISMA guidelines. The qualitative data were extracted using thematic analysis. PROSPERO Registration number: CRD42019126439. RESULTS: The main outcome measures were patients' motivations, decision-making factors, attitudes and experiences surrounding the use of PGT for aneuploidy and sex selection. Ten studies were included, four for PGT-A and six for sex selection. Attitudes towards PGT-A were positive, with the main motivating factors being decreasing miscarriage rate, reducing the risk of termination of pregnancy and reducing the time to pregnancy. Consistently raised concerns regarding PGT-A were the financial burden and moral beliefs. The vast majority of patients felt sufficiently knowledgeable to make the decision; however, studies did reveal that a minority mis-interpreted certain potential benefits of PGT-A. Studies investigating PGT for sex selection predominantly reported the main motivation was to achieve gender balance within the family dynamic, with most studies finding no difference between couples using PGT for gender selection to have male or female offspring. CONCLUSIONS: Although this systematic review was limited by the small number of studies investigating this topic, a significant minority of patients appeared to misunderstand certain benefits and limitations of PGT-A. Fertility clinics must ensure they provide adequate counseling to all patients using PGT-A. With the use of PGT-A on the rise globally, there is a need to develop decision support tools for couples who have an increasing number of genetic testing options becoming available to them.

Exploring women's attitudes, knowledge, and intentions to use oocyte freezing for non-medical reasons: A systematic review.

INTRODUCTION: Women are postponing childbearing and preventing age-related fertility decline with oocyte freezing for non-medical reasons (OFNMR). The objective of this systematic evaluation was to gain an understanding of women's attitudes and knowledge of, and intentions to use OFNMR among users of OFNMR and the general public. MATERIAL AND METHODS: A systematic search of MEDLINE, EMBASE, and PyschINFO databases was undertaken, for studies that examined the psychosocial attitudes among women toward OFNMR. The search was limited to English language and no time restriction was set for publications. Extracted data were analyzed using thematic analysis and the study was performed according to PRISMA guidelines with prospective PROSPERO registration (CRD4201912578). RESULTS: Overall, 35 studies met the inclusion criteria. Studies were broadly categorized into studies investigating users or potential users of OFNMR, and studies examining the views of members of the general public. Users of OFNMR have good knowledge of age-related fertility decline and awareness of the OFNMR procedure. Lack of partner was identified as the most common motivating factor to undertake OFNMR, with cost as a predominant concern. Knowledge among the general public of OFNMR is highly variable. Underestimation of age-related fertility decline is common among the general public. Intentions of women to use OFNMR also varied drastically between studies. CONCLUSIONS: Women are predominantly motivated to freeze eggs by the lack of a suitable partner, but cost is a significant barrier. Increasing the number of women pursuing OFNMR at an earlier stage may positively impact upon the risk of future involuntary childlessness. Better information should be made available to both women and men about their fertility and options to inform their reproductive decision-making.

Transcranial direct current stimulation combined with robotic therapy for upper and lower limb function after stroke: a systematic review and meta-analysis of randomized control trials.

BACKGROUND: Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation method able to modulate neuronal activity after stroke. The aim of this systematic review was to determine if tDCS combined with robotic therapy (RT) improves limb function after stroke when compared to RT alone. METHODS: A search for randomized controlled trials (RCTs) published prior to July 15, 2021 was performed. The main outcome was function assessed with the Fugl-Meyer motor assessment for upper extremities (FM/ue) and 10-m walking test (10MWT) for the lower limbs. As secondary outcomes, strength was assessed with the Motricity Index (MI) or Medical Research Council scale (MRC), spasticity with the modified Ashworth scale (MAS), functional independence with the Barthel Index (BI), and kinematic parameters. RESULTS: Ten studies were included for analysis (n = 368 enrolled participants). The results showed a non-significant effect for tDCS combined with RT to improve upper limb function [standardized mean difference (SMD) = - 0.12; 95% confidence interval (CI): - 0.35-0.11)]. However, a positive effect of the combined therapy was observed in the lower limb function (SMD = 0.48; 95% CI: - 0.15-1.12). Significant results favouring tDCS combined with RT were not found in strength (SMD = - 0.15; 95% CI: - 0.4-0.1), spasticity [mean difference (MD) = - 0.15; 95% CI: - 0.8-0.5)], functional independence (MD = 2.5; 95% CI: - 1.9-6.9) or velocity of movement (SMD = 0.06; 95% CI: - 0.3-0.5) with a "moderate" or "low" recommendation level according to the GRADE guidelines. CONCLUSIONS: Current findings suggest that tDCS combined with RT does not improve upper limb function, strength, spasticity, functional independence or velocity of movement after stroke. However, tDCS may enhance the effects of RT alone for lower limb function. tDCS parameters and the stage or type of stroke injury could be crucial factors that determine the effectiveness of this therapy.

High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare).

To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study.

Fine mapping of root lesion nematode (Pratylenchus thornei) resistance loci on chromosomes 6D and 2B of wheat.

KEY MESSAGE: Resistance QTL to root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were mapped to intervals of 3.5 cM/1.77 Mbp on chromosome 6D and 1.4 cM/2.19 Mbp on chromosome 2B, respectively. Candidate resistance genes were identified in the QTL regions and molecular markers developed for marker-assisted breeding. Two previously known resistance QTL for root lesion nematode (Pratylenchus thornei) in bread wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were fine-mapped using a Sokoll (moderately resistant) by Krichauff (susceptible) doubled haploid (DH) population and six newly developed recombinant inbred line populations. Bulked segregation analysis with the 90K wheat SNP array identified linked SNPs which were subsequently converted to KASP assays for mapping in the DH and RIL populations. On chromosome 6D, 60 KASP and five SSR markers spanned a total genetic distance of 23.7 cM. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Aegilops tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. On chromosome 2B, 41 KASP and 5 SSR markers produced a map spanning 19.9 cM. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high-confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid biosynthetic pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker-assisted breeding of P. thornei-resistant wheat cultivars.