Can large language models replace humans in the systematic review process? Evaluating GPT-4's efficacy in screening and extracting data from peer-reviewed and grey literature in multiple languages

Systematic reviews are vital for guiding practice, research, and policy, yet they are often slow and labour-intensive. Large language models (LLMs) could offer a way to speed up and automate systematic reviews, but their performance in such tasks has not been comprehensively evaluated against humans, and no study has tested GPT-4, the biggest LLM so far. This pre-registered study evaluates GPT-4's capability in title/abstract screening, full-text review, and data extraction across various literature types and languages using a 'human-out-of-the-loop' approach. Although GPT-4 had accuracy on par with human performance in most tasks, results were skewed by chance agreement and dataset imbalance. After adjusting for these, there was a moderate level of performance for data extraction, and - barring studies that used highly reliable prompts - screening performance levelled at none to moderate for different stages and languages. When screening full-text literature using highly reliable prompts, GPT-4's performance was 'almost perfect.' Penalising GPT-4 for missing key studies using highly reliable prompts improved its performance even more. Our findings indicate that, currently, substantial caution should be used if LLMs are being used to conduct systematic reviews, but suggest that, for certain systematic review tasks delivered under reliable prompts, LLMs can rival human performance.Comment: 9 pages, 2 figures, 1 tabl

Measuring the psychosocial, biological, and cognitive signatures of profound stress in humanitarian settings: Impacts, challenges, and strategies in the field

From Springer Nature via Jisc Publications RouterAlastair Ager - ORCID 0000-0002-9474-3563 https://orcid.org/0000-0002-9474-3563Background: Evidence of ‘what works’ in humanitarian programming is important for addressing the disruptive consequences of conflict and forced displacement. However, collecting robust scientific evidence, and ensuring contextual relevance, is challenging. We measured the biological, psychosocial, and cognitive impacts of a structured psychosocial intervention, implemented by Mercy Corps with Syrian refugees and Jordanian host-community youth. In this paper, we present a case analysis of this evaluation study and reflect on the scientific contributions of the work, the challenges experienced in its delivery, and the strategies deployed to address them.Discussion: We identified challenges with respect to study design, methods, and dissemination: these included the logistics and acceptability of implementing a randomized controlled trial in a humanitarian context, the selection and refinement of culturally-relevant research tools and community-based practices, and the dissemination of results to multiple stakeholders. We demonstrated beneficial and sustained impacts on self-reports of insecurity, stress, and mental health; developed a reliable and culturally-relevant measure of resilience; experimentally tested cognitive skills; and showed that levels of cortisol, a biomarker of chronic stress, reduced by one third in response to intervention. Using stress biomarkers offered proof-of-concept evidence, beyond self-reported data: interventions targeting mental health and psychosocial wellbeing can regulate physiological stress in the body as well as improve self-reported mental health and wellbeing. We built constructive dialogue between local communities, scholars, humanitarian practitioners, and policy-makers.Conclusions: Our work shows the value of rigorous research in humanitarian settings, emphasizing relevance for local communities and meaningful ways to build research ownership. Findings encourage the adoption of cognitive measures and stress biomarkers alongside self-report surveys in evaluating programme impacts. High-quality scientific research with youth can be feasible, useful, and ethical in humanitarian settings.pubpu

Is level of prematurity a risk/plasticity factor at three years of age?

Children born preterm have poorer outcomes than children born full-term, but the caregiving environment can ameliorate some of these differences. Recent research has proposed that preterm birth may be a plasticity factor, leading to better outcomes for preterm than full-term infants in higher quality environments. This analysis uses data from two waves of an Irish study of children (at 9 months and 3 years of age, n=11,134 children) and their caregivers (n=11,132 mothers, n=9,998 fathers) to investigate differences in how caregiving affects social, cognitive, and motor skills between full-term, late preterm, and very preterm children. Results indicate that parental emotional distress and quality of attachment are important for child outcomes. Both being born very preterm and late preterm continue to be risk factors for poorer outcomes at 3 years of age. Only fathers’ emotional distress significantly moderated the effect of prematurity on infants’ cognitive and social outcomes – no other interactions between prematurity and environment were significant. These interactions were somewhat in line with diathesis stress, but the effect sizes were too small to provide strong support for this model. There is no evidence that preterm birth is a plasticity factor

Sporadic Human Cryptosporidiosis Caused by Cryptosporidium cuniculus, United Kingdom, 2007–2008

To investigate sporadic human cryptosporidiosis trends in the United Kingdom, we tested 3,030 Cryptosporidium spp.–positive fecal samples, submitted for routine typing in 2007–2008, for C. cuniculus. C. cuniculus prevalence was 1.2%; cases were mostly indigenous and occurred across all age groups. Most occurred during August–October and may be linked to exposure opportunities

The Effects of a Reading-Based Intervention on Emotion Processing in Children Who Have Suffered Early Adversity and War Related Trauma

Early adversity and trauma can have profound effects on children’s affective development and mental health outcomes. Interventions that improve mental health and socioemotional development are essential to mitigate these effects. We conducted a pilot study examining whether a reading-based program (We Love Reading) improves emotion recognition and mental health through socialization in Syrian refugee (n = 49) and Jordanian non-refugee children (n = 45) aged 7–12 years old (M = 8.9, 57% girls) living in Jordan. To measure emotion recognition, children classified the expression in faces morphed between two emotions (happy–sad and fear–anger), while mental health was assessed using survey measures of optimism, depression, anxiety, distress, and insecurity. Prior to the intervention, both groups of children were significantly biased to interpret ambiguous facial expressions as sad, while there was no clear bias on the fear–anger spectrum. Following the intervention, we found changes in Syrian refugee children’s bias in emotion recognition away from sad facial expressions, although this returned to pre-intervention levels 2 months after the end of the program. This shift in the bias away from sad facial expressions was not associated with changes in self-reported mental health symptoms. These results suggest a potential positive role of the reading intervention on affective development, but further research is required to determine the longer-term impacts of the program

Trauma, resilience and mental health in migrant and non-migrant youth: : An international cross-sectional study across six countries

Resilience is a dynamic process of positive adaptation to significant adversity. While there has been substantial focus on risks and negative outcomes associated with youth migrancy, there is limited evidence of the relationship between the adversity of migration, and resilience, wellbeing, and positive mental health in adolescents. This international study aimed to explore the differences in resilience, wellbeing, and mental health behaviors in migrant and non-migrant adolescents tested across six countries (Australia, New Zealand, UK, China, South Africa, and Canada) with varying levels of trauma exposure. The study was a cross-sectional survey design with a convenience sample of 194 10-17 year old migrants and non-migrants. The migrant sample included both "internal" migrants (change of residence within a country) and "external" migrants (change of residence across national borders) for comparison. Across the sites, migrants reported a higher mean number of traumatic events for the past year than non-migrants, with internal migrants reporting more events than external migrants overall. South African adolescents reported a higher mean number of traumatic events for the past year than all other sites. External migrants reported higher resilience scores yet reduced prosocial behaviors relative to internal migrants and non-migrants, whereas both internal and external migrants reported higher peer problems than non-migrants. When considering the interacting effects of trauma, the presence or absence of trauma did not appear to impact migrant scores in terms of resilience, wellbeing, or conduct problems. In comparison, trauma-exposed non-migrants showed detriments relative to trauma-exposed migrant peers for all of these measures. In conclusion, the survey tool was found to be reliable and acceptable for use in international studies of different samples of adolescent migrants. Overall, migrant adolescents showed greater resilience resources than non-migrants and, although the migrants experienced more traumatic events, the impact of trauma on mental health outcomes was greater in the non-migrants. There is a need for further research with larger prospective sample sizes to investigate how levels of resilience and wellbeing vary over time and across countries, and the ways resilience can be promoted in adolescents exposed to trauma, regardless of migrancy status

Predictors of Literacy and Attitudes Toward Reading Among Syrian Refugee Children in Jordan

Refugee children often face disruptions to their education before and during displacement. However, little is known about either levels or predictors of refugee children’s literacy or about their attitudes toward reading in low- or middle-income countries. To address this, we conducted in-home literacy assessments using the Holistic Assessment of Learning and Development Outcomes with 322 Syrian refugee mother–child dyads who lived in Jordan (child age range 4–8 years, M = 6.32 years, 50% female). Overall, the children had quite low levels of literacy, although they indicated a strong enthusiasm for reading. Child age, maternal education, and maternal ability to read all predicted child literacy, although maternal literacy predicted it only among children enrolled in school. Among those enrolled in school (64.9% of the total sample, 88.7% of those aged ≥ 6), students attending hybrid classes had better literacy than those attending either solely in-person or solely online, although the frequency of school attendance did not predict literacy. A less consistent pattern emerged for predicting children’s attitudes toward reading. Our results suggest an urgent need to improve literacy skills among refugee children in Jordan, as well as a need for validated measures of attitudes toward reading for use with Arabic-speaking youth

Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples

BACKGROUND: Whole genome sequencing (WGS) of Cryptosporidium spp. has previously relied on propagation of the parasite in animals to generate enough oocysts from which to extract DNA of sufficient quantity and purity for analysis. We have developed and validated a method for preparation of genomic Cryptosporidium DNA suitable for WGS directly from human stool samples and used it to generate 10 high-quality whole Cryptosporidium genome assemblies. Our method uses a combination of salt flotation, immunomagnetic separation (IMS), and surface sterilisation of oocysts prior to DNA extraction, with subsequent use of the transposome-based Nextera XT kit to generate libraries for sequencing on Illumina platforms. IMS was found to be superior to caesium chloride density centrifugation for purification of oocysts from small volume stool samples and for reducing levels of contaminant DNA. RESULTS: The IMS-based method was used initially to sequence whole genomes of Cryptosporidium hominis gp60 subtype IbA10G2 and Cryptosporidium parvum gp60 subtype IIaA19G1R2 from small amounts of stool left over from diagnostic testing of clinical cases of cryptosporidiosis. The C. parvum isolate was sequenced to a mean depth of 51.8X with reads covering 100 % of the bases of the C. parvum Iowa II reference genome (Bioproject PRJNA 15586), while the C. hominis isolate was sequenced to a mean depth of 34.7X with reads covering 98 % of the bases of the C. hominis TU502 v1 reference genome (Bioproject PRJNA 15585). The method was then applied to a further 17 stools, successfully generating another eight new whole genome sequences, of which two were C. hominis (gp60 subtypes IbA10G2 and IaA14R3) and six C. parvum (gp60 subtypes IIaA15G2R1 from three samples, and one each of IIaA17G1R1, IIaA18G2R1, and IIdA22G1), demonstrating the utility of this method to sequence Cryptosporidium genomes directly from clinical samples. This development is especially important as it reduces the requirement to propagate Cryptosporidium oocysts in animal models prior to genome sequencing. CONCLUSION: This represents the first report of high-quality whole genome sequencing of Cryptosporidium isolates prepared directly from human stool samples

Meeting Report: Application of Genotyping Methods to Assess Risks from Cryptosporidium in Watersheds

A workshop titled “Application of Genotyping Methods to Assess Pathogen Risks from Cryptosporidium in Drinking Water Catchments” was held at the International Water Association biennial conference, Marrakech, Morocco, 23 September 2004. The workshop presented and discussed the findings of an interlaboratory trial that compared methods for genotyping Cryptosporidium oocysts isolated from feces. The primary goal of the trial and workshop was to assess the utility of current Cryptosporidium genotyping methods for determining the public health significance of oocysts isolated from feces in potable-water–supply watersheds. An expert panel of 16 watershed managers, public health practitioners, and molecular parasitologists was assembled for the workshop. A subordinate goal of the workshop was to educate watershed management and public health practitioners. An open invitation was extended to all conference delegates to attend the workshop, which drew approximately 50 interested delegates. In this report we summarize the peer consensus emerging from the workshop. Recommendations on the use of current methods by watershed managers and public health practitioners were proposed. Importantly, all the methods that were reported in the trial were mutually supporting and found to be valuable and worthy of further utility and development. Where there were choices as to which method to apply, the small-subunit ribosomal RNA gene was considered to be the optimum genetic locus to target. The single-strand conformational polymorphism method was considered potentially the most valuable for discriminating to the subtype level and where a large number of samples were to be analyzed. A research agenda for protozoan geneticists was proposed to improve the utility of methods into the future. Standardization of methods and nomenclature was promoted