Automated data analysis of unstructured grey literature in health research: A mapping review

\ua9 2023 The Authors. Research Synthesis Methods published by John Wiley & Sons Ltd. The amount of grey literature and ‘softer’ intelligence from social media or websites is vast. Given the long lead-times of producing high-quality peer-reviewed health information, this is causing a demand for new ways to provide prompt input for secondary research. To our knowledge, this is the first review of automated data extraction methods or tools for health-related grey literature and soft data, with a focus on (semi)automating horizon scans, health technology assessments (HTA), evidence maps, or other literature reviews. We searched six databases to cover both health- and computer-science literature. After deduplication, 10% of the search results were screened by two reviewers, the remainder was single-screened up to an estimated 95% sensitivity; screening was stopped early after screening an additional 1000 results with no new includes. All full texts were retrieved, screened, and extracted by a single reviewer and 10% were checked in duplicate. We included 84 papers covering automation for health-related social media, internet fora, news, patents, government agencies and charities, or trial registers. From each paper, we extracted data about important functionalities for users of the tool or method; information about the level of support and reliability; and about practical challenges and research gaps. Poor availability of code, data, and usable tools leads to low transparency regarding performance and duplication of work. Financial implications, scalability, integration into downstream workflows, and meaningful evaluations should be carefully planned before starting to develop a tool, given the vast amounts of data and opportunities those tools offer to expedite research

The Role of the Fc Region in CD70-specific Antibody Effects on Cardiac Transplant Survival

Background: The role of the CD70-specific antibody and the mechanisms by which it extends transplant survival are not known. Methods: Fully major histocompatibility complex-mismatched heterotopic heart transplantation (BALB/c to C57BL/6) was performed. Treated mice received intraperitoneal injections of wild-type (WT) CD70-specific antibody (FR70) or IgG1 or IgG2a chimeric antibodies on days 0, 2, 4, and 6 posttransplantation. Results: WT FR70 antibody significantly extended heart transplant survival to 19 days compared with untreated mice (median survival time [MST]=10 days). Graft survival using the nondepleting IgG1 antibody was significantly shorter (MST=14 days), whereas the survival using depleting IgG2a antibody (MST=18) was similar to that using WT FR70. The FR70 and IgG2a antibodies demonstrated a greater efficiency of fixing mouse complement over the IgG1 variant in vitro. CD4 and CD8 T-cell graft infiltration was reduced with treatment; however, this was most pronounced with WT FR70 and IgG2a antibody therapy compared with the IgG1 chimeric variant. Circulating donor-specific IgG alloantibodies were initially reduced with WT FR70 treatment (day 8 posttransplantation) but increased at days 15 and 20 posttransplantation to the level detected in untreated controls. Conclusion: We conclude that WT (FR70) and the IgG2a depleting variant of CD70-specific antibody reduce graft infiltrating CD4 and CD8 T cells, transiently reduce serum alloantibody levels, and extend graft survival. In contrast, the nondepleting IgG1 variant of this antibody showed lower efficacy. These data suggest that a depleting mechanism of action and not merely costimulation blockade plays a substantial role in the therapeutic effects of CD70-specific antibody

Cognitive or behavioural interventions (or both) to prevent or mitigate loneliness in adolescents, adults, and older adults

This is a protocol for a Cochrane Review (intervention). The objectives are as follows: To examine the effects of structured psychological interventions, based on cognitive behavioural therapy (CBT) techniques, compared to all comparators on loneliness in adolescents, adults, and older adults with diagnoses of common mental disorders, or at risk of loneliness. To examine the effects of structured psychological interventions, based on CBT techniques, compared to all comparators on depression severity, anxiety severity, social connectedness, or quality of life in adolescents, adults, and older adults, with diagnoses of common mental disorders, or at risk of loneliness

The hidden perils of read mapping as a quality assessment tool in genome sequencing

This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled. Precautions must also be undertaken when using long read sequencing technology, which may also lead to misassembled contigs

Evaluating high-cost technologies - no need to throw the baby out with the bathwater

INTRODUCTION: Evidence generation for the health technology assessment (HTA) of a new technology is a long and expensive process with no guarantees that the health technology will be adopted and implemented into a health-care system. This would suggest that there is a greater risk of failure for a company developing a high-cost technology and therefore incentives (such as increasing the funding available for research or additional market exclusivity) may be needed to encourage development of such technologies as has been seen with many high-cost orphan drugs. AREAS COVERED: This paper discusses some of the key issues relating to the evaluation of high-cost technologies through the use of existing HTA processes and what the challenges will be going forward. EXPERT OPINION: We propose that while the current HTA process is robust, its evolution into accommodating the incorporation of real-world data and evidence alongside a life-cycle HTA approach should better enable developers to produce the evidence required on effectiveness and cost-effectiveness. This should lead to reduced decision uncertainty for HTA agencies to make adoption decisions in a more timely and efficient manner. Furthermore, budget impact analysis remains important in understanding the actual financial impact on health-care systems and budgets outside of the cost-effectiveness framework used to aid decision-making

A systematic review and meta-analysis of the prevalence of common mental disorders in people with non-communicable diseases in Bangladesh, India, and Pakistan

Background: The prevalence of mental and physical comorbidities is unknown in South Asia, as estimates of mental ill health in patients with non-communicable diseases (NCDs) have predominantly come from studies based in the United States, Europe and Australasia. This systematic review and meta-analysis summarises evidence and provides pooled estimates of the prevalence of common mental disorders in adults with non-communicable diseases in South Asia. Methods: We included prevalence studies of depression and anxiety in adults with diabetes, cancer, cardiovascular disease, and chronic respiratory conditions in Bangladesh, India, and Pakistan, published from 1990 onwards in international and country-specific databases. Results: Out of 96 included studies, 83 provided data for random effects meta-analyses. The pooled prevalence of depression was 44% (95% confidence interval (CI) = 26 to 62) for patients with COPD, 40% (95% CI = 34 to 45) for diabetes, 39% (95% CI = 23 to 56) for stroke, 38% (95% CI = 32 to 45) for hypertension, and 37% (95% CI = 30 to 45) for cancer. The pooled prevalence of anxiety based on 28 studies was 29% (95% CI = 22 to 36). Many quality issues were identified in a critical appraisal of included studies, mostly relating to the sampling frame and selection process, the description of the methods and basic data, and the description of non-responders. Conclusions: Depression and anxiety are prevalent and underdiagnosed in people with physical comorbidities in Bangladesh, India, and Pakistan

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence

Background: A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin's (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2-3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris.Results: 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin's finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins.Conclusions: These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin's finches. © 2013 Rands et al.; licensee BioMed Central Ltd