Meta-analysis is a statistical procedure for analyzing the combined data from different studies, and can be a major source of concise up-to-date information. The overall conclusions of a ...meta-analysis, however, depend heavily on the quality of the meta-analytic process, and an appropriate evaluation of the quality of meta-analysis (meta-evaluation) can be challenging. We outline ten questions biologists can ask to critically appraise a meta-analysis. These questions could also act as simple and accessible guidelines for the authors of meta-analyses. We focus on meta-analyses using non-human species, which we term 'biological' meta-analysis. Our ten questions are aimed at enabling a biologist to evaluate whether a biological meta-analysis embodies 'mega-enlightenment', a 'mega-mistake', or something in between.
Food security concerns and the scarcity of new productive land have put productivity enhancement of degraded lands back on the political agenda. In such a context, salt‐affected lands are a valuable ...resource that cannot be neglected nor easily abandoned even with their lower crop yields, especially in areas where significant investments have already been made in irrigation and drainage infrastructure. A review of previous studies shows a very limited number of highly variable estimates of the costs of salt‐induced land degradation combined with methodological and contextual differences. Simple extrapolation suggests that the global annual cost of salt‐induced land degradation in irrigated areas could be US$ 27.3 billion because of lost crop production. We present selected case studies that highlight the potential for economic and environmental benefits of taking action to remediate salt‐affected lands. The findings indicate that it can be cost‐effective to invest in sustainable land management in countries confronting salt‐induced land degradation. Such investments in effective remediation of salt‐affected lands should form part of a broader strategy for food security and be defined in national action plans. This broader strategy is required to ensure the identification and effective removal of barriers to the adoption of sustainable land management, such as perverse subsidies. Whereas reversing salt‐induced land degradation would require several years, interim salinity management strategies could provide a pathway for effective remediation and further showcase the importance of reversing land degradation and the rewards of investing in sustainable land management.
ABSTRACT
Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta‐analytic methods to understand ecological and evolutionary phenomena. Meta‐analyses ...can resolve long‐standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta‐analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta‐analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta‐analysis should be trusted – and to be able to build upon the review – authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by ‘reporting quality’. To assess perceptions and standards of reporting quality of systematic reviews and meta‐analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta‐analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta‐Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta‐analysis community in ecology and evolutionary biology: PRISMA‐EcoEvo (version 1.0). PRISMA‐EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta‐analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA‐EcoEvo guideline both in the planning and writing stages of a systematic review and meta‐analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA‐EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta‐analyses.
The BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on ...BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius.
Type 1 diabetes (T1D) is one of the most widely studied complex genetic disorders, and the genes in HLA are reported to account for approximately 40–50% of the familial aggregation of T1D. The major ...genetic determinants of this disease are polymorphisms of class II HLA genes encoding DQ and DR. The DR-DQ haplotypes conferring the highest risk are
DRB1
*03:01-
DQA1
*05:01-
DQB1
*02:01 (abbreviated “DR3”) and
DRB1
*04:01/02/04/05/08-
DQA1
*03:01-
DQB1
*03:02/04 (or
DQB1
*02; abbreviated “DR4”). The risk is much higher for the heterozygote formed by these two haplotypes (OR = 16.59; 95% CI, 13.7–20.1) than for either of the homozygotes (DR3/DR3, OR = 6.32; 95% CI, 5.12–7.80; DR4/DR4, OR = 5.68; 95% CI, 3.91). In addition, some haplotypes confer strong protection from disease, such as
DRB1
*15:01-
DQA1
*01:02-
DQB1
*06:02 (abbreviated “DR2”; OR = 0.03; 95% CI, 0.01–0.07). After adjusting for the genetic correlation with DR and DQ, significant associations can be seen for HLA class II
DPB1
alleles, in particular,
DPB1
*04:02,
DPB1
*03:01, and
DPB1
*02:02. Outside of the class II region, the strongest susceptibility is conferred by class I allele B*39:06 (OR =10.31; 95% CI, 4.21–25.1) and other
HLA-B
alleles. In addition, several loci in the class III region are reported to be associated with T1D, as are some loci telomeric to class I. Not surprisingly, current approaches for the prediction of T1D in screening studies take advantage of genotyping HLA-DR and HLA-DQ loci, which is then combined with family history and screening for autoantibodies directed against islet-cell antigens. Inclusion of additional moderate HLA risk haplotypes may help identify the majority of children with T1D before the onset of the disease.
Summary
Background
Th2 cells have long been considered responsible for the switching of B cells to production of IgE during cognate interaction, primarily due to their expression of CD40L and ...secretion of IL‐4. This concept has been challenged by the more recent definition of follicular helper T cells (Tfh) as the key T cell subset in B cell isotype switching, due to their physical location at the boundary of T cell:B cell areas in lymphoid follicles and ability to express IL‐4 and CD40L.
Objective
To determine whether Tfh cells are responsible for IgE responses to Der p 1 allergen after house dust mite (HDM)‐induced allergic sensitization.
Methods
Mice deficient in Tfh cells were sensitized to HDM and Der p 1‐specific IgE measured by ELISA.
Results
Mice with a mutation in T cell‐expressed IL‐6R were unable to expand Tfh populations after HDM sensitization, and their anti‐Der p 1 IgE, IgG1 and total IgE responses were reduced by 80–90% compared with wild‐type mice. These animals displayed unaltered lung Th2 and eosinophilic responses after intranasal HDM challenge and normal IL‐4 production, but B cell infiltration of the airways was abrogated.
Conclusions and Clinical Relevance
Our data indicate that Tfh cells are largely responsible for switching B cells to IgE synthesis, most likely via an IgG1+ intermediate. However, Th2 cells are the major source of IL‐4 during HDM sensitization and this might contribute to IgE synthesis at a stage distal to Tfh‐mediated isotype switching. The IL‐6/follicular helper T cell pathway is a potential therapeutic target in allergic disease.
BACKGROUND: Congenital toxoplasmosis presents as severe, life-altering disease in North America. If mothers of infants with congenital toxoplasmosis could be identified by risks, it would provide ...strong support for educating pregnant women about risks, to eliminate this disease. Conversely, if not all risks are identifiable, undetectable risks are suggested. A new test detecting antibodies to sporozoites demonstrated that oocysts were the predominant source of Toxoplasma gondii infection in 4 North American epidemics and in mothers of children in the National Collaborative Chicago-based Congenital Toxoplasmosis Study (NCCCTS). This novel test offered the opportunity to determine whether risk factors or demographic characteristics could identify mothers infected with ocysts. METHODS: Acutely infected mothers and their congenitally infected infants were evaluated, including in-person interviews concerning risks and evaluation of perinatal maternal serum samples. RESULTS: Fifty-nine (78%) of 76 mothers of congenitally infected infants in NCCCTS had primary infection with oocysts. Only 49% of these mothers identified significant risk factors for sporozoite acquisition. Socioeconomic status, hometown size, maternal clinical presentations, and ethnicity were not reliable predictors. CONCLUSIONS: Undetected contamination of food and water by oocysts frequently causes human infections in North America. Risks are often unrecognized by those infected. Demographic characteristics did not identify oocyst infections. Thus, although education programs describing hygienic measures may be beneficial, they will not suffice to prevent the suffering and economic consequences associated with congenital toxoplasmosis. Only a vaccine or implementation of systematic serologic testing of pregnant women and newborns, followed by treatment, will prevent most congenital toxoplasmosis in North America.
Temperature as a modulator of sexual selection García‐Roa, Roberto; Garcia‐Gonzalez, Francisco; Noble, Daniel W.A. ...
Biological reviews of the Cambridge Philosophical Society,
December 2020, Letnik:
95, Številka:
6
Journal Article
Recenzirano
Odprti dostop
ABSTRACT
A central question in ecology and evolution is to understand why sexual selection varies so much in strength across taxa; it has long been known that ecological factors are crucial to this. ...Temperature is a particularly salient abiotic ecological factor that modulates a wide range of physiological, morphological and behavioural traits, impacting individuals and populations at a global taxonomic scale. Furthermore, temperature exhibits substantial temporal variation (e.g. daily, seasonally and inter‐seasonally), and hence for most species in the wild sexual selection will regularly unfold in a dynamic thermal environment. Unfortunately, studies have so far almost completely neglected the role of temperature as a modulator of sexual selection. Here, we outline the main pathways through which temperature can affect the intensity and form (i.e. mechanisms) of sexual selection, via: (i) direct effects on secondary sexual traits and preferences (i.e. trait variance, opportunity for selection and trait–fitness covariance), and (ii) indirect effects on key mating parameters, sex‐specific reproductive costs/benefits, trade‐offs, demography and correlated abiotic factors. Building upon this framework, we show that, by focusing exclusively on the first‐order effects that environmental temperature has on traits linked with individual fitness and population viability, current global warming studies may be ignoring eco‐evolutionary feedbacks mediated by sexual selection. Finally, we tested the general prediction that temperature modulates sexual selection by conducting a meta‐analysis of available studies experimentally manipulating temperature and reporting effects on the variance of male/female reproductive success and/or traits under sexual selection. Our results show a clear association between temperature and sexual selection measures in both sexes. In short, we suggest that studying the feedback between temperature and sexual selection processes may be vital to developing a better understanding of variation in the strength of sexual selection in nature, and its consequences for population viability in response to environmental change (e.g. global warming).
Summary
Background
Safety of individual probiotic strains approved under Investigational New Drug (IND) policies in cirrhosis with minimal hepatic encephalopathy (MHE) is not clear.
Aim
The primary ...aim of this phase I study was to evaluate the safety, tolerability of probiotic Lactobacillus GG (LGG) compared to placebo, while secondary ones were to explore its mechanism of action using cognitive, microbiome, metabolome and endotoxin analysis in MHE patients.
Methods
Cirrhotic patients with MHE patients were randomised 1:1 into LGG or placebo BID after being prescribed a standard diet and multi‐vitamin regimen and were followed up for 8 weeks. Serum, urine and stool samples were collected at baseline and study end. Safety was assessed at Weeks 4 and 8. Endotoxin and systemic inflammation, microbiome using multi‐tagged pyrosequencing, serum/urine metabolome were analysed between groups using correlation networks.
Results
Thirty MHE patients (14 LGG and 16 placebo) completed the study without any differences in serious adverse events. However, self‐limited diarrhoea was more frequent in LGG patients. A standard diet was maintained and LGG batches were comparable throughout. Only in the LGG‐randomised group, endotoxemia and TNF‐α decreased, microbiome changed (reduced Enterobacteriaceae and increased Clostridiales Incertae Sedis XIV and Lachnospiraceae relative abundance) with changes in metabolite/microbiome correlations pertaining to amino acid, vitamin and secondary BA metabolism. No change in cognition was found.
Conclusions
In this phase I study, Lactobacillus GG is safe and well‐tolerated in cirrhosis and is associated with a reduction in endotoxemia and dysbiosis.
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