Viral Pneumonia Is an Independent Risk Factor for Pulmonary Fibrosis: Results of Large-Scale Longitudinal Population-Level Data

2019 ◽  
Author(s):  
A. Shojaee ◽  
N. Kaminski ◽  
J.M. Siner ◽  
Y. Aryan ◽  
X. Yan ◽  
...  
Keyword(s):  
Risk Factor ◽  
Pulmonary Fibrosis ◽  
Large Scale ◽  
Independent Risk Factor ◽  
Population Level ◽  
Viral Pneumonia ◽  
Level Data

scholarly journals ‘Trust Us’: Open Data and Preregistration in Political Science and International Relations

2022 ◽  
Author(s):  
Bermond Scoggins ◽  
Matthew Peter Robertson
Keyword(s):  
International Relations ◽  
Political Science ◽  
Statistical Inference ◽  
Large Scale ◽  
Open Data ◽  
Population Level ◽  
Open Science ◽  
Science Practices ◽  
Level Data ◽  
Replication Crisis

The scientific method is predicated on transparency -- yet the pace at which transparent research practices are being adopted by the scientific community is slow. The replication crisis in psychology showed that published findings employing statistical inference are threatened by undetected errors, data manipulation, and data falsification. To mitigate these problems and bolster research credibility, open data and preregistration have increasingly been adopted in the natural and social sciences. While many political science and international relations journals have committed to implementing these reforms, the extent of open science practices is unknown. We bring large-scale text analysis and machine learning classifiers to bear on the question. Using population-level data -- 93,931 articles across the top 160 political science and IR journals between 2010 and 2021 -- we find that approximately 21% of all statistical inference papers have open data, and 5% of all experiments are preregistered. Despite this shortfall, the example of leading journals in the field shows that change is feasible and can be effected quickly.

scholarly journals Impact of increasing vegetarian availability on meal selection and sales in cafeterias

2019 ◽  
Vol 116 (42) ◽  
pp. 20923-20929 ◽  
Author(s):  
Emma E. Garnett ◽  
Andrew Balmford ◽  
Chris Sandbrook ◽  
Mark A. Pilling ◽  
Theresa M. Marteau
Keyword(s):  
Large Scale ◽  
Population Level ◽  
Field Studies ◽  
Individual Level ◽  
Rebound Effects ◽  
Percentage Points ◽  
Physical Environments ◽  
Meat Meal ◽  
Level Data ◽  
The Impact

Shifting people in higher income countries toward more plant-based diets would protect the natural environment and improve population health. Research in other domains suggests altering the physical environments in which people make decisions (“nudging”) holds promise for achieving socially desirable behavior change. Here, we examine the impact of attempting to nudge meal selection by increasing the proportion of vegetarian meals offered in a year-long large-scale series of observational and experimental field studies. Anonymized individual-level data from 94,644 meals purchased in 2017 were collected from 3 cafeterias at an English university. Doubling the proportion of vegetarian meals available from 25 to 50% (e.g., from 1 in 4 to 2 in 4 options) increased vegetarian meal sales (and decreased meat meal sales) by 14.9 and 14.5 percentage points in the observational study (2 cafeterias) and by 7.8 percentage points in the experimental study (1 cafeteria), equivalent to proportional increases in vegetarian meal sales of 61.8%, 78.8%, and 40.8%, respectively. Linking sales data to participants’ previous meal purchases revealed that the largest effects were found in the quartile of diners with the lowest prior levels of vegetarian meal selection. Moreover, serving more vegetarian options had little impact on overall sales and did not lead to detectable rebound effects: Vegetarian sales were not lower at other mealtimes. These results provide robust evidence to support the potential for simple changes to catering practices to make an important contribution to achieving more sustainable diets at the population level.

scholarly journals Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection

Genetics ◽  
2020 ◽  
Vol 215 (1) ◽  
pp. 173-192 ◽  
Author(s):  
Parul Johri ◽  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Large Scale ◽  
Demographic History ◽  
Null Model ◽  
Purifying Selection ◽  
Population Level ◽  
Population Variation ◽  
Theoretical Development ◽  
Level Data ◽  
Constant Operation ◽  
Adaptive Processes

The question of the relative evolutionary roles of adaptive and nonadaptive processes has been a central debate in population genetics for nearly a century. While advances have been made in the theoretical development of the underlying models, and statistical methods for estimating their parameters from large-scale genomic data, a framework for an appropriate null model remains elusive. A model incorporating evolutionary processes known to be in constant operation, genetic drift (as modulated by the demographic history of the population) and purifying selection, is lacking. Without such a null model, the role of adaptive processes in shaping within- and between-population variation may not be accurately assessed. Here, we investigate how population size changes and the strength of purifying selection affect patterns of variation at “neutral” sites near functional genomic components. We propose a novel statistical framework for jointly inferring the contribution of the relevant selective and demographic parameters. By means of extensive performance analyses, we quantify the utility of the approach, identify the most important statistics for parameter estimation, and compare the results with existing methods. Finally, we reanalyze genome-wide population-level data from a Zambian population of Drosophila melanogaster, and find that it has experienced a much slower rate of population growth than was inferred when the effects of purifying selection were neglected. Our approach represents an appropriate null model, against which the effects of positive selection can be assessed.

scholarly journals CanVar: A resource for sharing germline variation in cancer patients

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2813 ◽  
Author(s):  
Daniel Chubb ◽  
Peter Broderick ◽  
Sara E. Dobbins ◽  
Richard S. Houlston
Keyword(s):  
Cancer Patients ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Population Level ◽  
The Cancer Genome Atlas ◽  
Sequencing Data ◽  
Level Data ◽  
Germline Variation ◽  
Variant Frequency ◽  
Specific Frequency

The advent of high-throughput sequencing has accelerated our ability to discover genes predisposing to disease and is transforming clinical genomic sequencing. In both contexts knowledge of the spectrum and frequency of genetic variation in the general population and in disease cohorts is vital to the interpretation of sequencing data. While population level data is becoming increasingly available from publicly accessible sources, as exemplified by The Exome Aggregation Consortium (ExAC), the availability of large-scale disease-specific frequency information is limited. These data are of particular importance to contextualise findings from clinical mutation screens and small gene discovery projects. This is especially true for cancer, which is typified by a number of hereditary predisposition syndromes.  Although mutation frequencies in tumours are available from resources such as Cosmic and The Cancer Genome Atlas, a similar facility for germline variation is lacking. Here we present the Cancer Variation Resource (CanVar) an online database which has been developed using the ExAC framework to provide open access to germline variant frequency data from the sequenced exomes of cancer patients. In its first release, CanVar catalogues the exomes of 1,006 familial early-onset colorectal cancer (CRC) patients sequenced at The Institute of Cancer Research. It is anticipated that CanVar will host data for additional cancers, providing a resource for others studying cancer predisposition and an example of how the research community can utilise the ExAC framework to share sequencing data.

Type 1 Diabetes Mellitus is an Independent Risk Factor for Pulmonary Fibrosis

2014 ◽  
Vol 70 (2) ◽  
pp. 1385-1391 ◽  
Author(s):  
Yuxin Hu ◽  
Zhongsen Ma ◽  
Zhimin Guo ◽  
Fenglian Zhao ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 1 Diabetes ◽  
Risk Factor ◽  
Pulmonary Fibrosis ◽  
Type 1 Diabetes Mellitus ◽  
Independent Risk Factor

scholarly journals Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection

2019 ◽  
Author(s):  
Parul Johri ◽  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Large Scale ◽  
Demographic History ◽  
Null Model ◽  
Purifying Selection ◽  
Population Level ◽  
Population Variation ◽  
Theoretical Development ◽  
Level Data ◽  
Constant Operation ◽  
Adaptive Processes

ABSTRACTThe question of the relative evolutionary roles of adaptive and non-adaptive processes has been a central debate in population genetics for nearly a century. While advances have been made in the theoretical development of the underlying models, and statistical methods for estimating their parameters from large-scale genomic data, a framework for an appropriate null model remains elusive. A model incorporating evolutionary processes known to be in constant operation - genetic drift (as modulated by the demographic history of the population) and purifying selection – is lacking. Without such a null model, the role of adaptive processes in shaping within- and between-population variation may not be accurately assessed. Here, we investigate how population size changes and the strength of purifying selection affect patterns of variation at neutral sites near functional genomic components. We propose a novel statistical framework for jointly inferring the contribution of the relevant selective and demographic parameters. By means of extensive performance analyses, we quantify the utility of the approach, identify the most important statistics for parameter estimation, and compare the results with existing methods. Finally, we re-analyze genome-wide population-level data from a Zambian population of Drosophila melanogaster, and find that it has experienced a much slower rate of population growth than was inferred when the effects of purifying selection were neglected. Our approach represents an appropriate null model, against which the effects of positive selection can be assessed.

scholarly journals rs641738C>T near MBOAT7 is positively associated with liver fat, ALT, and histological severity of NAFLD: a meta-analysis

2019 ◽  
Author(s):  
Kevin Teo ◽  
Kushala W. M. Abeysekera ◽  
Leon Adams ◽  
Elmar Aigner ◽  
Jesus M. Banales ◽  
...  
Keyword(s):  
Risk Factor ◽  
Association Studies ◽  
Meta Analysis ◽  
Population Level ◽  
Recessive Model ◽  
Liver Fat ◽  
Genome Wide Association Studies ◽  
Serum Triglycerides ◽  
Alcoholic Fatty Liver ◽  
Level Data

ABSTRACTBackground & AimsA common genetic variant near MBOAT7 (rs641738C>T) has been previously associated with hepatic fat and advanced histology in non-alcoholic fatty liver disease (NAFLD), however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C>T is a risk factor across the spectrum of NAFLD and characterize its role in the regulation of related metabolic phenotypes through meta-analysis.MethodsWe performed meta-analysis of studies with data on the association between rs641738C>T genotype and: liver fat, NAFLD histology, and serum ALT, lipids, or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed random effects meta-analysis using recessive, additive, and dominant genetic models.ResultsData from 1,047,265 participants (8,303 with liver biopsies) across 42 studies was included in the meta-analysis. rs641738C>T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI: 0.02 - 0.05]) and diagnosis of NAFLD (OR 1.22 [95% CI 1.08 - 1.39]) in Caucasian adults. The variant was also positively associated with presence of severe steatosis, NASH, and advanced fibrosis (OR: 1.32 [95% CI: 1.06 - 1.63]) in Caucasian adults using a recessive model of inheritance (CC+CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (Pz=0.002) and lower serum triglycerides (Pz=1.5×10−4). rs641738C>T was not associated with fasting insulin and no effect was observed in children with NAFLD.ConclusionOur study validates rs641738C>T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent.

Corporal Punishment and the Law in Global Perspective

2019 ◽  
pp. 292-320 ◽  
Author(s):  
Joan E. Durrant
Keyword(s):  
New Zealand ◽  
Public Education ◽  
Corporal Punishment ◽  
Large Scale ◽  
Population Level ◽  
Global Perspective ◽  
Violence Against Children ◽  
Level Data ◽  
Primary Focus

Debates over corporal punishment’s effectiveness have come to an end. No study has shown it to have long-term benefits, while many have demonstrated its substantial and wide-ranging risks. Today, the primary focus is on ending it. The increasing recognition of children as rights-bearers is leading an ever-growing number of countries to legally prohibit corporal punishment of children. These laws are intended to foster recognition of children’s rights to protection from all violence, reduce approval and use of corporal punishment, and lower the threshold for tolerance of violence against children. Population-level data from Sweden, Germany, and New Zealand indicate that these changes are taking place. Additional research suggests that a combination of prohibition and large-scale public education is the most effective route to ending the corporal punishment of children.

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