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32
Date Added: Oct 8, 2021
Date Added: Oct 8, 2021
Fast growing scientific topics have famously been key harbingers of the new frontiers of science, yet, large-scale analyses of their genesis and impact are rare. We investigated one possible factor connected with a topic’s extraordinary growth: scientific prizes. Our longitudinal analysis of nearly all recognized prizes worldwide and over 11,000 scientific topics from 19 disciplines indicates that topics associated with a scientific prize experience extraordinary growth in productivity, impact, and new entrants. Relative to matched non-prizewinning topics, prizewinning topics produce 40% more papers and 33% more citations, retain 55% more scientists, and gain 37 and 47% more new entrants and star scientists, respectively, in the first five-to-ten years after the prize. Funding do not account for a prizewinning topic’s growth. Rather, growth is positively related to the degree to which the prize is discipline-specific, conferred for recent research, or has prize money. These findings reveal new dynamics behind scientific innovation and investment.
3
Date Added: May 25, 2021
Date Added: May 25, 2021
Quantitative ethnographers across a range of domains study complex collaborative thinking (CCT): the processes by which members of a group or team develop shared understanding by making cognitive connections from the statements and actions of the group. CCT is difficult to model because the actions of group members are interdependent—the activity of any individual is influenced by the actions of other members of the group. Moreover, the actions of group members engaged in some collaborative tasks may need to follow a particular order. However, current techniques can account for either interdependence or order, but not both. In this paper, we present directed epistemic network analysis (dENA), an extension of epistemic network analysis (ENA), as a method that can simultaneously account for the interdependent and ordered aspects of CCT. To illustrate the method, we compare a qualitative analysis of two U.S. Navy commanders working in a simulation to ENA and dENA analyses of their performance. We find that by accounting for interdependence but not order, ENA was not able to model differences between the commanders seen in the qualitative analysis, but by accounting for both interdependence and order, dENA was able to do so.
4
Date Added: Apr 14, 2021
Date Added: Apr 14, 2021
Accurate measurements of promoter activities are crucial for predictably building genetic systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of promoters in absolute units, the variability in their activity across a population, and their quantitative toll on cellular resources, all of which provide critical insights for cellular engineering.
5
Date Added: Mar 3, 2021
Date Added: Mar 3, 2021
To help researchers conduct a systematic review or meta-analysis as efficiently and transparently as possible, we designed a tool to accelerate the step of screening titles and abstracts. For many tasks—including but not limited to systematic reviews and meta-analyses—the scientific literature needs to be checked systematically. Scholars and practitioners currently screen thousands of studies by hand to determine which studies to include in their review or meta-analysis. This is error prone and inefficient because of extremely imbalanced data: only a fraction of the screened studies is relevant. The future of systematic reviewing will be an interaction with machine learning algorithms to deal with the enormous increase of available text. We therefore developed an open source machine learning-aided pipeline applying active learning: ASReview. We demonstrate by means of simulation studies that active learning can yield far more efficient reviewing than manual reviewing while providing high quality. Furthermore, we describe the options of the free and open source research software and present the results from user experience tests. We invite the community to contribute to open source projects such as our own that provide measurable and reproducible improvements over current practice.
63
Date Added: Jul 31, 2020
Date Added: Jul 31, 2020
Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80–93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93–98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89–98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.
8
Date Added: Sep 29, 2020
Date Added: Sep 29, 2020
For almost half a century, Paul Meehl educated psychologists about how themindless use of null-hypothesis significance tests made research on theories in thesocial sciences basically uninterpretable (Meehl, 1990). In response to the replicationcrisis, reforms in psychology have focused on formalising procedures for testinghypotheses. These reforms were necessary and impactful. However, as an unexpectedconsequence, psychologists have begun to realise that they may not be ready to testhypotheses. Forcing researchers to prematurely test hypotheses before they haveestablished a sound ‘derivation chain’ between test and theory is counterproductive.Instead, various non-confirmatory research activities should be used to obtain theinputs necessary to make hypothesis tests informative. Before testing hypotheses,researchers should spend more time forming concepts, developing valid measures,establishing the causal relationships between concepts and their functional form, andidentifying boundary conditions and auxiliary assumptions. Providing these inputsshould be recognised and incentivised as a crucial goal in and of itself. In this article,we discuss how shifting the focus to non-confirmatory research can tie togethermany loose ends of psychology’s reform movement and help us lay the foundation todevelop strong, testable theories, as Paul Meehl urged us to.
7
Date Added: Oct 9, 2020
Date Added: Oct 9, 2020
Researcher degrees of freedom can lead to a multiple comparisons problem, even in settings where researchers perform only a single analysis on their data. The problem is there can be a large number of potential comparisons when the details of data analysis are highly contingent on data, without the researcher having to perform any conscious procedure of fishing or examining multiple p-values. We discuss in the context of several examples of published papers where data-analysis decisions were theoretically-motivated based on previous literature, but where the details of data selection and analysis were not pre-specified and, as a result, were contingent on data
15
Date Added: Jul 21, 2020
Date Added: Jul 21, 2020
A single nuclear gene can be translated into a dual localized protein that distributes between the cytosol and mitochondria. Accumulating evidences show that mitoproteomes contain lots of these dual localized proteins termed echoforms. Unraveling the existence of mitochondrial echoforms using current GFP (Green Fluorescent Protein) fusion microscopy approaches is extremely difficult because the GFP signal of the cytosolic echoform will almost inevitably mask that of the mitochondrial echoform. We therefore engineered a yeast strain expressing a new type of Split-GFP that we termed Bi-Genomic Mitochondrial-Split-GFP (BiG Mito-Split-GFP). Because one moiety of the GFP is translated from the mitochondrial machinery while the other is fused to the nuclear-encoded protein of interest translated in the cytosol, the self-reassembly of this Bi-Genomic-encoded Split-GFP is confined to mitochondria. We could authenticate the mitochondrial importability of any protein or echoform from yeast, but also from other organisms such as the human Argonaute 2 mitochondrial echoform.
3
Date Added: Oct 12, 2020
Date Added: Oct 12, 2020
We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) tissue, allowing us to track membrane puncta in pioneer neurons, and 2) , which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.
39
Date Added: Jul 31, 2020
Date Added: Jul 31, 2020
Background: Rapid economic growth in China in the past decades has been accompanied by dramatic changes in lifestyle and environmental exposures. The burdens of non-communicable diseases, such as cardiovascular diseases, diabetes and cancer, have also increased substantially.Methods/design: We initiated a large prospective cohort–the Taizhou Longitudinal Study–in Taizhou (a medium-size city in China) to explore the environmental and genetic risk factors for common non-communicable diseases. The sample size of the cohort will be at least 100,000 adultsaged 30–80 years drawn from the general residents of the districts of Hailin, Gaogang, and Taixing (sample frame, 1.8 million) of Taizhou. A three-stage stratified sampling method will be applied.Baseline investigations include interviewer-administered questionnaire, anthropometric measurements, and collection of buccal mucosal cells and blood specimens. DNA will be extracted for genetic studies and serum samples will be used for biochemical examinations. A follow-upsurvey will be conducted every three years to obtain information on disease occurrence and information on selected lifestyle exposures. Study participants will be followed-up indefinitely by using a chronic disease register system for morbidity and cause-specific mortality. Information onnon-fatal events will be obtained for certain major categories of disease (e.g., cancer, stroke, myocardial infarction) through established registry systems.Discussion: The Taizhou Longitudinal Study will provide a good basis for exploring the roles of many important environmental factors (especially those concomitant with the economic transformation in China) for common chronic diseases, solely or via interaction with genetic factors.