scholarly journals Evolution of anatomical concept usage over time: Mining 200 years of biodiversity literature

Author(s):  
Prashanti Manda ◽  
Todd J Vision

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted an ontology-based temporal data mining analysis of biodiversity literature from the 1700s to 2000s to quantitatively measure how the context of usage for vertebrate anatomical concepts has changed over time. The corpus of literature was divided into nine non-overlapping time periods with comparable amounts of data and context vectors of anatomical concepts were compared to measure the magnitude of concept drift both between adjacent time periods and cumulatively relative to the initial state. Surprisingly, we found that while anatomical concept drift between adjacent time periods was substantial (55% to 68%), it was of the same magnitude as cumulative concept drift across multiple time periods. Such a process, bound by an overall mean drift, fits the expectations of a mean-reverting process.

2017 ◽  
Author(s):  
Prashanti Manda ◽  
Todd J Vision

The scientific literature contains an historic record of the changing ways in which we describe the world. Shifts in understanding of scientific concepts are reflected in the introduction of new terms and the changing usage and context of existing ones. We conducted an ontology-based temporal data mining analysis of biodiversity literature from the 1700s to 2000s to quantitatively measure how the context of usage for vertebrate anatomical concepts has changed over time. The corpus of literature was divided into nine non-overlapping time periods with comparable amounts of data and context vectors of anatomical concepts were compared to measure the magnitude of concept drift both between adjacent time periods and cumulatively relative to the initial state. Surprisingly, we found that while anatomical concept drift between adjacent time periods was substantial (55% to 68%), it was of the same magnitude as cumulative concept drift across multiple time periods. Such a process, bound by an overall mean drift, fits the expectations of a mean-reverting process.


Author(s):  
Stefan Verweij ◽  
Barbara Vis

Abstract Qualitative Comparative Analysis (QCA) – a configurational research approach – has become often-used in political science. In its original form, QCA is relatively static and does not analyze configurations over time. Since many key questions in political science – and other social sciences – have a temporal dimension, this is a major drawback of QCA. Therefore, we discuss and compare three QCA-related strategies that enable researchers to track configurations over time: (1) Multiple Time Periods, Single QCA; (2) Multiple QCAs, Different Time Periods; and (3) Fuzzy-Set Ideal Type Analysis. We use existing datasets to empirically demonstrate and visualize the strategies. By comparing the strategies, we also contribute to existing overviews on how to address time in QCA. We conclude by formulating an agenda for the further development of the three strategies in applied research, in political science and beyond.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Koen F. Tieskens ◽  
Prasad Patil ◽  
Jonathan I. Levy ◽  
Paige Brochu ◽  
Kevin J. Lane ◽  
...  

Abstract Background Associations between community-level risk factors and COVID-19 incidence have been used to identify vulnerable subpopulations and target interventions, but the variability of these associations over time remains largely unknown. We evaluated variability in the associations between community-level predictors and COVID-19 case incidence in 351 cities and towns in Massachusetts from March to October 2020. Methods Using publicly available sociodemographic, occupational, environmental, and mobility datasets, we developed mixed-effect, adjusted Poisson regression models to depict associations between these variables and town-level COVID-19 case incidence data across five distinct time periods from March to October 2020. We examined town-level demographic variables, including population proportions by race, ethnicity, and age, as well as factors related to occupation, housing density, economic vulnerability, air pollution (PM2.5), and institutional facilities. We calculated incidence rate ratios (IRR) associated with these predictors and compared these values across the multiple time periods to assess variability in the observed associations over time. Results Associations between key predictor variables and town-level incidence varied across the five time periods. We observed reductions over time in the association with percentage of Black residents (IRR = 1.12 [95%CI: 1.12–1.13]) in early spring, IRR = 1.01 [95%CI: 1.00–1.01] in early fall) and COVID-19 incidence. The association with number of long-term care facility beds per capita also decreased over time (IRR = 1.28 [95%CI: 1.26–1.31] in spring, IRR = 1.07 [95%CI: 1.05–1.09] in fall). Controlling for other factors, towns with higher percentages of essential workers experienced elevated incidences of COVID-19 throughout the pandemic (e.g., IRR = 1.30 [95%CI: 1.27–1.33] in spring, IRR = 1.20 [95%CI: 1.17–1.22] in fall). Towns with higher proportions of Latinx residents also had sustained elevated incidence over time (IRR = 1.19 [95%CI: 1.18–1.21] in spring, IRR = 1.14 [95%CI: 1.13–1.15] in fall). Conclusions Town-level COVID-19 risk factors varied with time in this study. In Massachusetts, racial (but not ethnic) disparities in COVID-19 incidence may have decreased across the first 8 months of the pandemic, perhaps indicating greater success in risk mitigation in selected communities. Our approach can be used to evaluate effectiveness of public health interventions and target specific mitigation efforts on the community level.


2019 ◽  
Vol 53 (1) ◽  
pp. 79-83
Author(s):  
Kim Quaile Hill

ABSTRACTA growing body of research investigates the factors that enhance the research productivity and creativity of political scientists. This work provides a foundation for future research, but it has not addressed some of the most promising causal hypotheses in the general scientific literature on this topic. This article explicates the latter hypotheses, a typology of scientific career paths that distinguishes how scientific careers vary over time with respect to creative ambitions and achievements, and a research agenda based on the preceding components for investigation of the publication success of political scientists.


2021 ◽  
Vol 45 (5) ◽  
pp. 1340-1348
Author(s):  
Maryam Meshkinfamfard ◽  
Jon Kristian Narvestad ◽  
Johannes Wiik Larsen ◽  
Arezo Kanani ◽  
Jørgen Vennesland ◽  
...  

Abstract Background Resuscitative emergency thoracotomy is a potential life-saving procedure but is rarely performed outside of busy trauma centers. Yet the intervention cannot be deferred nor centralized for critically injured patients presenting in extremis. Low-volume experience may be mitigated by structured training. The aim of this study was to describe concurrent development of training and simulation in a trauma system and associated effect on one time-critical emergency procedure on patient outcome. Methods An observational cohort study split into 3 arbitrary time-phases of trauma system development referred to as ‘early’, ‘developing’ and ‘mature’ time-periods. Core characteristics of the system is described for each phase and concurrent outcomes for all consecutive emergency thoracotomies described with focus on patient characteristics and outcome analyzed for trends in time. Results Over the study period, a total of 36 emergency thoracotomies were performed, of which 5 survived (13.9%). The “early” phase had no survivors (0/10), with 2 of 13 (15%) and 3 of 13 (23%) surviving in the development and mature phase, respectively. A decline in ‘elderly’ (>55 years) patients who had emergency thoracotomy occurred with each time period (from 50%, 31% to 7.7%, respectively). The gender distribution and the injury severity scores on admission remained unchanged, while the rate of patients with signs on life (SOL) increased over time. Conclusion The improvement over time in survival for one time-critical emergency procedure may be attributed to structured implementation of team and procedure training. The findings may be transferred to other low-volume regions for improved trauma care.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ermanno Cordelli ◽  
Paolo Soda ◽  
Giulio Iannello

Abstract Background Biological phenomena usually evolves over time and recent advances in high-throughput microscopy have made possible to collect multiple 3D images over time, generating $$3D+t$$ 3 D + t (or 4D) datasets. To extract useful information there is the need to extract spatial and temporal data on the particles that are in the images, but particle tracking and feature extraction need some kind of assistance. Results This manuscript introduces our new freely downloadable toolbox, the Visual4DTracker. It is a MATLAB package implementing several useful functionalities to navigate, analyse and proof-read the track of each particle detected in any $$3D+t$$ 3 D + t stack. Furthermore, it allows users to proof-read and to evaluate the traces with respect to a given gold standard. The Visual4DTracker toolbox permits the users to visualize and save all the generated results through a user-friendly graphical user interface. This tool has been successfully used in three applicative examples. The first processes synthetic data to show all the software functionalities. The second shows how to process a 4D image stack showing the time-lapse growth of Drosophila cells in an embryo. The third example presents the quantitative analysis of insulin granules in living beta-cells, showing that such particles have two main dynamics that coexist inside the cells. Conclusions Visual4DTracker is a software package for MATLAB to visualize, handle and manually track $$3D+t$$ 3 D + t stacks of microscopy images containing objects such cells, granules, etc.. With its unique set of functions, it remarkably permits the user to analyze and proof-read 4D data in a friendly 3D fashion. The tool is freely available at https://drive.google.com/drive/folders/19AEn0TqP-2B8Z10kOavEAopTUxsKUV73?usp=sharing


2021 ◽  
Vol 11 (13) ◽  
pp. 6078
Author(s):  
Tiffany T. Ly ◽  
Jie Wang ◽  
Kanchan Bisht ◽  
Ukpong Eyo ◽  
Scott T. Acton

Automatic glia reconstruction is essential for the dynamic analysis of microglia motility and morphology, notably so in research on neurodegenerative diseases. In this paper, we propose an automatic 3D tracing algorithm called C3VFC that uses vector field convolution to find the critical points along the centerline of an object and trace paths that traverse back to the soma of every cell in an image. The solution provides detection and labeling of multiple cells in an image over time, leading to multi-object reconstruction. The reconstruction results can be used to extract bioinformatics from temporal data in different settings. The C3VFC reconstruction results found up to a 53% improvement on the next best performing state-of-the-art tracing method. C3VFC achieved the highest accuracy scores, in relation to the baseline results, in four of the five different measures: Entire structure average, the average bi-directional entire structure average, the different structure average, and the percentage of different structures.


2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Alison C. Bartenslager ◽  
Nirosh D. Althuge ◽  
John Dustin Loy ◽  
Matthew M. Hille ◽  
Matthew L. Spangler ◽  
...  

Abstract Background Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, strategies to prevent IBK are limited, with most cases resulting in treatment with antibiotics once the disease has developed. Longitudinal studies evaluating establishment of the ocular microbiota may identify critical risk periods for IBK outbreaks or changes in the microbiota that may predispose animals to IBK. Results In an attempt to characterize the establishment and colonization patterns of the bovine ocular microbiota, we conducted a longitudinal study consisting of 227 calves and evaluated the microbiota composition over time using amplicon sequence variants (ASVs) based on 16S rRNA sequencing data and culture-based approaches. Beef calves on trial consisted of both male (intact) and females. Breeds were composed of purebred Angus and composites with varying percentages of Simmental, Angus, and Red Angus breeds. Average age at the start of the trial was 65 days ±15.02 and all calves remained nursing on their dam until weaning (day 139 of the study). The trial consisted of 139 days with four sampling time points on day 0, 21, 41, and 139. The experimental population received three different vaccination treatments (autogenous, commercial (both inactivated bacteria), and adjuvant placebo), to assess the effectiveness of different vaccines for IBK prevention. A significant change in bacterial community composition was observed across time periods sampled compared to the baseline (p < 0.001). However, no treatment effect of vaccine was detected within the ocular bacterial community. The bacterial community composition with the greatest time span between sampling time periods (98d span) was most similar to the baseline sample collected, suggesting re-establishment of the ocular microbiota to baseline levels over time after perturbation. The effect of IgA levels on the microbial community was investigated in a subset of cattle within the study. However, no significant effect of IgA was observed. Significant changes in the ocular microbiota were identified when comparing communities pre- and post-clinical signs of IBK. Additionally, dynamic changes in opportunistic pathogens Moraxella spp. were observed and confirmed using culture based methods. Conclusions Our results indicate that the bovine ocular microbiota is well represented by opportunistic pathogens such as Moraxella and Mycoplasma. Furthermore, this study characterizes the diversity of the ocular microbiota in calves and demonstrates the plasticity of the ocular microbiota to change. Additionally, we demonstrate the ocular microbiome in calves is similar between the eyes and the perturbation of one eye results in similar changes in the other eye. We also demonstrate the bovine ocular microbiota is slow to recover post perturbation and as a result provide opportunistic pathogens a chance to establish within the eye leading to IBK and other diseases. Characterizing the dynamic nature of the ocular microbiota provides novel opportunities to develop potential probiotic intervention to reduce IBK outbreaks in cattle.


2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Jiekun He ◽  
Siliang Lin ◽  
Jiatang Li ◽  
Jiehua Yu ◽  
Haisheng Jiang

AbstractThe Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.


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