scholarly journals Intrinsic limitations in mainstream methods of identifying network motifs in biology

2018 ◽  
Author(s):  
James Fodor ◽  
Michael Brand ◽  
Rebecca J Stones ◽  
Ashley M Buckle
Keyword(s):  
Gene Regulation ◽  
Statistical Analysis ◽  
Synthetic Biology ◽  
Biological Networks ◽  
Rational Design ◽  
Statistical Significance ◽  
Biological Systems ◽  
Network Motifs ◽  
Motif Identification ◽  
Spurious Results

Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, interactomes, and metabolomes. Network motifs may also become pivotal in the rational design and engineering of complex biological systems underpinning the field of synthetic biology. Distinguishing true motifs from arbitrary substructures, however, remains a challenge. Here we demonstrate both theoretically and empirically that implicit assumptions present in mainstream methods for motif identification do not necessarily hold, with the ramification that motif studies using these mainstream methods are less able to effectively differentiate between spurious results and events of true statistical significance than is often presented. We show that these difficulties cannot be overcome without revising the methods of statistical analysis used to identify motifs. The implications of these findings are therefore far-reaching across diverse areas of biology.

Synthetic biology: insights into biological computation

2016 ◽  
Vol 8 (4) ◽  
pp. 518-532 ◽  
Author(s):  
Romilde Manzoni ◽  
Arturo Urrios ◽  
Silvia Velazquez-Garcia ◽  
Eulàlia de Nadal ◽  
Francesc Posas
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Biological Systems ◽  
Biological Computation

Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology.

Evolving protocells to prototissues: rational design of a missing link

2013 ◽  
Vol 41 (5) ◽  
pp. 1159-1165 ◽  
Author(s):  
Shiksha Mantri ◽  
K. Tanuj Sapra
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Structural Elements ◽  
Bottom Up ◽  
Missing Link ◽  
Hierarchical Assembly ◽  
Artificial Cell

Realization of a functional artificial cell, the so-called protocell, is a major challenge posed by synthetic biology. A subsequent goal is to use the protocellular units for the bottom-up assembly of prototissues. There is, however, a looming chasm in our knowledge between protocells and prototissues. In the present paper, we give a brief overview of the work on protocells to date, followed by a discussion on the rational design of key structural elements specific to linking two protocellular bilayers. We propose that designing synthetic parts capable of simultaneous insertion into two bilayers may be crucial in the hierarchical assembly of protocells into a functional prototissue.

scholarly journals Characteristics of anteroposterior curvatures of the spine in soccer and futsal players

2017 ◽  
Vol 18 (4) ◽  
Author(s):  
Krystyna Chromik ◽  
Anna Burdukiewicz ◽  
Jadwiga Pietraszewska ◽  
Aleksandra Stachoń ◽  
Paweł Wolański ◽  
...  
Keyword(s):  
College Students ◽  
Statistical Analysis ◽  
Injury Prevention ◽  
Analysis Of Variance ◽  
Statistical Significance ◽  
Body Posture ◽  
Soccer Players ◽  
Prevention Training ◽  
The Difference ◽  
Post Hoc

AbstractPurpose. The aim of the study was to determine differences in anteroposterior spine curvatures between futsal players, soccer players, and non-training students. The results may contribute to the development of present-day knowledge of posturometry, and its implementation in training can help reduce the risk of body posture disorders in athletes. Methods. The examined group consisted of 48 athletes and 38 non-training college students. Body posture parameters were measured with the use of Posturometr-S. The normality of distribution was checked with the Shapiro-Wilk test, and the differences between the groups were measured with ANOVA and the Bonferroni post-hoc test. The level of statistical significance was set at p < 0.05. Results. The analysis of angle values revealed the widest and most similar measurements in the group of futsal players and soccer players. The analysis of variance proved statistically significant differences between the soccer players and futsal players (p = 0.003). The difference between the soccer players and non-training students was statistically significant. The highest γ angular value was measured in non-training students, followed by futsal players and soccer players. The statistical analysis revealed significant differences between the non-training students and futsal players, as well as non-training students and soccer players (p < 0.001). Conclusions. A complex assessment of athletes’ body posture is crucial in injury prevention. Training overloads may often lead to disorders of the organ of locomotion and affect the correct body posture in athletes. This, in turn, may result in pains and injuries.

Do longitudinal orthodontic trials use appropriate statistical analyses? A meta-epidemiological study

2021 ◽  
Author(s):  
Samer Mheissen ◽  
Haris Khan ◽  
Mohammed Almuzian ◽  
Emad Eddin Alzoubi ◽  
Nikolaos Pandis
Keyword(s):  
Statistical Analysis ◽  
Epidemiological Study ◽  
Data Extraction ◽  
Statistical Significance ◽  
Repeated Measure ◽  
Exact Test ◽  
Optimal Analysis ◽  
Study Characteristics ◽  
Measure Analysis ◽  
Repeated Measure Analysis

Summary Background In orthodontic trials, longitudinal designs with multiple outcome measurements over time are common. The aim of this epidemiological study was to examine whether optimal statistical analysis approaches have been used in longitudinal orthodontic trials. Methods Pubmed was searched in August 2021 for longitudinal orthodontic trials with at least three time points of outcome assessment published in the 2017–20 period. Study selection and data extraction were done independently and in duplicate. The analysis approaches undertaken were tabulated and associations between study characteristics and the use of optimal analysis or not were assessed using Fisher’s exact test and logistic regression. Results One hundred forty-seven out of 563 unique records were deemed eligible for inclusion. Only 26.50% of these trials used an optimal statistical analysis for longitudinal data where the data structure is accounted for. None of the study characteristics except the statistical significance of the results were associated with the appropriateness of the statistical analysis. The odds of significant results in studies with suboptimal analyses were higher than that in studies with optimal longitudinal analyses (odds ratio: 3.48, 95% confidence interval: 1.62, 7.46, P = 0.001). For the studies with optimal analysis, the most frequent test was repeated-measure analysis of variance (RM-ANOVA). The reporting of the statistical analysis section was suboptimal in the majority of the trials. Conclusion Most longitudinal orthodontic trials are not analysed using optimal statistical approaches. Inferences and interpretation of their results are likely to be compromised.

Wybrane parametry jakości ucisku i relaksacji klatki piersiowej wykonywanej przez personel pielęgniarski w ramach pozaszpitalnego nagłego zatrzymania krążenia ? badanie pilotażowe

2018 ◽  
Vol 21 (4) ◽  
Author(s):  
Paweł Więch ◽  
Marek Muster ◽  
Dariusz Bazaliński ◽  
Grzegorz Kucaba ◽  
Izabela Sałacińska ◽  
...  
Keyword(s):  
Health Care ◽  
Primary Health Care ◽  
Statistical Analysis ◽  
Discharge Rate ◽  
Statistical Significance ◽  
Sudden Cardiac Arrest ◽  
Initial Examination ◽  
Relaxation Parameters ◽  
Primary Health

Introduction. Sudden cardiac arrest (SCA) in out-of-hospital conditions is a frequent condition of immediate life-emergency of cardiological background. The survival and discharge rate in SCA patients treated by medical services is still at a low level. Aim. The aim of the study was to analyze selected parameters of the quality of chest compressions and relaxation performed by nursing staff as part of out-of-hospital SCA. Material and methods. The study covered a group of 48 nurses working in primary health care in branches of conservative (PRE/C = 24 people, mean age 33.04 ± 9.20) and surgery profile (PRE/I = 24 people, average age 31.88 ± 9.97), participating in the research project of the Center for Medical and Natural Sciences Research and Innovation, University of Rzeszów in Rzeszów. Two months after the initial examination and intervention, the test was repeated. The assessment of selected compression and relaxation parameters was performed using the True CPR Resuscitation Assistant. The statistical analysis of the collected material was carried out with the SPSS Statistics 20 software. The statistical analysis used the analysis of variables using parametric and non-parametric tests. The statistical significance was assumed at p < 0.05. Results. Initially, a high percentage of the effectiveness of the most important compression and relaxation parameters of the chest was obtained during 2-minute out-of-hospital cardiopulmonary resuscitation with no statistically significant differences between the two groups (PRE/C: 51 mm depth, 83.92% relaxation, frequency 115.46 vs. PRE/I: depth: 47.58 mm, relaxation: 92.54, frequency: 109.96, p < 0.05). After two months, similar parametric values were observed with no statistical significance (p < 0.05). Conclusions. The initial high quality of compressions and relaxation was found in nurses participating in the simulated out-of-hospital SCA, while there were no significant differences between primary health care nurses working at conservative departments and nurses from surgical ones. After a two-month interval from the initial examination and training, high CPR effectiveness was observed based on the guidelines of the European Resuscitation Council from 2015.

scholarly journals Three Evidence Based Methods to Compensate for a Lack of Subject Background when Ordering Chemistry Monographs

2008 ◽  
Vol 3 (3) ◽  
pp. 3
Author(s):  
Robert A. Wright
Keyword(s):  
Statistical Analysis ◽  
Statistical Significance ◽  
Evidence Base ◽  
Circulation Rate ◽  
Evidence Based ◽  
Practical Application ◽  
Present Evidence ◽  
Library System ◽  
Over Time ◽  
Selection Of

Objective – The aim of this article is to present evidence based methods for the selection of chemistry monographs, particularly for librarians lacking a background in chemistry. These methods will be described in detail, their practical application illustrated, and their efficacy tested by analyzing circulation data. Methods – Two hundred and ninety-five chemistry monographs were selected between 2005 and 2007 using rigorously-applied evidence based methods involving the Library's integrated library system (ILS), Google, and SciFinder Scholar. The average circulation rate of this group of monographs was compared to the average circulation rate of 254 chemistry monographs selected between 2002 and 2004 when the methods were not used or were in an incomplete state of development. Results – Circulations/month were on average 9% greater in the cohort of monographs selected with the rigorously-applied evidence based methods. Further statistical analysis, however, finds that this result can not be attributed to the different application of these methods. Conclusion – The methods discussed in this article appear to provide an evidence base for the selection of chemistry monographs, but their application does not change circulation rates in a statistically significant way. Further research is needed to determine if this lack of statistical significance is real or a product of the organic development and application of these methods over time, making definitive comparisons difficult.

scholarly journals Independent control of amplitude and period in a synthetic oscillator circuit with modified repressilator

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Fengyu Zhang ◽  
Yanhong Sun ◽  
Yihao Zhang ◽  
Wenting Shen ◽  
Shujing Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Biological Systems ◽  
Reporter Genes ◽  
Quantitative Model ◽  
Theoretical Level ◽  
Independent Control ◽  
Oscillator Circuit ◽  
Biological Circuits

AbstractSynthetic Biology aims to create predictable biological circuits and fully operational biological systems. Although there are methods to create more stable oscillators, such as repressilators, independently controlling the oscillation of reporter genes in terms of their amplitude and period is only on theoretical level. Here, we introduce a new oscillator circuit that can be independently controlled by two inducers in Escherichia coli. Some control components, including σECF11 and NahR, were added to the circuit. By systematically tuning the concentration of the inducers, salicylate and IPTG, the amplitude and period can be modulated independently. Furthermore, we constructed a quantitative model to forecast the regulation results. Under the guidance of the model, the expected oscillation can be regulated by choosing the proper concentration combinations of inducers. In summary, our work achieved independent control of the oscillator circuit, which allows the oscillator to be modularized and used in more complex circuit designs.

scholarly journals Therapeutic Effect of Oral Administration and External Therapy of Traditional Chinese Medicine on Cervical Tuberculous

2019 ◽  
Vol 3 (3) ◽  
Author(s):  
Guoqiang Yang ◽  
Jin Zhang
Keyword(s):  
Statistical Analysis ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Oral Administration ◽  
Total Effective Rate ◽  
Statistical Significance ◽  
Effective Rate ◽  
Control Group ◽  
Treatment Data ◽  
Experimental Group

Objective: To analyze the clinical effect and value of oral administration and external therapy of traditional Chinese medicine for treatment of cervical tuberculous lymphadenopathy. Methods: A total of 56 patients with cervical tuberculous lymphadenopathy admitted to our hospital from January 1 to January 2018 were recruited. By using double-blind method, the patients were divided into control group (n=28) and experimental group (n=28). Control group comprised of patients with conventional anti-tuberculosis treatment, while the experimental group comprised of patients treated with oral administration and external therapy of traditional Chinese medicine. Total effective rate, incidence of complication and level of T lymphocyte subsets were compared between the two groups of cervical tuberculous lymphadenopathy patients. Results: Post-treatment data of total effective rate, complication rate, CD3+, CD4+, CD8+, CD4+/CD8+ of the experimental group were compared with the control group. P<0.05; statistical analysis showed statistical significance. Post-treatment data of CD3+, CD4+, CD8+, CD4+/CD8+ of both control and experimental groups were compared with pre-treatment data. P<0.05; statistical analysis showed statistical significance. Conclusion: Oral administration and external therapy of traditional Chinese medicine possesses significant effect in treatment of cervical tuberculous lymphadenopathy.

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