scholarly journals Boolean implication analysis unveils candidate universal relationships in microbiome data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Daniella Vo ◽  
Shayal Charisma Singh ◽  
Sara Safa ◽  
Debashis Sahoo
Keyword(s):  
Disease Diagnosis ◽  
Biological Properties ◽  
Clinical Settings ◽  
Human Environment ◽  
Linear Relationships ◽  
Critical Components ◽  
General Populations ◽  
Almost All ◽  
Microbiome Data ◽  
Boolean Implication

Abstract Background Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correlation to determine linear relationships between microbes and diseases. Weak correlations due to nonlinearity between microbe pairs may cause researchers to overlook critical components of the data. With the abundance of available microbiome, we need a method that comprehensively studies microbiomes and how they are related to each other. Results We collected publicly available datasets from human, environment, and animal samples to determine both symmetric and asymmetric Boolean implication relationships between a pair of microbes. We then found relationships that are potentially invariants, meaning they will hold in any microbe community. In other words, if we determine there is a relationship between two microbes, we expect the relationship to hold in almost all contexts. We discovered that around 330,000 pairs of microbes universally exhibit the same relationship in almost all the datasets we studied, thus making them good candidates for invariants. Our results also confirm known biological properties and seem promising in terms of disease diagnosis. Conclusions Since the relationships are likely universal, we expect them to hold in clinical settings, as well as general populations. If these strong invariants are present in disease settings, it may provide insight into prognostic, predictive, or therapeutic properties of clinically relevant diseases. For example, our results indicate that there is a difference in the microbe distributions between patients who have or do not have IBD, eczema and psoriasis. These new analyses may improve disease diagnosis and drug development in terms of accuracy and efficiency.

scholarly journals Boolean Implication Analysis Unveils Candidate Universal Relationships in Microbiome Data

2020 ◽  
Author(s):  
Daniella Vo ◽  
Shayal Charisma Singh ◽  
Sara Safa ◽  
Debashis Sahoo
Keyword(s):  
Disease Diagnosis ◽  
Biological Properties ◽  
Clinical Settings ◽  
Human Environment ◽  
Linear Relationships ◽  
Critical Components ◽  
General Populations ◽  
Almost All ◽  
Microbiome Data ◽  
Boolean Implication

Abstract Background: Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correlation to determine linear relationships between microbes and diseases. Weak correlations due to nonlinearity between microbe pairs may cause researchers to overlook critical components of the data. With the abundance of available microbiome, we need a method that comprehensively studies microbiomes and how they are related to each other.Results: We collected publicly available datasets from human, environment, and animal samples to determine both symmetric and asymmetric Boolean implication relationships between a pair of microbes. We then found relationships that are potentially invariants, meaning they will hold in any microbe community. In other words, if we determine there is a relationship between two microbes, we expect the relationship to hold in almost all contexts. We discovered that around 330,000 pairs of microbes universally exhibit the same relationship in almost all the datasets we studied, thus making them good candidates for invariants. Our results also confirm known biological properties and seem promising in terms of disease diagnosis. Conclusions: Since the relationships are likely universal, we expect them to hold in clinical settings, as well as general populations. If these strong invariants are present in disease settings, it may provide insight into prognostic, predictive, or therapeutic properties of clinically relevant diseases. For example, our results indicate that there is a difference in the microbe distributions between patients who have or do not have IBD, eczema and psoriasis. These new analyses may improve disease diagnosis and drug development in terms of accuracy and efficiency.

scholarly journals Boolean Implication Analysis Unveils Candidate Universal Relationships in Microbiome Data

2020 ◽  
Author(s):  
Daniella Vo ◽  
Shayal Charisma Singh ◽  
Sara Safa ◽  
Debashis Sahoo
Keyword(s):  
Disease Diagnosis ◽  
Biological Properties ◽  
Weak Correlation ◽  
Human Environment ◽  
Asymmetric Data ◽  
Therapeutic Properties ◽  
Almost All ◽  
Microbiome Data ◽  
The Relationship ◽  
Boolean Implication

Abstract Background: Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Some previous analyses of microbiomes focus on the relationships between specific microbiomes and a particular disease. These typically use correlation which is fundamentally symmetric with respect to pairs of microbes. Correlation focuses on the symmetry of the data distribution, and asymmetric data is often discarded as having a weak correlation. With all the data available on the microbiome, there is a need for a method that comprehensively studies microbiomes and how they are related to each other.Results: We collect publicly available datasets from human, environment, and animal samples to determine both symmetric and asymmetric Boolean relationships between a pair of microbes. We then find relationships that are potentially invariants, meaning they will hold in any microbe community. In other words, if we determine there is a relationship between two microbes, we expect the relationship to hold in almost all context. We discovered that certain pairs of microbes always exhibit the same relationship in almost all the datasets we studied, thus making them good candidates for universal relationships. Our results confirm known biological properties and seem promising in terms of disease diagnosis.Conclusions: Since the relationships are likely universal, we expect that they will hold in a clinical setting as well as in the general population. Strong universal relationships may provide insight on prognostic, predictive, or therapeutic properties of a clinically relevant disease. These new analyses may improve disease diagnosis and drug development in terms of accuracy and efficiency.

scholarly journals E2F activity is regulated by cell cycle-dependent changes in subcellular localization.

1997 ◽  
Vol 17 (12) ◽  
pp. 7268-7282 ◽  
Author(s):  
R Verona ◽  
K Moberg ◽  
S Estes ◽  
M Starz ◽  
J P Vernon ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Subcellular Localization ◽  
Nuclear Localization ◽  
Mammalian Cells ◽  
Critical Role ◽  
Biological Properties ◽  
Dependent Manner ◽  
Restriction Point ◽  
Cycle Dependent ◽  
Almost All

E2F directs the cell cycle-dependent expression of genes that induce or regulate the cell division process. In mammalian cells, this transcriptional activity arises from the combined properties of multiple E2F-DP heterodimers. In this study, we show that the transcriptional potential of individual E2F species is dependent upon their nuclear localization. This is a constitutive property of E2F-1, -2, and -3, whereas the nuclear localization of E2F-4 is dependent upon its association with other nuclear factors. We previously showed that E2F-4 accounts for the majority of endogenous E2F species. We now show that the subcellular localization of E2F-4 is regulated in a cell cycle-dependent manner that results in the differential compartmentalization of the various E2F complexes. Consequently, in cycling cells, the majority of the p107-E2F, p130-E2F, and free E2F complexes remain in the cytoplasm. In contrast, almost all of the nuclear E2F activity is generated by pRB-E2F. This complex is present at high levels during G1 but disappears once the cells have passed the restriction point. Surprisingly, dissociation of this complex causes little increase in the levels of nuclear free E2F activity. This observation suggests that the repressive properties of the pRB-E2F complex play a critical role in establishing the temporal regulation of E2F-responsive genes. How the differential subcellular localization of pRB, p107, and p130 contributes to their different biological properties is also discussed.

scholarly journals Possibilities for interprofessional learning at a Swedish acute healthcare ward not dedicated to interprofessional education: an ethnographic study

BMJ Open ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. e027590 ◽  
Author(s):  
Ann Hägg-Martinell ◽  
Håkan Hult ◽  
Peter Henriksson ◽  
Anna Kiessling
Keyword(s):  
Nursing Students ◽  
Interprofessional Education ◽  
Ethnographic Study ◽  
Clinical Settings ◽  
Interprofessional Learning ◽  
Staff Members ◽  
Questions And Answers ◽  
Field Notes ◽  
Almost All ◽  
Acute Healthcare

ObjectivesAlmost all healthcare today is team-based in collaboration over professional borders, and numerous students have work-based learning in such contexts. However, interprofessional learning (IPL) in clinical settings has mostly been systematically explored in specially designed contexts dedicated to interprofessional education (IPE). This study aimed to explore the possibilities for IPL activities, and if or how they occur, in an acute ward context not dedicated to IPE.Design and settingBetween 2011 and 2013 ethnographic observations were performed of medical and nursing students’ interactions and IPL during early clerkship at an acute internal medicine ward in Sweden. Field notes were taken and analysed based on the framework of IPE:learning with, from and about.Participants21 medical, 4 nursing students and 30 supervisors participated.ResultsLearning with—there were no organised IPE activities. Instead, medical and nursing students learnt in parallel. However, students interacted with staff members from other professions.Learning from—interprofessional supervision was frequent. Interprofessional supervision of nursing students by doctors focused on theoretical questions and answers, while interprofessional supervision of medical students by nurses focused on the performance of technical skills.Learning about—students were observed to actively observe interactions between staff and learnt how staff conducted different tasks.ConclusionThis study shows that there were plenty of possibilities for IPL activities, but the potential was not fully utilised or facilitated. Serendipitous IPL activities differed between observed medical and nursing students. Although interprofessional supervision was fairly frequent, students were not learning with, from or about each other over professional borders.

scholarly journals Quantification of one Prenylated Flavanone from Eysenhardtia platycarpa and four derivatives in Ex Vivo Human Skin Permeation Samples Applying a Validated HPLC Method

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 889
Author(s):  
Paola Bustos-Salgado ◽  
Berenice Andrade-Carrera ◽  
María Luisa Garduño-Ramírez ◽  
Helen Alvarado ◽  
Ana Calpena-Campmany
Keyword(s):  
Human Skin ◽  
Ex Vivo ◽  
Skin Permeation ◽  
Correlation Coefficients ◽  
Biological Properties ◽  
Cell System ◽  
Hplc Method ◽  
Linear Relationships ◽  
Relative Standard ◽  
Instrumental System

Prenylated flavanones are polyphenols that have diverse biological properties. The present paper focuses on a HPLC method validation for the quantification of prenylated flavanones (2S)-5,7-dihydroxy-6-(3-methyl-2-buten-1-yl)-2-phenyl-2,3-dihydro-4H-1Benzopyran-4-one 1 and derivatives (2S)-5,7-bis(acetyloxy)-6-(3-methyl-2-buten-1-yl)-2-phenyl-2,3-dihydro-4H-1-Benzopyran-4-one A; (2S)-5-hydroxy-7-methoxy-6-(3-methyl-2-buten-1-yl)-2-phenyl-2,3-dihydro-4H-1-Benzopyran-4-one B; (8S)-5-hydroxy-2,2-dimethyl-8-phenyl-3,4,7,8-tetrahydro-2H,6H-Benzo[1,2-b:5,4-bˈ]dipyran-6-one C; and (8S)-5-hydroxy-2,2-dimethyl-8-phenyl-7,8-dihydro-2H,6H-Benzo[1,2-b:5,4-bˈ]dipyran-6-one D applied in biopharmaceutic studies. The linear relationships are proven with significant correlation coefficients (R2 ˃ 0.999) in the range of 1.56 to 200 μg/mL with low limits of detection and quantification, on average of 0.4 μg/mL and 1.2 μg/mL, respectively. The validation method used in this work is highly accurate and precise, with values lower than 15%. The relative standard deviation values of repeatability of the instrumental system are demonstrated with less than 0.6% for all studied flavanones. Therefore, the applicability method of the quantification of the prenylated flavanones was established using the permeation of human skin in the Franz cell system. During the method previously described, there was no interference observed from human skin components in ex vivo permeation studies.

scholarly journals Survey on Management of Spotted Pod Borer (Maruca vitrata Fabricius) on Yardlong Bean in Chitwan, Nepal

2016 ◽  
Vol 4 (1) ◽  
pp. 39-43
Author(s):  
Rajendra. Regmi ◽  
Sundar Tiwari ◽  
Resham Bhadur Thapa ◽  
Ranju Maharjan ◽  
Sujata poudel Poudel ◽  
...  
Keyword(s):  
Management Practice ◽  
Insect Pest ◽  
Household Survey ◽  
Human Environment ◽  
Commercial Grower ◽  
Pod Borer ◽  
Major Pest ◽  
Yardlong Bean ◽  
Almost All ◽  
Chemical Pesticides

A household survey was conducted during January 2012 in Gunjanagar, Dibyanagar and Sukranagar Village Development Committee of Chitwan district to know the socioeconomic status, status of spotted pod borer and its management practice. The survey included purposive random sampling methods in 35 yardlong bean growers. Most of commercial farmers have been growing since 3-7 years. Nearly three fourth of the farmers considered spotted pod borer as a major pest of yarldlong bean in Chitwan. Most of them considered more than 60% loss caused by spotted pod borer if no management practice is applied. Almost all sprayed chemical pesticides for management of spotted pod borer and nearly three fourth of them used more than one chemical pesticides alternately for management of spotted pod borer.One third farmers (31.43%) applied chemical pesticides in 4-7 days interval and one third of them (31.43%) applied chemical pesticides in 7-10 days interval after beginning of flowering for management of spotted pod borer. Almost all farmers (94.29%) knew adverse effect of pesticides on human, environment, natural enemies and other animal. Majority (94.29%) of farmers harvested pods after 1-3 day of spray of chemical pesticides and very few (14.29%) of commercial grower of this area get training in insect pest management.Int J Appl Sci Biotechnol, Vol 4(1): 39-43

Magnetic Nanoparticles: Current Trends and Future Aspects in Diagnostics and Nanomedicine

2019 ◽  
Vol 20 (6) ◽  
pp. 457-472 ◽  
Author(s):  
Naga Veera Srikanth Vallabani ◽  
Sanjay Singh ◽  
Ajay Singh Karakoti
Keyword(s):  
Magnetic Nanoparticles ◽  
Biomedical Applications ◽  
Antimicrobial Agents ◽  
Superparamagnetic Iron Oxide ◽  
Disease Diagnosis ◽  
Imaging Modalities ◽  
Clinical Settings ◽  
Current Trends ◽  
Recent Developments ◽  
Near Future

Background: Biomedical applications of Magnetic Nanoparticles (MNPs) are creating a major impact on disease diagnosis and nanomedicine or a combined platform called theranostics. A significant progress has been made to engineer novel and hybrid MNPs for their multifunctional modalities such as imaging, biosensors, chemotherapeutic or photothermal and antimicrobial agents. MNPs are successfully applied in biomedical applications due to their unique and tunable properties such as superparamagnetism, stability, and biocompatibility. Approval of ferumoxytol (feraheme) for MRI and the fact that several Superparamagnetic Iron Oxide Nanoparticles (SPIONs) are currently undergoing clinical trials have paved a path for future MNPs formulations. Intensive research is being carried out in designing and developing novel nanohybrids for multiple applications in nanomedicine. Objective: The objective of the present review is to summarize recent developments of MNPs in imaging modalities like MRI, CT, PET and PA, biosensors and nanomedicine including their role in targeting and drug delivery. Relevant theory and examples of the use of MNPs in these applications have been cited and discussed to create a thorough understanding of the developments in this field. Conclusion: MNPs have found widespread use as contrast agents in imaging modalities, as tools for bio-sensing, and as therapeutic and theranostics agents. Multiple formulations of MNPs are in clinical testing and may be accepted in clinical settings in near future.

scholarly journals Polyphenols in Dental Applications

2020 ◽  
Vol 7 (3) ◽  
pp. 72 ◽  
Author(s):  
Naji Kharouf ◽  
Youssef Haikel ◽  
Vincent Ball
Keyword(s):  
Surface Chemistry ◽  
Biological Activities ◽  
Broad Class ◽  
Dental Materials ◽  
Biological Properties ◽  
Dental Tissues ◽  
Metallic Cations ◽  
Almost All ◽  
Dental Applications ◽  
Large Repertoire

(1) Background: polyphenols are a broad class of molecules extracted from plants and have a large repertoire of biological activities. Biomimetic inspiration from the effects of tea or red wine on the surface of cups or glass lead to the emergence of versatile surface chemistry with polyphenols. Owing to their hydrogen bonding abilities, coordination chemistry with metallic cations and redox properties, polyphenols are able to interact, covalently or not, with a large repertoire of chemical moieties, and can hence be used to modify the surface chemistry of almost all classes of materials. (2) Methods: the use of polyphenols to modify the surface properties of dental materials, mostly enamel and dentin, to afford them with better adhesion to resins and improved biological properties, such as antimicrobial activity, started more than 20 years ago, but no general overview has been written to our knowledge. (3) Results: the present review is aimed to show that molecules from all the major classes of polyphenolics allow for low coast improvements of dental materials and engineering of dental tissues.

scholarly journals Wireless E-Nose Sensors to Detect Volatile Organic Gases through Multivariate Analysis

Micromachines ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 597
Author(s):  
Saifur Rahman ◽  
Abdullah S. Alwadie ◽  
Muhammed Irfan ◽  
Rabia Nawaz ◽  
Mohsin Raza ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Gas Sensors ◽  
Chemical Engineering ◽  
Disease Diagnosis ◽  
Medical Diagnostics ◽  
Pollution Monitoring ◽  
Oxide Semiconductor ◽  
Food And Beverage ◽  
Critical Components ◽  
Mos Sensor

Gas sensors are critical components when adhering to health safety and environmental policies in various manufacturing industries, such as the petroleum and oil industry; scent and makeup production; food and beverage manufacturing; chemical engineering; pollution monitoring. In recent times, gas sensors have been introduced to medical diagnostics, bioprocesses, and plant disease diagnosis processes. There could be an adverse impact on human health due to the mixture of various gases (e.g., acetone (A), ethanol (E), propane (P)) that vent out from industrial areas. Therefore, it is important to accurately detect and differentiate such gases. Towards this goal, this paper presents a novel electronic nose (e-nose) detection method to classify various explosive gases. To detect explosive gases, metal oxide semiconductor (MOS) sensors are used as reliable tools to detect such volatile gases. The data received from MOS sensors are processed through a multivariate analysis technique to classify different categories of gases. Multivariate analysis was done using three variants—differential, relative, and fractional analyses—in principal components analysis (PCA). The MOS sensors also have three different designs: loading design, notch design, and Bi design. The proposed MOS sensor-based e-nose accurately detects and classifies three different gases, which indicates the reliability and practicality of the developed system. The developed system enables discrimination of these gases from the mixture. Based on the results from the proposed system, authorities can take preventive measures to deal with these gases to avoid their potential adverse impacts on employee health.

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