Phenotyping Research Articles

Особливості фенотипування лімфоцитів у хворих з активованою рецидивуючою герпетичною інфекцією першого/другого типу та порушенням репродукції

Метою дослідження був аналіз особливостей змін субпопуляції лімфоцитів за даними імунограми у хворих із рецидивуючою герпетичною інфекцією та репродуктивними порушеннями. Матеріали та методи. Вивчено особливості фенотипування лімфоцитів у 120 хворих з активованою рецидивуючою герпетичною інфекцією першого/другого типу (ВПГ 1/2), серед яких у 63 пацієнтів була діагностована безплідність. Результати. Виявлено збільшення рівня кілерних клітин: CD16+/56+ (NK-клітин) при помірно рецидивуючій інфекції (1–5 рецидивів протягом року) та CD3+/8+ (Т-супресорів/кілерів) при часто рецидивуючій інфекції (6 і більше рецидивів протягом року). Висновки. У безплідних хворих із рецидивуючою інфекцією ВПГ 1/2 спостерігався дефіцит клітин із супресорною активністю: CD4+CD25+CD127–-лімфоцитів (регуляторних Т-клітин) та CD3+/8+-лімфоцитів (Т-супресорів/кілерів).

Kinect Sensor Moving for Low-Cost Mobile Phenotyping of 3D Plant Structures

Kinect Sensor Moving for Low-Cost Mobile Phenotyping of 3D Plant Structures

Exploratory Analysis of HIV Status Knowledge and Associated Factors Using Data from Electronic Medical Records.

Despite recommendations for the routine HIV testing of all sexually active individuals, a significant percentage of HIV-positive adults are unaware of their HIV status. Therefore, a number of strategies have been implemented to expand HIV testing, which in turn makes it necessary to develop tools for identifying patients with unknown HIV status. This study presents the results of an external validation of an electronic phenotyping algorithm for identifying HIV status and its application on a retrospective cohort in order to explore temporal trends of HIV knowledge status and associated factors.

Behavioural Phenotyping of Daily Activities Relevant to Social Functioning Based on Smartphone-Collected Geolocation Data.

Smartphones offer new opportunities to monitor health-related behaviours in the real world. This allows researchers to go beyond traditional data collection methods, such as interviews and questionnaires that suffer from recall bias and low spatio-temporal resolution. In this study, we present an experiment that uses advanced analytical methods to identify daily activities relevant to assess social functioning, from geolocation data. Twenty-one healthy volunteers used a smartphone to continuously record their GPS location for up to 10 days. Participants also completed a diary to record their daily activities that was used as ground truth. Using clustering algorithms and semantic enrichment methods we were able to predict these activities from the GPS data with a precision of 0.75 (standard deviation [SD] 0.13) and a recall of 0.60 (SD 0.11). Although performed on a limited sample, our study shows potential for continuous, and passive geolocation-based monitoring of patient behaviour in mental health.

Extended phenotyping of blood group antigens: Towards improved transfusion practices

Even though the International Society of Blood Transfusion has defined 38 blood group systems, only ABO and RhD are matched while selecting a compatible unit for blood recipients of Indian origin. Genetic disparity between a donor and a patient with reference to minor blood group antigens creates the risk of alloimmunization. The presence of red blood cell alloantibodies further creates the potential for serologic incompatibility, makes the selection of appropriate units for future transfusion more difficult, delays blood transfusion, and presents the risk of hemolytic disease of the newborn. Hence, there is a need to carry out extended blood group typing for antigens of clinical importance among donors and patients so that prophylactic antigen-matched blood can be given to a patient. Provision of antigen-matched blood will help in management of alloimmunized transfused-dependent patients carrying alloantibodies and/or autoantibodies. Typing of blood group antigens among large number of donors will also help in the development of antigen-negative inventories, develop indigenous red cell panels, and identify rare donors. Selection of blood group antigens for typing is important as it may not be always feasible to phenotype all the antigens. Based on the prevalence and immunogenicity of an antigen in a population, specific antigens have to be selected for typing so that the risk of alloimmunization reduces by strategic level of antigen matching. The aim of this review is to highlight the need for extended blood group phenotyping in different case scenarios and the methods available to do so. This review was performed by searching for keywords such as blood transfusion, red cell alloimmunization, partial antigen matching, rare blood donors, multitransfused patients, transfusion in thalassemics, molecular blood group genotyping, serology, and reagent red cell panels in PubMed and Google databases.

Resolving crossmatch incompatibility due to daratumumab in multiple myeloma

Daratumumab (DARA) is an anti-CD38 monoclonal antibody which has promising results in relapsed and refractory multiple myeloma. DARA interferes with blood compatibility testing by causing panagglutination in the indirect antiglobulin test. In all incompatibilities, immunohematology workup must be done to rule out allo- or autoantibody and to issue compatible unit to the patient. Transfusion support is vital for all these patients with incompatibility and should not be delayed. We encountered one such patient who was undergoing treatment with DARA for refractory multiple myeloma and had incompatibility during crossmatching. Many methods are available to sort out this problem. These include anti-CD38 idiotypes, cord blood, trypsin, papain, dithiothreitol (DTT) treatment, phenotyping, and genotyping. We hereby report resolving the above discrepancy by one of the simplest, cheapest, and feasible methods, i.e., DTT treatment in our blood centers.

Genotyping of Vancomycin Resistance and Investigation of Virulence Traits in Foodborne Enterococci

The study was performed to determine the presence of vancomycin phenotyping genes and some virulence traits in enterococci species. For this purpose, a total of 42 enterococci including 6 vancomycin-resistant and 36 vancomycin-susceptible strains originated from meat/meat products and milk/dairy products were assessed for the van A, van B and van C phenoyping genes and agg , esp , gel E, ace and efa A virulence trait genes by using polymerase chain reaction or multiplex polymerase chain reaction. The van A type gene was found in 12% (n=5) of the strains and van C type gene in 50% (n=21). From these, three van A- ( E. faecalis , E. durans , E. casseliflavus ) and two van C-positive ( E. durans ) strains had a minimum inhibitory concentrations of > 256 mg/ml, previously determined with the E-test . The isolates, expressing vancomycin susceptibility and originating from ready-to-eat food, carried van A (n=1) and van C (n=5) genes. On the other hand, the van B gene was not identified among strains. Also any of the strains were not found to harbor virulence traits studied. Our results indicated that resistant or susceptible enterococci strains to antibiotic vancomycin from foods of animal origin can be a possible reservoir of van A type genes potentially transferred between enterococci or to various other bacteria. Furthermore, to develop epidemiological surveillance systems for foodborne antibiotic resistant pathogens as vancomycin-resistant enterococci and their genes responsible for resistance, primarily van A, van B, continues to be an essential issue all around the world. The present work provides data for foodborne enterococci isolates harboring van A type gene from Turkey.

Molecular characteristics of qnrS1-positive Escherichia coli resistant to quinolone

Objective To analyze the molecular characteristics of qnrS-positive Escherichia coli (E.coli) strains resistant to quinolone. Methods A total of 57 qnrS1-positive clinical isolates were collected from Fujian Medical University Union Hospital. Plasmid-mediated quinolone resistance (PMQR) genes [qnrA, qnrB, qnrC, qnrD, aac(6′)-Ib-cr, qepA and oqxAB] and β-lactamase genes (blaCTX-M-1, blaCTX-M-2, blaCTX-M-8, blaCTX-M-9, blaSHV and blaTEM) were detected by PCR and then sequenced. Agar dilution method was used to analyze the antimicrobial susceptibility of the qnrS1-positive strains. Phylogenetic analysis was conducted using PCR. Multilocus sequence typing (MLST) was performed for phenotyping. Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) was used to evaluate the genetic similarity between those isolates. Transferability of the qnrS1 genes carried by the 57 strains was examined by conjugation test with the sodiumazide-resistant E. coli J53 as the recipient strain. Mutations in the quinolone resistance-determining regions (QRDR) in those strains were analyzed by PCR. Results All of the qnrS1-positive E. coli strains showed high resistance to quinolones. PMQR genes were harbored by 14 (24.6%) isolates. Extended spectrum β-lactamases (ESBLs)-producing isolates accounted for 68.4%. Mutations in the QRDR of gyrA, gyrB, parC and parE genes were found in 56 (98.2%) strains and the most frequent point mutations were S83L (89.5%) in gyrA gene, S80I (54.4%) in parC gene and P415V (28.1%) in parE gene. The qnrS1 gene was successful transferred from 13 (22.8%) isolates to E. coli J53 by conjugation. Five plasmid incompatibility groups were detected. Phylogenetic analysis showed that there were 36 (63.2%), 13 (22.8%), 1 (1.8%) and 7 (12.3%) isolates belonging to groups A, B1, B2 and D, respectively. The 57 qnrS1-positive E. coli strains were assigned to 50 ERIC types and 39 sequence types (ST) based on the results of ERIC-PCR and MLST. Conclusions Mutations in the QRDR in E. coli strains were associated with qnrS1 gene and might play a critical role in the dissemination of quinolone-resistant bacteria. Key words: qnrS; Escherichia coli; Quinolone resistance; Plasmid-mediated quinolone resistance; Quinolone resistance-determining region

Quantification of serum apolipoprotein E and patient phenotyping using isotope dilution liquid chromatography-tandem mass spectrometry

Objective To establish an isotope dilution liquid chromatography tandem mass spectrometry method (ID-LC-MS) for quantification of serum apolipoprotein E and phenotyping. Methods Method establishment. Samples underwent denaturing, alkylation and trypsin digestion with addition of internal standards as isotope labelling arginine. SB-C18 column was used for the liquid chromatographic separation and mass spectrometry positive ion mode and multiple reaction monitoring were employed for quantification and phenotyping. Precision, accuracy and linearity were investigated for method evaluation. 40 serum samples from Shanghai Dongfang Hospital during Oct. to Dec., 2018 were used for method comparison between ID-LC-MS and immunoassay. Deming regression and Bland-Altman were used for method comparison analysis and SPSS 24 for linearity. Results Target peptides reached their releasing maximum within 4 hours and SE did at 3 hours. 3 phenotyping of ApoE were observed, such as E3/E3, E2/E3 and E3/E4. The imprecision of IQC was 5.2%. The relative bias for low and high levels of accuracy-based samples was 7.6% and 3.6%, respectively. Deming regression showed the intercept with 95% confidence interval (CI) was 6.44-11.44 (P<0.05 and the 95% confidence interval for the slopewas 0.77-0.89 (P<0.05). The coefficient was r=0.97. The mean difference was -2.95 mg/L with 95% CI -4.26--1.65 mg/L. The linearity covered from 16.9 to 58.5 mg/L. Conclusion ID-LC-MS can be used to quantify serum apolipoprotein E and simultaneously detect its phenotyping. Key words: Apolipoproteins E; Phenotype; Chromatography, liquid; Tandem mass spectrometry

Late-onset spondyloarthritis: a study of 133 patients in Dakar, Senegal.

Reports of late-onset spondyloarthritis in sub-Saharan Africa are sparse. This series allows us to describe the characteristics of this disease in Senegal. This is a retrospective study conducted in the Rheumatology Department of the Dantec University Hospital (Dakar) where we reviewed records of spondyloarthritis cases. Its diagnosis met the modified ASAS and New York criteria. Late-onset was defined as after the age of 55 years. During the study period, the department managed 133 late-onset patients, or 38% of all spondyloarthritis cases (350). Age ranged from 65 to 74 years, with a mean of 66. HLA B 27 phenotyping was performed in 89 patients; 39 patients were HLA B27 positive (29%). The treatments were based on DMARDs (salazopyrin and methotrexate).

Towards patient-driven phenotyping and similarity for precision medicine

Towards patient-driven phenotyping and similarity for precision medicine

Systematic approach in identification and management of multiple alloantibody: A case of triple alloantibody

Alloimmunization is an adverse consequence of exposition to red blood cell antigens through transfusion, pregnancy, or transplantation. Alloimmunization to red cell antigens creates problem not only in immunohematological testing but also causes difficulty in finding compatible blood for those patients who develop multiple alloantibodies. Moreover, the development of multiple alloantibodies can significantly complicate transfusion therapy and/or provokes hemolytic transfusion reactions, the severity of which can vary from mild to extremely severe. We are presenting an interesting case with multiple alloantibodies. Patient's samples were investigated for antibody screening using commercially available three cell panels, and the antibody was identified using different lots of identification panel. Red cell phenotyping was done with minor blood group antisera. After workup, antigen-negative compatible blood was provided for transfusion.

ApoE genotyping and its clinical significance

Apolipoprotein E has a dominant function in the metabolic process of triglyceride and cholesterol in multiple tissues of human. The allele of ApoE has three variants e2, e3, e4 and six genotypes e2/e2, e3/e3, e4/e4, e2/e3, e2/e4, e3/e4, due to polymorphisms of two common SNPs. These genotypes associated with kinds of diseases, such as hyperlipidemia, ASCVD, and AD. In addition, they are also related to the treatment effect of statins. Thus, the detection of the ApoE genotypes is valuable and meaningful in the clinic. In this article, there is a simple discussion about the methodology of the ApoE genotypes, from the protein electrophoresis phenotyping to the rapid, precise and convenient genotyping methods, and its clinical significances.(Chin J Lab Med, 2018, 41: 963-967) Key words: Apolipoproteins E; Genotype; Polymorphism, single nucleotide; Genotyping techniques

Phenotyping of poplar seedling leaves based on a 3D visualization method

In plant research, there is a demand for non-destructive and non-invasive trait measurement methods for phenotyping that can be used to accurately analyze various aspects of plants, such as stem length, leaf area, and leaf inclination. In this study, a method for measuring the leaf geometric characteristics of poplar seedlings based on 3D visualization via the use of time-of-flight (ToF) and digital cameras was proposed. Firstly, the average distance density function method was applied to process outliers of leaves. Secondly, to improve the accuracy of data fitting, a specific method using the angle of adjacent two-point normal vectors was introduced to filter redundant data, kept essential sample values as the control points, and then used the control points to fit the leaf surface based on non-uniform rational B-splines (NURBS). At the same time, NURBS was used to fit the trunk according to its control points and an iterative method to fit the other branches. Finally, 3D visualization of poplar seedlings was achieved, and leaf traits, including leaf width, leaf length, leaf area, and leaf inclination angle, were calculated. To obtain accurate results, multiple experiments were conducted including assessments of poplar seedlings exhibiting normal growth and those grown under water shortage. The results of the proposed method were compared with the real values of the leaves. The RMSE for leaf width, leaf length, leaf area, and leaf angle were 0.18 cm, 0.21 cm, 1.14 cm2, and 1.97°, respectively. The results proved that this approach could be used to accurately measure the leaf characteristics of poplar seedlings via visualization. Keywords: NURBS, poplar seedling, 3D visualization, leaf geometrical characteristics DOI: 10.25165/j.ijabe.20181106.4110 Citation: Hu C H, Li P P, Pan Z. Phenotyping of poplar seedling leaves based on a 3D visualization method. Int J Agric & Biol Eng, 2018; 11(6): 145–151.

Automated extraction of corn leaf points from unorganized terrestrial LiDAR point clouds

Terrestrial LiDAR data can be used to extract accurate structure parameters of corn plant and canopy, such as leaf area, leaf distribution, and 3D model. The first step of these applications is to extract corn leaf points from unorganized LiDAR point clouds. This paper focused on an automated extraction algorithm for identifying the points returning on corn leaf from massive, unorganized LiDAR point clouds. In order to mine the distinct geometry of corn leaves and stalk, the Difference of Normal (DoN) method was proposed to extract corn leaf points. Firstly, the normals of corn leaf surface for all points were estimated on multiple scales. Secondly, the directional ambiguity of the normals was eliminated to obtain the same normal direction for the same leaf distribution. Finally, the DoN was computed and the computed DoN results on the optimal scale were used to extract leave points. The quantitative accuracy assessment showed that the overall accuracy was 94.10%, commission error was 5.89%, and omission error was 18.65%. The results indicate that the proposed method is effective and the corn leaf points can be extracted automatically from massive, unorganized terrestrial LiDAR point clouds using the proposed DoN method. Keywords: corn leaves, terrestrial LiDAR, cloud points, automatic extraction, crop growth monitoring, phenotyping, difference of normal (DoN), directional ambiguity of the normals DOI: 10.25165/j.ijabe.20181103.3177 Citation: Su W, Zhang M Z, Liu J M. Automated extraction of corn leaf points from unorganized terrestrial LiDAR point clouds. Int J Agric & Biol Eng, 2018; 11(3): 166–170.

Sensors for measuring plant phenotyping: A review

Food crisis is a matter of prime importance because it becomes more severe as the global population grows. Among the solutions to this crisis, breeding is deemed one of the most effective ways. However, traditional phenotyping in breeding is time consuming and laborious, and the database is insufficient to meet the requirements of plant breeders, which hinders the development of breeding. Accordingly, innovations in phenotyping are urgent to solve this bottleneck. The morphometric and physiological parameters of plant are particularly interested to breeders. Numerous sensors have been employed and novel algorithms have been proposed to collect data on such parameters. This paper presents a brief review on the parameter measurement for phenotyping to describe its development in recent years. Some parameters that have been measured in phenotyping are introduced and discussed, including plant height, leaf parameters, in-plant space, chlorophyll, water stress, and biomass. And the measurement methods of each parameter with different sensors were classified and compared. Some comprehensive measurement platforms were also summarized, which are able to measure several parameters simultaneously. Besides, some deficiencies of phenotyping should be addressed, and novel methods should be proposed to reduce cost, improve efficiency, and promote phenotyping in the future. Keywords: plant phenotype, high-throughput phenotyping, sensor, morphometric parameters, physiological parameters DOI: 10.25165/j.ijabe.20181102.2696 Citation: Qiu R C, Wei S, Zhang M, Sun H, Li H, Liu G, et al. Sensors for measuring plant phenotyping: A review. Int J Agric & Biol Eng, 2018; 11(2): 1–17.

Polyarteritis nodosa revisited: a review of historical approaches, subphenotypes and a research agenda.

Polyarteritis nodosa (PAN) is a rare form of primary systemic vasculitis with heterogeneous presentations, treatments and disease course. Historical approaches to classification and diagnostic terminology are reviewed. Since differentiation of PAN from microscopic polyangiitis (MPA) and other ANCA vasculitides by the Chapel Hill conference statements, and with hepatitis associated PAN defined as a secondary vasculitis, the phenotyping and subclassification of PAN has received little attention. Monogenic disorders similar to PAN have been described (familial Mediterranean fever, Adenosine Deaminase-2 deficiency), and cutaneous PAN and single organ vasculitis, discussed. The overlapping phenotypes between PAN and other primary vasculitic syndromes and subphenotypes within PAN are explored. This work will underpin development of newer treatment regimens and future genetic and related aetiologic studies.

Quantitative Radiomic Phenotyping of Cervix Cancer

Quantitative Radiomic Phenotyping of Cervix Cancer

Colorectal cancer heterogeneity: genotype, phenotype and clinical manifestation

Colorectal cancer is the third high-incidence of malignant tumors in the world, and also a kind of tumor with good biological behavior and good efficacy. Colorectal cancer heterogeneity is a very important trait of its biological behavior, which can be reflected in many different aspects, including tumor type, pathogenesis, molecular phenotyping and time-space heterogeneity. Different pathogenesis produces different tumor phenotypes, which are generated in the process of natural evolution and intervention. Various phenotypes show the difference among different individuals of colorectal cancer, in terms of clinical characteristics, treatment response and prognosis. Understanding the heterogeneity of colorectal cancer has important clinical value for individualized treatment.

Role of CYP3A4 in kinase inhibitor metabolism and assessment of CYP3A4 activity

Tyrosine kinase inhibitors (TKIs) are small pharmacologically active molecules, which are administered orally at fixed doses to combat tumor cells. Although oral administration is advantageous, the variability of exposure is important for drug efficacy. Hence, the impact of individual CYP3A activity as one of the most important enzymes regulating exposure is important to know. To assess the relevance of CYP3A’s contribution to the clearance of TKIs, 31 TKI European public assessment reports (EPAR) were evaluated. AUC ratios (AUCR) from drug-drug interactions studies with ketoconazole (strong CYP3A inhibitor) and rifampicin (strong CYP3A inducer) were calculated and a significant linear regression was found between both AUCRs (r 2 =0.6951) after nonlinear regression analysis of the log transformed data. In general, if CYP3A contributes to more than 50% to the overall clearance, dose adaptations should be applied. Phenotyping CYP3A by midazolam microdosing might be an applicable option in future to adjust the TKI dose to the individual CYP3A activity, which should then be validated by therapeutic drug monitoring (TDM) to achieve optimal—efficacious but non-toxic—drug concentrations.