scholarly journals Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description

2004 ◽  
Vol 3 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Lee A Newberg ◽  
Charles E Lawrence

Under the assumption that a significant motivation for sequencing the genomes of mammals is the resulting ability to help us locate and characterize functional DNA segments shared with humans, we have developed a statistical analysis to quantify the expected advantage. Examining uncertainty in terms of the width of a confidence interval, we show that uncertainty in the rate of nucleotide mutation can be shrunk by a factor of nearly four when nine mammals; human, chimpanzee, baboon, cat, dog, cow, pig, rat, mouse; are used instead of just two; human and mouse. Contrastingly, we show confidence interval shrinkage by a factor of only 1.5 for measurements of the distribution of nucleotides at an aligned sequence site. These additional genomes should greatly help in identifying conserved DNA sites, but would be much less effective at precisely describing the expected pattern of nucleotides at those sites.

2020 ◽  
Author(s):  
Hideya Kawasaki ◽  
Hiromi Suzuki ◽  
Masato Maekawa ◽  
Takahiko Hariyama

BACKGROUND As pathogens such as influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can easily cause pandemics, rapid diagnostic tests are crucial for implementing efficient quarantine measures, providing effective treatments to patients, and preventing or containing a pandemic infection. Here, we developed the immunochromatography-NanoSuit® method, an improved immunochromatography method combined with a conventional scanning electron microscope (SEM), which enables observation of immunocomplexes labeled with a colloidal metal. OBJECTIVE A total of 197 clinical samples from patients suspected to be suffering from influenza were provided by a general hospital at the Hamamatsu University School of Medicine for examination using the Flu kit. METHODS Immunochromatography kit The ImunoAce® Flu kit (NP antigen detection), a human influenza commercial diagnosis kit, was purchased from TAUNS Laboratories, Inc. (Shizuoka, Japan). Au/Pt nanoparticles were utilized to visualize the positive lines. A total of 197 clinical samples from patients suspected to be suffering from influenza were provided by a general hospital at the Hamamatsu University School of Medicine for examination using the Flu kit. After macroscopic diagnosis using the Flu kit, the samples were stored in a biosafety box at room temperature (20-25 °C / 68 - 77 °F). The IgM detection immunochromatography kit against SARS-CoV-2 was obtained from Kurabo Industries, Ltd. (Osaka, Japan). One step rRT-PCR for influenza A rRT-PCR for influenza A was performed as described previously using Flu A universal primers. A Ct within 38.0 was considered as positive according to the CDC protocol. The primer/probe set targeted the human RNase P gene and served as an internal control for human nucleic acid as described previously. SEM image acquisition The immunochromatography kit was covered with a modified NanoSuit® solution based on previously published components (Nisshin EM Co., Ltd., Tokyo, Japan), placed first onto the wide stage of the specimen holder, and then placed in an Lv-SEM (TM4000Plus, Hitachi High-Technologies, Tokyo, Japan). Images were acquired using backscattered electron detectors with 10 or 15 kV at 30 Pa. Particle counting In fields containing fewer than 50 particles/field, the particles were counted manually. Otherwise, ImageJ/Fiji software was used for counting. ImageJ/Fiji uses comprehensive particle analysis algorithms that effectively count various particles. Images were then processed and counting was performed according to the protocol. Diagnosis and statistics The EM diagnosis and criteria for a positive test were defined as follows: particle numbers from 6 fields from the background area and test-line were statistically analyzed using the t-test. If there were more than 5 particles in one visual field and a significant difference (P < 0.01) was indicated by the t-test, the result was considered positive. Statistical analysis using the t-test was performed in Excel software. Statistical analysis of the assay sensitivity and specificity with a 95% confidence interval (95% CI) was performed using the MedCalc statistical website. The approximate line, correlation coefficient, and null hypothesis were calculated with Excel software. RESULTS Our new immunochromatography-NanoSuit® method suppresses cellulose deformity and makes it possible to easily focus and acquire high-resolution images of gold/platinum labeled immunocomplexes of viruses such as influenza A, without the need for conductive treatment as with conventional SEM. Electron microscopy (EM)-based diagnosis of influenza A exhibited 94% clinical sensitivity (29/31) (95% confidence interval [95%CI]: 78.58–99.21%) and 100% clinical specificity (95%CI: 97.80–100%). EM-based diagnosis was significantly more sensitive (71.2%) than macroscopic diagnosis (14.3%), especially in the lower influenza A-RNA copy number group. The detection ability of our method is comparable to that of real-time reverse transcription-polymerase chain reaction. CONCLUSIONS This simple and highly sensitive quantitative analysis method involving immunochromatography can be utilized to diagnose various infections in humans and livestock, including highly infectious diseases such as COVID-19.


2021 ◽  
Vol 28 ◽  
pp. 146-150
Author(s):  
L. A. Atramentova

Using the data obtained in a cytogenetic study as an example, we consider the typical errors that are made when performing statistical analysis. Widespread but flawed statistical analysis inevitably produces biased results and increases the likelihood of incorrect scientific conclusions. Errors occur due to not taking into account the study design and the structure of the analyzed data. The article shows how the numerical imbalance of the data set leads to a bias in the result. Using a dataset as an example, it explains how to balance the complex. It shows the advantage of presenting sample indicators with confidence intervals instead of statistical errors. Attention is drawn to the need to take into account the size of the analyzed shares when choosing a statistical method. It shows how the same data set can be analyzed in different ways depending on the purpose of the study. The algorithm of correct statistical analysis and the form of the tabular presentation of the results are described. Keywords: data structure, numerically unbalanced complex, confidence interval.


Pharmaceutics ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 318 ◽  
Author(s):  
Jordi Ocaña ◽  
Toni Monleón-Getino ◽  
Virginia Merino ◽  
Daniel Peris ◽  
Lluís Soler

This study examines the statistical implications, and their possible implementation, of the “Draft guideline on quality and equivalence of topical products” issued by the European Medicines Agency in 2018, with particular focus on the section devoted to quality equivalence of physical properties. A new confidence interval to conduct the quality equivalence test and a way to cope with the multiplicity of quality parameters are presented and discussed. As an example, the results and the statistical analysis of a study on betamethasone 0.5 mg/g ointment are presented. It is suggested that the equivalence limits proposed in the draft guideline are overly strict: It is as difficult to declare quality equivalence between two packaging formats of the same reference product as to declare quality equivalence between the reference and the test product.


Author(s):  
David Corinaldi ◽  
Massimo Callegari ◽  
Matteo-Claudio Palpacelli ◽  
Giacomo Palmieri

The paper presents the preliminary design of a novel gripper able to grasp large non-rigid materials that has been conceived to face the challenge of automatic handling tasks in the leather industry. The design has been driven by the requirements to limit production costs and the complexity of the grasping device. A statistical analysis of the different templates sizes has allowed to identify a fixed configuration of the gripping points able to properly pick all the sheets within a great confidence interval. According to the varying shape of the leather templates themselves, that is due to their stacking in plies on the beam, the trajectory of the gripping points has been studied and arranged. Due to the irregular shape of the large sheets that are handled, the edges of the non-rigid materials out of the gripping area might flutter during the transferring phase: a four-bar linkage has been specifically designed, so that the motion of its end-effector prevents unwanted leather creases.


1989 ◽  
Vol 72 (2) ◽  
pp. 237-241
Author(s):  
Gerald L Stahl ◽  
D Dal Kratzer ◽  
Charles W Kasson

Abstract A modification of the AOAC microbiological determination of neomycin in feeds was collaboratively studied by 12 laboratories. The official method was modified by substituting a constant salt concentration diluent for the feed extract diluent, preparing the agar medium in tris buffer, and performing the test with a monolayer plating system. Each laboratory performed single assays on 8 samples in a randomized sequence. The samples included duplicates of a cattle and swine feed at 2 different marketed concentrations. The mean recovery across all laboratories was 110.7% of theory with a range of means of 69.4-128.6 across the 12 laboratories. The results of one laboratory and 2 additional values from different laboratories were deemed outliers and excluded from statistical analysis. The statistical analysis gave a confidence interval of ± 26% for individual assays.


1998 ◽  
Vol 26 (1) ◽  
pp. 46-51 ◽  
Author(s):  
Anna M. Demirdjian ◽  
Scott G. Petrie ◽  
Carlos A. Guanche ◽  
Kevin A. Thomas

The Noyes and Lysholm knee scoring questionnaires, commonly used for follow-up assessment after knee surgery, were developed based on knees with preexisting pathologic changes and have not been standardized to normal knees. We administered both questionnaires to normal subjects. Any subject reporting a history of injury or surgery to either knee, or preexisting knee pathologic changes, was excluded. From a total of 492 knees evaluated, 418 knees (253 male, 165 female) qualified for statistical analysis. The average age of the group was 17.6 years (range, 13 to 25). For male subjects, the total Noyes and Lysholm scores averaged 99.10 (range, 68 to 100) and 99.10 (range, 77 to 100), respectively. For female subjects, the average Noyes and Lysholm scores were 97.82 (range, 72 to 100) and 97.16 (range, 75 to 100), respectively. The 95% confidence interval computed for each of these groups did not contain the maximal value of 100. The female athletes reported significantly lower total scores than the male athletes on both questionnaires. For the Lysholm questionnaire, the male athletes scored significantly lower than the maximum in all categories except support and stair climbing, and the female athletes scored significantly lower than the maximum in all categories except limp and thigh atrophy. The range of scores found in this highly selected, “normal” population exemplifies the need for more accurate instruments in the evaluation of knee surgical outcomes.


1983 ◽  
Vol 3 (8) ◽  
pp. 1389-1402 ◽  
Author(s):  
K T Jeang ◽  
G S Hayward

A single 880-base-pair region within the genome of simian cytomegalovirus strain Colburn contains sequences that hybridize intensely with both human and mouse total genome DNA probes. This sequence was also found in a second simian cytomegalovirus isolate and was retained in both plaque-purified virus subclones and in plasmid DNA clones containing the SalI P fragment. Cleaved genomic DNAs from several mammalian species all exhibited strong dispersed hybridization with the SalI-P probes, and over 70% of the lambda clones in a mouse genomic library plus several selected clones containing globin, 45S rDNA, or 5S rDNA genes all formed hybrids with SalI-P. The appropriate region of cytomegalovirus SalI-P contains relatively A + T-rich unique sequences interrupted by three stretches of the simple alternating dinucleotides, (CA)15, (CA)22, and (CA)21, which we show to be responsible for most of the cell-virus homology. We conclude that discrete, tandemly repeated (CA) dinucleotide tracts capable of forming left-handed Z-DNA helices punctuate mammalian genomes at greater than 10(5) copies per cell and that three adjacent copies of what appear to be a family of interspersed repetitive elements containing these (CA)n stretches are carried in the genomes of simian cytomegaloviruses.


2019 ◽  
Vol 15 (1) ◽  
pp. 53-70
Author(s):  
Lailla Hidayatul Amin

This study aims to reveal the influence of teachers' perceptions of school leadership and academic qualifications of teachers on teacher performance SDIT Ulul Albab 1 and 2 Purworejo. The approach used in this study is the quantitative approach. The research sample is determined by the formula nomogram Herry King. A population of 58 people with 95% confidence interval, are used to determine 56 people. Based on the results of the descriptive statistical analysis of the variables of school leadership gained a mean of 3.1379, academic qualifications obtained by mean of 2.4483 and teacher performance obtained by mean of 3.8276. There is a positive and significant impact of school leadership on teacher performance of 5.5%. There are no significant negative influence and academic qualifications of teachers on teacher performance of (-) 2.1%. There is the influence of positive and significant impact of school leadership and teachers' academic qualifications together on teacher performance by 0.4%.


1983 ◽  
Vol 3 (8) ◽  
pp. 1389-1402
Author(s):  
K T Jeang ◽  
G S Hayward

A single 880-base-pair region within the genome of simian cytomegalovirus strain Colburn contains sequences that hybridize intensely with both human and mouse total genome DNA probes. This sequence was also found in a second simian cytomegalovirus isolate and was retained in both plaque-purified virus subclones and in plasmid DNA clones containing the SalI P fragment. Cleaved genomic DNAs from several mammalian species all exhibited strong dispersed hybridization with the SalI-P probes, and over 70% of the lambda clones in a mouse genomic library plus several selected clones containing globin, 45S rDNA, or 5S rDNA genes all formed hybrids with SalI-P. The appropriate region of cytomegalovirus SalI-P contains relatively A + T-rich unique sequences interrupted by three stretches of the simple alternating dinucleotides, (CA)15, (CA)22, and (CA)21, which we show to be responsible for most of the cell-virus homology. We conclude that discrete, tandemly repeated (CA) dinucleotide tracts capable of forming left-handed Z-DNA helices punctuate mammalian genomes at greater than 10(5) copies per cell and that three adjacent copies of what appear to be a family of interspersed repetitive elements containing these (CA)n stretches are carried in the genomes of simian cytomegaloviruses.


PEDIATRICS ◽  
1987 ◽  
Vol 79 (3) ◽  
pp. 487-487
Author(s):  
JOSEPH OREN ◽  
DOROTHY H. KELLY ◽  
DANIEL C. SHANNON

In Reply.— Dr Cummins' letter raises two questions regarding the statistical analysis in our report and we forward the following explanations. First, we agree that the Fisher exact test is superior to the χ2 statistic in analyzing associations between small subgroups. However, as we have already shown, in response to Dr Leblanc's letter (Pediatrics 1986;78:957), the results of the Fisher exact test are in good agreement with the published values using χ2 analysis. Second, in Figs 1 and 2 the ordinate depicts the 95% confidence interval of the relative risk and not the relative risk per se.


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