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1.  Validity of visual inspection of diagnostic peritoneal lavage fluid 
Canadian Journal of Surgery  1996;39(2):114-119.
To determine the positive and negative predictive values of visual inspection of peritoneal lavage fluid and the threshold concentration of erythrocytes for diagnosing significant hemoperitoneum by this method.
Nineteen residents in surgery and 21 staff surgeons were asked to inspect mock peritoneal lavage fluid and state whether they would proceed with urgent laparotomy.
Main Results
The overall positive and negative predictive values for visual inspection were 52.0% and 98.9%, respectively. The threshold for diagnosing significant hemoperitoneum by visual inspection was between 10 000 and 20 000 erythrocytes/mL for most subjects. There were no significant differences between residents and staff surgeons.
Visual inspection of peritoneal lavage fluid has good negative but poor positive predictive value, and the threshold for diagnosing significant hemoperitoneum by visual inspection is less than 100 000 erythrocytes/mL. Therefore, patients whose condition is stable and for whom visual inspection of lavage fluid indicates apparently significant hemoperitoneum should not undergo laparotomy without confirmation by laboratory testing.
PMCID: PMC3949848  PMID: 8769921
2.  Vaccine Storage Practices and the Effects of Education in Some Private Medical Institutions 
Although vaccination rates have increased, problems still remain in the storage and handling of vaccines. This study focused on inspecting actual vaccine storage status and awareness, and comparing them before and after education was provided.
In the primary inspection, a status survey checklist was completed by visual inspection. A questionnaire on the awareness of proper vaccine storage and handling was also administered to vaccine administrators in private medical institutions in 4 regions in Gyeongsangbuk-province. One-on-one education was then carried out, and our self-produced manual on safe vaccine storage and management methods was provided. In the secondary inspection, the investigators visited the same medical institutions and used the same questionnaire and checklist used during the primary inspection. The results before and after education were compared, by treating each appropriate answer as 1 point.
The average checklists score was 9.74 (out of 15 points), which increased significantly after education was provided (by 0.84, p<0.001). The participants demonstrated improved practices in recording storage temperatures (p=0.016), storing vaccines in the center of the refrigerator (p=0.004), storing vaccines with other medication and non-medical items (p=0.031) after education. The average score calculated from the questionnaires was 10.48 (out of 14 points), which increased after education (by 1.03, p<0.001).
This study suggests that vaccine storage practices and awareness are inadequate, but can be partially improved by providing relevant education. Repetitive education and policy-making are required to store vaccines safely because one-off education and unenforced guidelines offer limited efficacy.
PMCID: PMC3324719  PMID: 22509448
Awareness; Checklist; Education; Questionnaires; Vaccines
3.  Online Fabric Defect Inspection Using Smart Visual Sensors 
Sensors (Basel, Switzerland)  2013;13(4):4659-4673.
Fabric defect inspection is necessary and essential for quality control in the textile industry. Traditionally, fabric inspection to assure textile quality is done by humans, however, in the past years, researchers have paid attention to PC-based automatic inspection systems to improve the detection efficiency. This paper proposes a novel automatic inspection scheme for the warp knitting machine using smart visual sensors. The proposed system consists of multiple smart visual sensors and a controller. Each sensor can scan 800 mm width of web, and can work independently. The following are considered in dealing with broken-end defects caused by a single yarn: first, a smart visual sensor is composed of a powerful DSP processor and a 2-megapixel high definition image sensor. Second, a wavelet transform is used to decompose fabric images, and an improved direct thresholding method based on high frequency coefficients is proposed. Third, a proper template is chosen in a mathematical morphology filter to remove noise. Fourth, a defect detection algorithm is optimized to meet real-time demands. The proposed scheme has been running for six months on a warp knitting machine in a textile factory. The actual operation shows that the system is effective, and its detection rate reaches 98%.
PMCID: PMC3673105  PMID: 23571669
machine vision; fabric defect inspection; smart visual sensor; wavelet transform; mathematical morphology filter
4.  Real-Time Rotation Estimation Using Histograms of Oriented Gradients 
PLoS ONE  2014;9(3):e92137.
This paper focuses on real-time rotation estimation for model-based automated visual inspection. In the case of model-based inspection, spatial alignment is essential to distinguish visual defects from normal appearance variations. Defects are detected by comparing the inspected object with its spatially aligned ideal reference model. Rotation estimation is crucial for the inspection of rotationally symmetric objects where mechanical manipulation is unable to ensure the correct object rotation. We propose a novel method for in-plane rotation estimation. Rotation is estimated with an ensemble of nearest-neighbor estimators. Each estimator contains a spatially local representation of an object in a feature space for all rotation angles and is constructed with a semi-supervised self-training approach from a set of unlabeled training images. An individual representation in a feature space is obtained by calculating the Histograms of Oriented Gradients (HOG) over a spatially local region. Each estimator votes separately for the estimated angle; all votes are weighted and accumulated. The final estimation is the angle with the most votes. The method was evaluated on several datasets of pharmaceutical tablets varying in size, shape, and color. The results show that the proposed method is superior in robustness with comparable speed and accuracy to previously proposed methods for rotation estimation of pharmaceutical tablets. Furthermore, all evaluations were performed with the same set of parameters, which implies that the method requires minimal human intervention. Despite the evaluation focused on pharmaceutical tablets, we consider the method useful for any application that requires robust real-time in-plane rotation estimation.
PMCID: PMC3963882  PMID: 24662954
5.  Prerelease intent predicts smoking behavior postrelease following a prison smoking ban 
Nicotine & Tobacco Research  2009;12(2):152-158.
More than 2 million persons are incarcerated in the United States. Most are young minority men, soon to reenter the community. The majority are also lifelong smokers with high rates of health-related problems. As prisons implement smoking bans, it is not known whether health behavior change that is mandated, rather than selected, can be maintained. The Wisconsin Department of Corrections smoking ban is a unique opportunity to investigate determinants of smoking behavior after release from prison.
A convenience sample of 49 incarcerated men near release participated in two interviews (1-month prerelease, in prison, and 1-month postrelease via telephone). Descriptive analyses and multivariate modeling were conducted to determine associations with postrelease smoking.
Participants had a mean age of 36.7 years, 12.4 years of education, and a 2.3-year incarceration; 47% were Black and 41% White. They had smoked 14.5 years. Most (67%) believed that their health was improved after the smoking ban. Paired t tests revealed decreases in Positive and Negative Affect Scale negative affect (p = .001) and Patient Health Questionnaire-8 depression (p = .009) postrelease. Univariate analysis showed correlations of intent to smoke upon release with smoking relapse postrelease (p = .001), White race with smoking relapse postrelease (p = .045), and perceived better health since the prison smoking ban with nonsmoking on release (p = .01). There was a trend toward use of alcohol with smoking relapse on release (p = .061).
Prerelease smoking intention predicted postrelease behavior. Belief in improved health after the prison smoking ban correlated with nonsmoking on release. Targeted relapse prevention interventions are needed for people reentering the community.
PMCID: PMC2902915  PMID: 20038510
6.  The Use of Spinning-Disk Confocal Microscopy for the Intravital Analysis of Platelet Dynamics in Response to Systemic and Local Inflammation 
PLoS ONE  2011;6(9):e25109.
Platelets are central players in inflammation and are an important component of the innate immune response. The ability to visualize platelets within the live host is essential to understanding their role in these processes. Past approaches have involved adoptive transfer of labelled platelets, non-specific dyes, or the use of fluorescent antibodies to tag platelets in vivo. Often, these techniques result in either the activation of the platelet, or blockade of specific platelet receptors. In this report, we describe two new methods for intravital visualization of platelet biology, intravenous administration of labelled anti-CD49b, which labels all platelets, and CD41-YFP transgenic mice, in which a percentage of platelets express YFP. Both approaches label endogenous platelets and allow for their visualization using spinning-disk confocal fluorescent microscopy. Following LPS-induced inflammation, we were able to measure a significant increase in both the number and size of platelet aggregates observed within the vasculature of a number of different tissues. Real-time observation of these platelet aggregates reveals them to be large, dynamic structures that are continually expanding and sloughing-off into circulation. Using these techniques, we describe for the first time, platelet recruitment to, and behaviour within numerous tissues of the mouse, both under control conditions and following LPS induced inflammation.
PMCID: PMC3176312  PMID: 21949865
7.  Feasibility study for identifying adverse events attributable to vaccination by record linkage. 
Epidemiology and Infection  1995;114(3):475-480.
To investigate the feasibility of using a record linkage method for identifying vaccine attributable adverse events, computerized hospital admissions and vaccination records from South East Kent district were linked and checked for accuracy. Records for 90% of children under 2 years of age admitted to hospital over a 2-year period were matched with vaccination records using a computer algorithm based on name, date of birth, sex, and post-code supplemented by visual inspection. Relative to this gold standard, matching on date of birth, sex and postcode alone had a sensitivity of 60% and an incorrect match rate of 0.2% after matches to more than one vaccine recipient were excluded. Manual checking of a sample of admissions showed that only 4% had been assigned incorrect International Classification of Disease (ICD) codes. Routine record linkage of ICD admission codes to vaccination records therefore yields data of good quality which may be used for surveillance purposes.
PMCID: PMC2271302  PMID: 7781735
8.  Angiogenic factor-enriched platelet-rich plasma enhances in vivo bone formation around alloplastic graft material 
Although most researchers agree that platelet-rich plasma (PRP) is a good source of autogenous growth factors, its effect on bone regeneration is still controversial. The purpose of this study was to evaluate whether increasing angiogenic factors in the human PRP to enhance new bone formation through rapid angiogenesis.
In vitro, the human platelets were activated with application of shear stress, 20 µg/ml collagen, 2 mM CaCl2 and 10U thrombin/1 × 109 platelets. Level of vascular endothelial growth factor (VEGF) and platelet microparticle (PMP) in the activated platelets were checked. In the animal study, human angiogenic factors-enriched PRP was tested in 28 athymic rat's cranial critical bone defects with β-TCP. Angiogenesis and osteogenesis were evaluated by laser Doppler perfusion imaging, histology, dual energy X-ray densinometry, and micro-computed tomography.
In vitro, this human angiogenic factors-enriched PRP resulted in better cellular proliferation and osteogenic differentiation. In vivo, increasing angiogenic potential of the PRP showed significantly higher blood perfusion around the defect and enhanced new bone formation around acellular bone graft material.
Angiogenic factor-enriched PRP leads to faster and more extensive new bone formation in the critical size bone defect. The results implicate that rapid angiogenesis in the initial healing period by PRP could be supposed as a way to overcome short term effect of the rapid angiogenesis.
PMCID: PMC2984511  PMID: 21165181
Platelet-rich plasma; Angiogenesis; Human; Athymic rat; Cranial defect
9.  Platelet aggregation and quality control of platelet concentrates produced in the Amazon Blood Bank 
The study of platelet aggregation is essential to assess in vitro platelet function by different platelet activation pathways.
To assess aggregation and biochemical parameters of random platelet concentrates produced at the Fundação HEMOAM using the quality control tests defined by law.
Whole blood samples from 80 donors and the respective platelet concentrate units were tested. Platelet concentrates were tested (platelet count, aggregation and pH) on days 1, 3 and 5 of storage. Additionally a leukocyte count was done only on day 1 and microbiological tests on day 5 of storage. Collagen and adenosine diphosphate were used as inducing agonists for platelet aggregation testing.
Donor whole blood had normal aggregation (aggregation with adenosine diphosphate = 67% and with collagen = 78%). The median aggregation in platelet concentrates with adenosine diphosphate was low throughout storage (18% on day 1, 7% on day 3 and 6% on day 5) and the median aggregation with collagen was normal only on day 1 and low thereafter (54.4% on day 1, 20.5% on day 3 and 9% on day 5).
Although the results were within the norms required by law, platelet concentrates had low aggregation rates. We suggest the inclusion of a functional assessment test for the quality control of platelet concentrates for a more effective response to platelet replacement therapy.
PMCID: PMC3520634  PMID: 23284257
Hemostasis; Quality control; Collagen; Blood component transfusion; Blood banks; Platelet aggregation
10.  Accuracy of direct digital radiography for detecting occlusal caries in primary teeth compared with conventional radiography and visual inspection: an in vitro study 
Dentomaxillofacial Radiology  2010;39(6):362-367.
The diagnosis of caries lesions is still a matter of concern in dentistry. The diagnosis of dental caries by digital radiography has a number of advantages over conventional radiography; however, this method has not been explored fully in the field of paediatric dentistry. This in vitro research evaluated the accuracy of direct digital radiography compared with visual inspection and conventional radiography in the diagnosis of occlusal caries lesions in primary molars.
50 molars were selected and evaluated under standardized conditions by 2 previously calibrated examiners according to 3 diagnostic methods (visual inspection, conventional radiography and direct digital radiography). Direct digital radiographs were obtained with the Dixi3 system (Planmeca, Helsinki, Finland) and the conventional radiographs with InSight film (Kodak Eastman Co., Rochester, NY). The images were scored and a reference standard was obtained histologically. The interexaminer reliability was calculated using Cohen's kappa test and the specificity, sensitivity and accuracy of the methods were calculated.
Examiner reliability was good. For lesions limited to the enamel, visual inspection showed significantly higher sensitivity and accuracy than both radiographic methods, but no significant difference was found in specificity. For teeth with dentinal caries, no significant differences were found for any parameter when comparing visual and radiographic evaluation.
Although less accurate than the visual method for detecting caries lesions confined to the enamel, the direct digital radiographic method is as effective as conventional radiographic examination and visual inspection of primary teeth with occlusal caries when the dentine is involved.
PMCID: PMC3520238  PMID: 20729186
direct digital radiography; conventional radiography; dental caries; primary teeth
11.  Interaction of lipoteichoic acid of group A streptococci with human platelets. 
Infection and Immunity  1977;16(2):649-654.
The interaction of group A streptococcal lipoteichoic acid (LTA) with mammalian cell membranes was studied in human platelets. The binding of LTA to platelets was platelet concentration and time dependent. Binding approached a maximum within 10 min of incubation. The bound LTA could be displaced by adding a 50-fold excess of unlabeled LTA. An association constant of 1.9 X 10(-7) M was calculated, and only one population of binding sites was detected. Immuno-ferritin labeling of LTA-treated platelets demonstrated a patchy distribution of LTA binding sites on the platelet surface. LTA inhibited collagen- and alpha1 chain-induced platelet aggregation, but not the platelet release reaction, suggesting that the LTA and collagen binding sites on human platelets are distinct. Apparently, LTA binds to platelets and interferes with collagen-induced aggregation although collagen is still able to attach to binding sites to trigger the release reaction.
PMCID: PMC421005  PMID: 324916
12.  Platelet gel in the treatment of cutaneous ulcers: the experience of the Immunohaematology and Transfusion Centre of Parma 
Blood Transfusion  2010;8(4):237-247.
Platelet gel is being ever more frequently used to promote healing of cutaneous ulcers. However, the factors that determine the often variable clinical outcome of this procedure are still incompletely understood.
The aims of this study were to demonstrate that platelet gel, even when obtained under strictly controlled conditions, produces highly variable outcomes in patients with cutaneous ulcers and to propose a method for in vitro standardisation of the biological properties of platelet gel.
Material and methods.
Patients were enrolled on the basis of a pre-defined protocol. Platelet concentrate was produced with standard methods, with a variability in platelet count among the different samples of less than 10%. The platelet gel for clinical use was obtained, under strictly standardized conditions, by adding thrombin and calcium gluconate to the concentrates. For in vitro studies, platelet gel, obtained from platelet-rich plasma from four donors, was frozen and thawed twice so as to increase gel contraction. The supernatant was used to modify cell proliferation, protein synthesis, and the expression of selected genes in cultures of human diploid fibroblasts.
Seventeen patients (aged 44–78 years) with ulcers (4 diabetic, 11 vascular, 1 post-traumatic, 1 decubitus) were treated with platelet gel (4 autologous, 13 homologous). Complete re-epithelialisation of four ulcers (1 diabetic, 1 post-traumatic, 2 vascular) was obtained after applications of platelet gel (2 autologous, 2 homologous); in 11 other cases there was a greater than 50% reduction in the size of the ulcer. Two patients had no benefit. The supernatant of the platelet gel was able to promote dose-dependent proliferation and changes in gene expression as well as in metabolic activities related to protein synthesis.
Although the use of platelet gel in the treatment of cutaneous ulcers is increasing, and conditions for its production are better standardised, very considerable variability of clinical outcomes is still observed, even within single centres, suggesting that there are differences in biological properties of platelet concentrates from individual patients which cannot be readily controlled with current techniques. The biological effects of the platelet gel supernatant described in this article may provide the basis for a simple biological validation of platelet preparations before their clinical use, so as to reduce this potentially important source of variability.
PMCID: PMC2957488  PMID: 20967164
platelet gel; fibroblasts; ulcers; cell proliferation
13.  GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes 
BMC Bioinformatics  2014;15:12.
Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required.
In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions.
Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at
PMCID: PMC3897944  PMID: 24423161
Molecular recognition; Ligand binding site; Protein–ligand interactions; Protein structure; Protein function; Pattern recognition; Database; Web-server
14.  Endotracheal tube defects: Hidden causes of airway obstruction 
Saudi Journal of Anaesthesia  2010;4(2):108-110.
Manufacturing defects of endotracheal tube (ETT) are still encountered in anesthesia practice. Many such defects go unnoticed during routine inspection prior to their use. Such defects in ETT may lead to partial or complete airway obstruction in an intubated patient. We report a case of partial airway obstruction with a prepacked, single use, uncuffed ETT due to a manufacturing defect in the form of a plastic meniscus at the distal end of the tube. This case report highlights the significance of standard monitoring of ventilation and the role of a vigilant clinician in detecting such defects in avoiding critical events as can arise from the use of such defective ETTs. It also emphasizes the need for double checking ETTs prior to their use.
PMCID: PMC2945507  PMID: 20927272
Endotracheal tube; ventilation; monitoring; intubation
15.  Data management for prospective research studies using SAS® software 
Maintaining data quality and integrity is important for research studies involving prospective data collection. Data must be entered, erroneous or missing data must be identified and corrected if possible, and an audit trail created.
Using as an example a large prospective study, the Missouri Lower Respiratory Infection (LRI) Project, we present an approach to data management predominantly using SAS software. The Missouri LRI Project was a prospective cohort study of nursing home residents who developed an LRI. Subjects were enrolled, data collected, and follow-ups occurred for over three years. Data were collected on twenty different forms. Forms were inspected visually and sent off-site for data entry. SAS software was used to read the entered data files, check for potential errors, apply corrections to data sets, and combine batches into analytic data sets. The data management procedures are described.
Study data collection resulted in over 20,000 completed forms. Data management was successful, resulting in clean, internally consistent data sets for analysis. The amount of time required for data management was substantially underestimated.
Data management for prospective studies should be planned well in advance of data collection. An ongoing process with data entered and checked as they become available allows timely recovery of errors and missing data.
PMCID: PMC2546431  PMID: 18786262
16.  Unreliable Detection of Mycobacterium xenopi by the Nonradiometric Bactec MGIT 960 Culture System▿  
Journal of Clinical Microbiology  2009;47(3):804-806.
From June 2006 to December 2007, 3,648 clinical specimens consecutively received for mycobacterial culture were investigated. Each processed sample was inoculated into Bactec MGIT 960 liquid medium and a Löwenstein-Jensen slant. Tubes that were flagged as positive by the instrument as well as those determined to be negative after 42 days of incubation were removed, visually inspected for growth, and checked for the presence of acid-fast bacilli. Three hundred sixty-nine mycobacterial strains were recovered; of the 44 Mycobacterium xenopi isolates recovered by MGIT medium, only 13 were detected by the instrument (P < 0.0001). Most tubes yielding M. xenopi exhibited a peculiar pattern of growth characterized by a scant number of round, yellow-pigmented granules instead of the fine, evenly dispersed clumps usually observed for mycobacteria. It is suggested to check all individual tubes discarded by the MGIT 960 system at the end of the incubation period to prevent a significant amount of previously undetected growth from being missed.
PMCID: PMC2650918  PMID: 19144802
17.  Hydroxyl Radical Modification of Collagen Type II Increases Its Arthritogenicity and Immunogenicity 
PLoS ONE  2012;7(2):e31199.
The oxidation of proteins by endogenously generated free radicals causes structural modifications in the molecules that lead to generation of neo-antigenic epitopes that have implications in various autoimmune disorders, including rheumatoid arthritis (RA). Collagen induced arthritis (CIA) in rodents (rats and mice) is an accepted experimental model for RA.
Methodology/Principal Findings
Hydroxyl radicals were generated by the Fenton reaction. Collagen type II (CII) was modified by •OH radical (CII-OH) and analysed by ultraviolet-visible (UV-VIS), fluorescence and circular dichroism (CD) spectroscopy. The immunogenicity of native and modified CII was checked in female Lewis rats and specificity of the induced antibodies was ascertained by enzyme linked immunosorbent assay (ELISA). The extent of CIA was evaluated by visual inspection. We also estimated the oxidative and inflammatory markers in the sera of immunized rats. A slight change in the triple helical structure of CII as well as fragmentation was observed after hydroxyl radical modification. The modified CII was found to be highly arthritogenic and immunogenic as compared to the native form. The CII-OH immunized rats exhibited increased oxidative stress and inflammation as compared to the CII immunized rats in the control group.
Neo-antigenic epitopes were generated on •OH modified CII which rendered it highly immunogenic and arthritogenic as compared to the unmodified form. Since the rodent CIA model shares many features with human RA, these results illuminate the role of free radicals in human RA.
PMCID: PMC3272010  PMID: 22319617
18.  Quantifying Morphological Parameters of the Terminal Branching Units in a Mouse Lung by Phase Contrast Synchrotron Radiation Computed Tomography 
PLoS ONE  2013;8(5):e63552.
An effective technique of phase contrast synchrotron radiation computed tomography was established for the quantitative analysis of the microstructures in the respiratory zone of a mouse lung. Heitzman’s method was adopted for the whole-lung sample preparation, and Canny’s edge detector was used for locating the air-tissue boundaries. This technique revealed detailed morphology of the respiratory zone components, including terminal bronchioles and alveolar sacs, with sufficiently high resolution of 1.74 µm isotropic voxel size. The technique enabled visual inspection of the respiratory zone components and comprehension of their relative positions in three dimensions. To check the method’s feasibility for quantitative imaging, morphological parameters such as diameter, surface area and volume were measured and analyzed for sixteen randomly selected terminal branching units, each consisting of a terminal bronchiole and a pair of succeeding alveolar sacs. The four types of asymmetry ratios concerning alveolar sac mouth diameter, alveolar sac surface area, and alveolar sac volume are measured. This is the first ever finding of the asymmetry ratio for the terminal bronchioles and alveolar sacs, and it is noteworthy that an appreciable degree of branching asymmetry was observed among the alveolar sacs at the terminal end of the airway tree, despite the number of samples was small yet. The series of efficient techniques developed and confirmed in this study, from sample preparation to quantification, is expected to contribute to a wider and exacter application of phase contrast synchrotron radiation computed tomography to a variety of studies.
PMCID: PMC3660418  PMID: 23704918
19.  Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software 
Croatian Medical Journal  2014;55(2):115-120.
To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors.
We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; by means of two mtDNA data sets that were submitted for quality control.
The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data.
Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables.
PMCID: PMC4020147  PMID: 24778097
20.  Relative moldiness index as predictor of childhood respiratory illness 
The results of a traditional visual mold inspection were compared to a mold evaluation based on the Relative Moldiness Index (RMI). The RMI is calculated from mold-specific quantitative PCR (MSQPCR) measurements of the concentration of 36 species of molds in floor dust samples. These two prospective mold evaluations were used to classify the mold condition in 271 homes of infants. Later, the development of respiratory illness was measured in the infants living in these homes and the predictive value of each classification system was evaluated.
The binary classification of homes as either moldy or non-moldy by on-site visual home inspection was not predictive of the development of respiratory illness (wheeze and/or rhinitis) (P = 0.27). Conversely, a method developed and validated in this paper, using the RMI index fit to a logistic function, can be used to predict the occurrence of illness in homes and allows stake-holders the choice among various levels of risk.
PMCID: PMC2233948  PMID: 17033680
mold-specific quantitative PCR; mold; infants; wheezing; relative moldiness index
21.  Assessment of Riboflavin as a Tracer Substance: Comparison of a Qualitative to a Quantitative Method of Riboflavin Measurement 
Drug and alcohol dependence  2012;128(1-2):77-82.
Noncompliance with medications may have major impacts on outcomes measured in research, potentially distorting the validity of controlled clinical trials. Riboflavin is frequently used in trials as a marker of adherence. It can be combined with study medication and is excreted in urine where it fluoresces under UV light. This study compares qualitative visual inspection of fluorescence to quantitative fluorometric analysis of riboflavin concentration in its ability to detect the presence of riboflavin in urine.
Twenty-four volunteers received 0 mg, 25 mg, and 50 mg doses of riboflavin under single-blind conditions, with 20 also receiving a 100 mg dose. Five serial urine samples were collected over the following 36 hours. Quantitative measurement of riboflavin by fluorometric analysis and qualitative assessment of each sample using visual inspection were performed.
The overall false positive rate for qualitative assessment was 53%. For quantitative assessment, a riboflavin concentration of 900 ng/mL was established to classify positive samples. More than 80% of samples were positive 2 to 24 hours following ingestion of 25 mg and 50 mg, and less than 80% were positive at 36 hours. At least 95% of observations for the 100 mg dose were above 900 ng/mL at all timepoints.
Quantitative fluorometric assessment is superior to qualitative visual inspection alone in determining medication adherence. The combination of 25–50 mg of daily riboflavin and a cut-off level of 900 ng/mL allows for the acceptable sensitivity of missing detection of non-compliant participants while preserving a high level of power to detect all cases of medication compliance.
PMCID: PMC3556739  PMID: 22921475
adherence; quantitative; qualitative; riboflavin; tracer
22.  “Flow valve” microfluidic devices for simple, detectorless and label-free analyte quantitation 
Analytical chemistry  2012;84(16):7057-7063.
Simplified analysis systems that offer the performance of benchtop instruments but the convenience of portability are highly desirable. We have developed novel, miniature devices that feature visual inspection readout of a target’s concentration from a ~1 μL volume of solution introduced into a microfluidic channel. Microchannels are constructed within an elastomeric material, and channel surfaces are coated with receptors to the target. When a solution is flowed into the channel, the target crosslinks multiple receptors on the surface, resulting in constriction of the first few millimeters of the channel and stopping of flow. Quantitation is performed by measuring the distance traveled by the target solution in the channel before flow stops. A key advantage of our approach is that quantitation is accomplished by simple visual inspection of the channel, without the need for complex detection instrumentation. We have tested these devices using the model system of biotin as a receptor and streptavidin as the target. We have also characterized three factors that influence flow distance: solution viscosity, device thickness, and channel height. We found that solution capillary flow distance scales with the negative logarithm of target concentration and have detected streptavidin concentrations as low as 1 ng/mL. Finally, we have identified and evaluated a plausible mechanism wherein time-dependent channel constriction in the first few millimeters leads to concentration-dependent flow distances. Their simplicity coupled with performance makes these “flow valve” systems especially attractive for a host of analysis applications.
PMCID: PMC3426352  PMID: 22881075
23.  Differential Proteomic Analysis of Platelets Suggested Possible Signal Cascades Network in Platelets Treated with Salvianolic Acid B 
PLoS ONE  2011;6(2):e14692.
Salvianolic acid B (SB) is an active component isolated from Danshen, a traditional Chinese medicine widely used for the treatment of cardiovascular disorders. Previous study suggested that SB might inhibit adhesion as well as aggregation of platelets by a mechanism involving the integrin α2β1. But, the signal cascades in platelets after SB binding are still not clear.
Methodology/Principal Findings
In the present study, a differential proteomic analysis (two-dimensional electrophoresis) was conducted to check the protein expression profiles of rat platelets with or without treatment of SB. Proteins altered in level after SB exposure were identified by MALDI-TOF MS/MS. Treatment of SB caused regulation of 20 proteins such as heat shock-related 70 kDa protein 2 (hsp70), LIM domain protein CLP-36, copine I, peroxiredoxin-2, coronin-1 B and cytoplasmic dynein intermediate chain 2C. The regulation of SB on protein levels was confirmed by Western blotting. The signal cascades network induced by SB after its binding with integrin α2β1 was predicted. To certify the predicted network, binding affinity of SB to integrin α2β1 was checked in vitro and ex vivo in platelets. Furthermore, the effects of SB on protein levels of hsp70, coronin-1B and intracellular levels of Ca(2+) and reactive oxygen species (ROS) were checked with or without pre-treatment of platelets using antibody against integrin α2β1. Electron microscopy study confirmed that SB affected cytoskeleton structure of platelets.
Integrin α2β1 might be one of the direct target proteins of SB in platelets. The signal cascades network of SB after binding with integrin α2β1 might include regulation of intracellular Ca(2+) level, cytoskeleton-related proteins such as coronin-1B and cytoskeleton structure of platelets.
PMCID: PMC3040754  PMID: 21379382
24.  Transparency in Nigeria's public pharmaceutical sector: perceptions from policy makers 
Pharmaceuticals are an integral component of health care systems worldwide, thus, regulatory weaknesses in governance of the pharmaceutical system negatively impact health outcomes especially in developing countries [1]. Nigeria is one of a number of countries whose pharmaceutical system has been impacted by corruption and has struggled to curtail the production and trafficking of substandard drugs. In 2001, the National Agency for Food and Drug Administration and Control (NAFDAC) underwent an organizational restructuring resulting in reforms to reduce counterfeit drugs and better regulate pharmaceuticals [2]. Despite these changes, there is still room for improvement. This study assessed the perceived level of transparency and potential vulnerability to corruption that exists in four essential areas of Nigeria's pharmaceutical sector: registration, procurement, inspection (divided into inspection of ports and of establishments), and distribution.
Standardized questionnaires were adapted from the World Health Organization assessment tool and used in semi-structured interviews with key stakeholders in the public and private pharmaceutical system. The responses to the questions were tallied and converted to scores on a numerical scale where lower scores suggested greater vulnerability to corruption and higher scores suggested lower vulnerability.
The overall score for Nigeria's pharmaceutical system was 7.4 out of 10, indicating a system that is marginally vulnerable to corruption. The weakest links were the areas of drug registration and inspection of ports. Analysis of the qualitative results revealed that the perceived level of corruption did not always match the qualitative evidence.
Despite the many reported reforms instituted by NAFDAC, the study findings suggest that facets of the pharmaceutical system in Nigeria remain fairly vulnerable to corruption. The most glaring deficiency seems to be the absence of conflict of interest guidelines which, if present and consistently administered, limit the promulgation of corrupt practices. Other major contributing factors are the inconsistency in documentation of procedures, lack of public availability of such documentation, and inadequacies in monitoring and evaluation. What is most critical from this study is the identification of areas that still remain permeable to corruption and, perhaps, where more appropriate checks and balances are needed from the Nigerian government and the international community.
PMCID: PMC2775729  PMID: 19874613
25.  Platelet lipidomics: a modern day perspective on lipid discovery and characterization in platelets 
Circulation research  2014;114(7):1185-1203.
Lipids are diverse families of biomolecules that perform essential structural and signaling roles in platelets. Their formation and metabolism is tightly controlled by enzymes and signal transduction pathways, and their dysregulation leads to significant defects in platelet function and disease. Platelet activation is associated with significant changes to membrane lipids, and formation of diverse bioactive lipids that play essential roles in hemostasis. In recent years, new generation mass spectrometry analysis of lipids (termed “lipidomics”) has begun to alter our understanding of how these molecules participate in key cellular processes. While, the application of lipidomics to platelet biology is still in its infancy, seminal earlier studies have shaped our knowledge of how lipids regulate key aspects of platelet biology, including aggregation, shape change, coagulation and degranulation, as well as how lipids generated by platelets influence other cells, such as leukocytes and the vascular wall, and thus how they regulate hemostasis, vascular integrity and inflammation, as well as contribute to pathologies including arterial/deep vein thrombosis and atherosclerosis. This review will provide a brief historical perspective on the characterization of lipids in platelets, then an overview of the new generation lipidomic approaches, their recent application to platelet biology, and future perspectives for research in this area. The major platelet-regulatory lipid families, their formation, metabolism, and their role in health and disease, will be summarized.
PMCID: PMC4021279  PMID: 24677238
Platelets; Lipidomics; Mass spectrometry

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