Performance of an automated multiplex immunofluorescence assay for detection of Chlamydia trachomatis immunoglobulin G.

Chlamydia serology is indicated to investigate etiology of miscarriage, infertility, pelvic inflammatory disease, and ectopic pregnancy. Here, we assessed the reliability of a new automated-multiplex immunofluorescence assay (InoDiag test) to detect specific anti-C. trachomatis immunoglobulin G. Considering immunofluorescence assay (IF) as gold standard, InoDiag tests exhibited similar sensitivities (65.5%) but better specificities (95.1%-98%) than enzyme-linked immunosorbent assays (ELISAs). InoDiag tests demonstrated similar or lower cross-reactivity rates when compared to ELISA or IF.

Discordant prevalence of hypertension using two different automated blood pressure measurement devices: a population-based study in Dar es Salaam (Tanzania).

OBJECTIVE: The estimation of blood pressure is dependent on the accuracy of the measurement devices. We compared blood pressure readings obtained with an automated oscillometric arm-cuff device and with an automated oscillometric wrist-cuff device and then assessed the prevalence of defined blood pressure categories. METHODS: Within a population-based survey in Dar es Salaam (Tanzania), we selected all participants with a blood pressure >/= 160/95 mmHg (n=653) and a random sample of participants with blood pressure <160/95 mmHg (n=662), based on the first blood pressure reading. Blood pressure was reassessed 2 years later for 464 and 410 of the participants, respectively. In these 874 subjects, we compared the prevalence of blood pressure categories as estimated with each device. RESULTS: Overall, the wrist device gave higher blood pressure readings than the arm device (difference in systolic/diastolic blood pressure: 6.3 +/- 17.3/3.7 +/- 11.8 mmHg, P<0.001). However, the arm device tended to give lower readings than the wrist device for high blood pressure values. The prevalence of blood pressure categories differed substantially depending on which device was used, 29% and 14% for blood pressure <120/80 mmHg (arm device versus wrist device, respectively), 30% and 33% for blood pressure 120-139/80-89 mmHg, 17% and 26% for blood pressure 140-159/90-99 mmHg, 12% and 13% for blood pressure 160-179/100-109 mmHg and 13% and 14% for blood pressure >/= 180/110 mmHg. CONCLUSIONS: A large discrepancy in the estimated prevalence of blood pressure categories was observed using two different automatic measurement devices. This emphasizes that prevalence estimates based on automatic devices should be considered with caution.

Automated DNA extraction using the QIAsymphony platform: Estimation of DNA recovery from simulated forensic stains

The aim of this study was to evaluate the forensic protocol recently developed by Qiagen for the QIAsymphony automated DNA extraction platform. Samples containing low amounts of DNA were specifically considered, since they represent the majority of samples processed in our laboratory. The analysis of simulated blood and saliva traces showed that the highest DNA yields were obtained with the maximal elution volume available for the forensic protocol, that is 200 ml. Resulting DNA extracts were too diluted for successful DNA profiling and required a concentration. This additional step is time consuming and potentially increases inversion and contamination risks. The 200 ml DNA extracts were concentrated to 25 ml, and the DNA recovery estimated with real-time PCR as well as with the percentage of SGM Plus alleles detected. Results using our manual protocol, based on the QIAamp DNA mini kit, and the automated protocol were comparable. Further tests will be conducted to determine more precisely DNA recovery, contamination risk and PCR inhibitors removal, once a definitive procedure, allowing the concentration of DNA extracts from low yield samples, will be available for the QIAsymphony.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

A fully automated hot-wall multiplasma-monochamber reactor for thin film deposition

We present a study on the development and the evaluation of a fully automated radio-frequency glow discharge system devoted to the deposition of amorphous thin film semiconductors and insulators. The following aspects were carefully addressed in the design of the reactor: (1) cross contamination by dopants and unstable gases, (2) capability of a fully automated operation, (3) precise control of the discharge parameters, particularly the substrate temperature, and (4) high chemical purity. The new reactor, named ARCAM, is a multiplasma-monochamber system consisting of three separated plasma chambers located inside the same isothermal vacuum vessel. Thus, the system benefits from the advantages of multichamber systems but keeps the simplicity and low cost of monochamber systems. The evaluation of the reactor performances showed that the oven-like structure combined with a differential dynamic pumping provides a high chemical purity in the deposition chamber. Moreover, the studies of the effects associated with the plasma recycling of material from the walls and of the thermal decomposition of diborane showed that the multiplasma-monochamber design is efficient for the production of abrupt interfaces in hydrogenated amorphous silicon (a-Si:H) based devices. Also, special attention was paid to the optimization of plasma conditions for the deposition of low density of states a-Si:H. Hence, we also present the results concerning the effects of the geometry, the substrate temperature, the radio frequency power and the silane pressure on the properties of the a-Si:H films. In particular, we found that a low density of states a-Si:H can be deposited at a wide range of substrate temperatures (100°C

Corticosterone promotes scramble competition over sibling negotiation in Barn Owl nestlings (Tyto alba)

In species with parental care, siblings compete for access to food resources. Typically, they vocally signal their level of need to each other and to parents, and jostle for the position in the nest where parents deliver food. Although food shortage and social interactions are stressful, little is known about the effect of stress on the way siblings resolve the conflict over how food is shared among them. Because glucocorticoid hormones mediate physiological and behavioral responses to stressors, we tested whether corticosterone, the main glucocorticoid in birds, modulates physical and vocal signaling used by barn owl siblings (Tyto alba) to compete for food. Although corticosterone-implanted (cort-) nestlings and placebo-nestlings were similarly successful to monopolize food, they employed different behavioral strategies. Compared to placebo-nestlings, cort-individuals reduced the rate of vocally communicating with their siblings (but not with their parents) but were positioned closer to the nest-box entrance where parents predictably deliver food. Therefore, corticosterone induced nestlings to increase their effort in physical competition for the best nest position at the expense of investment in sib-sib communication without modifying vocal begging signals directed to parents. This suggests that in the barn owl stress alters nestlings' behavior and corticosterone could mediate the trade-off between scramble competition and vocal sib-sib communication. We conclude that stressful environments may prevent the evolution of sib-sib communication as a way to resolve family conflicts peacefully.

Automated Recording of Bridge Inspection Data in the Pontis Format Final Report, HR-364 April 1995

A large percentage of bridges in the state of Iowa are classified as structurally or fiinctionally deficient. These bridges annually compete for a share of Iowa's limited transportation budget. To avoid an increase in the number of deficient bridges, the state of Iowa decided to implement a comprehensive Bridge Management System (BMS) and selected the Pontis BMS software as a bridge management tool. This program will be used to provide a selection of maintenance, repair, and replacement strategies for the bridge networks to achieve an efficient and possibly optimal allocation of resources. The Pontis BMS software uses a new rating system to evaluate extensive and detailed inspection data gathered for all bridge elements. To manually collect these data would be a highly time-consuming job. The objective of this work was to develop an automated-computerized methodology for an integrated data base that includes the rating conditions as defined in the Pontis program. Several of the available techniques that can be used to capture inspection data were reviewed, and the most suitable method was selected. To accomplish the objectives of this work, two userfriendly programs were developed. One program is used in the field to collect inspection data following a step-by-step procedure without the need to refer to the Pontis user's manuals. The other program is used in the office to read the inspection data and prepare input files for the Pontis BMS software. These two programs require users to have very limited knowledge of computers. On-line help screens as well as options for preparing, viewing, and printing inspection reports are also available. The developed data collection software will improve and expedite the process of conducting bridge inspections and preparing the required input files for the Pontis program. In addition, it will eliminate the need for large storage areas and will simplify retrieval of inspection data. Furthermore, the approach developed herein will facilitate transferring these captured data electronically between offices within the Iowa DOT and across the state.

Seizure detection with automated EEG analysis: a validation study focusing on periodic patterns.

OBJECTIVE: To evaluate an automated seizure detection (ASD) algorithm in EEGs with periodic and other challenging patterns. METHODS: Selected EEGs recorded in patients over 1year old were classified into four groups: A. Periodic lateralized epileptiform discharges (PLEDs) with intermixed electrical seizures. B. PLEDs without seizures. C. Electrical seizures and no PLEDs. D. No PLEDs or seizures. Recordings were analyzed by the Persyst P12 software, and compared to the raw EEG, interpreted by two experienced neurophysiologists; Positive percent agreement (PPA) and false-positive rates/hour (FPR) were calculated. RESULTS: We assessed 98 recordings (Group A=21 patients; B=29, C=17, D=31). Total duration was 82.7h (median: 1h); containing 268 seizures. The software detected 204 (=76.1%) seizures; all ictal events were captured in 29/38 (76.3%) patients; in only in 3 (7.7%) no seizures were detected. Median PPA was 100% (range 0-100; interquartile range 50-100), and the median FPR 0/h (range 0-75.8; interquartile range 0-4.5); however, lower performances were seen in the groups containing periodic discharges. CONCLUSION: This analysis provides data regarding the yield of the ASD in a particularly difficult subset of EEG recordings, showing that periodic discharges may bias the results. SIGNIFICANCE: Ongoing refinements in this technique might enhance its utility and lead to a more extensive application.

Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library.

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.

Visualization Resources for Iowa State University and the Iowa DOT: An Automated Design Model to Simulator Converter, November 2012

This project developed an automatic conversion software tool that takes input a from an Iowa Department of Transportation (DOT) MicroStation three-dimensional (3D) design file and converts it into a form that can be used by the University of Iowa’s National Advanced Driving Simulator (NADS) MiniSim. Once imported into the simulator, the new roadway has the identical geometric design features as in the Iowa DOT design file. The base roadway appears as a wireframe in the simulator software. Through additional software tools, textures and shading can be applied to the roadway surface and surrounding terrain to produce the visual appearance of an actual road. This tool enables Iowa DOT engineers to work with the universities to create drivable versions of prospective roadway designs. By driving the designs in the simulator, problems can be identified early in the design process. The simulated drives can also be used for public outreach and human factors driving research.

Visualization Resources for Iowa State University and the Iowa DOT: An Automated Design Model to Simulator Converter, November 2012

The creation of three-dimensional (3D) drawings for proposed designs for construction, re-construction and rehabilitation activities are becoming increasingly common for highway designers, whether by department of transportation (DOT) employees or consulting engineers. However, technical challenges exist that prevent the use of these 3D drawings/models from being used as the basis of interactive simulation. Use of driving simulation to service the needs of the transportation industry in the US lags behind Europe due to several factors, including lack of technical infrastructure at DOTs, cost of maintaining and supporting simulation infrastructure—traditionally done by simulation domain experts—and cost and effort to translate DOT domain data into the simulation domain.

Visualization Resources for Iowa State University and the Iowa DOT: An Automated Design Model to Simulator Converter, November 2012

The creation of three-dimensional (3D) drawings for proposed designs for construction, re-construction and rehabilitation activities are becoming increasingly common for highway designers, whether by department of transportation (DOT) employees or consulting engineers. However, technical challenges exist that prevent the use of these 3D drawings/models from being used as the basis of interactive simulation. Use of driving simulation to service the needs of the transportation industry in the US lags behind Europe due to several factors, including lack of technical infrastructure at DOTs, cost of maintaining and supporting simulation infrastructure—traditionally done by simulation domain experts—and cost and effort to translate DOT domain data into the simulation domain.