Validation of the BIOCHIP test for the diagnosis of bullous pemphigoid, pemphigus vulgaris and pemphigus foliaceus.

BACKGROUND: The BIOCHIP is a novel multiplex indirect immunofluorescence technique used in the serological diagnosis of bullous pemphigoid and pemphigus. The BIOCHIP method combines the screening of autoantibodies and target antigen-specific substrates in a single miniature incubation field. OBJECTIVE: To evaluate the diagnostic accuracy of the new immunofluorescence BIOCHIP multiplex tool in pemphigus and bullous pemphigoid. METHODS: For the validation of the BIOCHIP, sera from patients with BP (n = 38), PF (n = 8) and pemphigus vulgaris (PV) (n = 23) were used. In addition, sera from disease control patients (n = 63) and healthy volunteers (n = 39) were used. The multiplex BIOCHIP and direct immunofluorescence (DIF) were performed for all BP, PF and PV patients. Additional indirect immunofluorescence (IIF) was performed on patients with BP, and ELISA was performed on patients with pemphigus. RESULTS: The BIOCHIP mosaic showed a sensitivity of 86.8% and specificity of 85% for BP180 or BP230 being positive in BP. It demonstrated a sensitivity of 75% and specificity of 97.7% for Dsg1 in PF. The BIOCHIP was found to have a sensitivity of 60.9% and specificity of 73.6% for Dsg3 in PV. CONCLUSION: The BIOCHIP mosaic-based immunofluorescence test is potentially a simple, time and effort saving test that can aid in the diagnosis and screening of BP, PV and PF. However, there is potential for interpretation bias and a learning curve that needs to be taken into consideration.

Inter-rater reliability of the BIOCHIP indirect immunofluorescence dermatology mosaic in bullous pemphigoid and pemphigus patients.

BACKGROUND: The BIOCHIP (Dermatology Mosaic 7; EUROIMMUN, Lubeck, Germany) is a novel multiplex indirect immunofluorescence (IIF) technique used in the serological diagnosis of bullous pemphigoid (BP) and pemphigus. OBJECTIVE: To validate the accuracy and inter-rater reliability (IRR) of the BIOCHIP in the diagnosis of BP, pemphigus foliaceus (PF) and pemphigus vulgaris (PV). METHODS: Sera from patients with BP (n = 38), PF (n = 8), PV (n = 23), control patients (n = 64) and healthy control volunteers (n = 39) were tested. Sera were collected and analysed during the course of the disease at 1-5 different time points. The BIOCHIP was performed for all patients, digital images were captured of each incubated field, and the images were shared with 10 dermatologists experienced in reading IF from around the world to report. There were 312 BIOCHIP slides consisting of 1872 photos in total. All patients were de-identified. Fleiss Kappa was used to estimate the IRR. RESULTS: Fleiss Kappa was computed for each category (Oesophagus, Oesophagus immunofluorescence pattern, Salt-Split Skin (SSS), SSS immunofluorescence location, BP180, BP230, Dsg 1 and Ds3). The inter-rater agreement between the 10 raters varied between fair and moderate for all categories. Those that demonstrated fair concordance included monkey oesophagus (k = 0.257, P < 0.0001), oesophagus pattern (k = 0.357, P < 0.0001), Dsg1 (k = 0.390, P < 0.0001) and BP230 (k = 0.281, P < 0.0001). Moderate agreement was demonstrated for SSS (k = 0.416, P < 0.0001), SSS immunofluorescence location (k = 0.505, P < 0.0001), Dsg3 (k = 0.437, P < 0.0001) and BP180 (k = 0.559, P < 0.0001). CONCLUSION: The BIOCHIP mosaic-based immunofluorescence test is a simple, time and effort saving test that can aid in the diagnosis and screening of BP, PV and PF. However, the level of agreement was relatively low. The authors found the most common causes to be variable levels of training, indicating the presence of a learning curve in the interpretation of the results and ambiguous staining patterns leading to incongruent results.

3D-QSAR pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation toward identifying lead compounds for NS2B-NS3 protease inhibitors.

NS2B-NS3 protease has been identified to serve as lead drug design target due to its significant role in West Nile viral (WNV) and dengue virus (DENV) reproduction and replication. There are currently no approved chemotherapeutic drugs and effective vaccines to inhibit DENV and WNV infections. In this work, 3D-QSAR pharmacophore model has been developed to discover potential inhibitory candidates. Validation through Fischer's model and decoy test indicate that the developed 3D pharmacophore model is highly predictive for DENV inhibitors, which was then employed to screen ZINC chemical library to obtain reasonable hits. Following ADMET filtering, 15 hits were subjected to further filter through molecular docking and CoMFA modeling. Finally, top three hits were identified as lead compounds or potential inhibitory candidates with IC50 values of ∼0.4637 µM and fitness of ∼57.73. It is implied from CoMFA modeling that substituents at the side site of benzotriazole such as a p-nitro group (e.g. biphenyl head) and a carbonyl (e.g. carboxylate function) at the side site of furan or amino group may improve bioactivity of ZINC85645245, respectively. Molecular dynamics simulations (MDS) were performed to discover new interactions and reinforce the binding modes from docking for the hits also. The QSAR and MDS results obtained from this work should be useful in determining structural requirements for inhibitor development as well as in designing more potential inhibitors for NS2B-NS3 protease.

Irrigation, organic matter addition, and tarping as methods of reducing emissions of methyl iodide from agricultural soil.

Methyl iodide (MeI) is increasingly being used as a highly effective alternative to the soil fumigant methyl bromide. Due to its volatile and toxic nature, MeI draws wide attention on its potential atmospheric emission following field fumigation treatment. Using soil columns that make it possible to determine emissions and gas phase distribution of soil fumigants, we studied MeI behavior in two soils differing in organic matter content. Additionally, the effectiveness of surface irrigation and tarping with virtually impermeable film (VIF) was assessed. In the lower organic matter, bare soil (control), emissions of MeI were rapid and high (83% of total). Although the peak emission flux was reduced by irrigation, the total loss was very similar to the control (82%). Tarping with VIF dramatically reduced emissions (0.04% total emissions). In the higher organic matter soil, degradation rate of MeI was increased around 4-fold, leading to a significant reduction in emissions (63% total emissions). The work suggests that surface tarping with VIF would be highly effective as an emissions reduction strategy and would also result in the maintenance of high soil gas concentrations (important for pest control). Ripping of the tarp after two weeks led to an immediate spike release of MeI, but, even so, the flux rate at this time was almost 20 times lower than the peak flux rate in the control. Even with tarp ripping, the total emission loss from the VIF treatment remained low (6%).

1,3-dichloropropene and chloropicrin emissions following simulated drip irrigation to raised beds under plastic films.

Using laboratory soil chambers a nonscaled representation of an agricultural raised bed was constructed. For a sandy loam soil, 1,3-dichloropropene (1,3-D) and chloropicrin (CP) were applied at 5 cm depth with an excess of water (simulated drip irrigation). Application was made under both high density polyethylene (HDPE) and virtually impermeable film (VIF) covering the soil bed (the furrow was left uncovered). Soil gas distribution of the fumigants, together with emissions into the headspace above the bed, sidewall and furrow were determined over time. Total emissions from the HDPE treatment were cis 1,3-D 28%, trans 1,3-D 24%, and CP 8%. Due to its lower permeability, the values for VIF were 13%, 7%, and 1.5%, respectively. With HDPE, the majority (86-93%) of the emissions occurred from the bed, while for VIF the majority (92-99%) of the emissions was from the furrow. Compared to a range of literature values for shank injection, the use of drip application appears to offer a benefit in reducing 1,3-D and CP emissions. However, the most meaningful comparison is with our previous data for simulated shank injection where the same soil was covered (completely) with the same plastic films (1). In this comparison, only 1,3-D emissions under HDPE were lower with drip application; 1,3-D emissions under VIF and CP emissions under both films were greater with the drip application.

Laboratory assessment of emission reduction strategies for the agricultural fumigants 1,3-dichloropropene and chloropicrin.

With the increased use of the agricultural fumigants 1,3-dichloropropene (1,3-D) and chloropicrin (CP), it is important that strategies to reduce emissions of these fumigant from soil to the air are assessed to protect air quality. Using an established soil column approach, the following emission reduction strategies were compared to a control: (1) spray application of ammonium thiosulfate to the soil surface; (2) deep injection at 46 cm depth; (3) high density polyethylene sealed over the soil surface; (4) virtually impermeable film sealed over the soil surface; and (5) irrigation with ammonium thiosulfate solution. Relative to the control, 1,3-D emissions were reduced by 26.1, 1.0, 0.01, 94.2, and 42.5%, for treatments 1 through 5, respectively. For CP the reductions were 41.6, 23.3, 94.6, 99.9, and 87.5% for treatments 1 through 5, respectively. Virtually impermeable film gave the greatest reductions for both fumigants, while HDPE was very effective only for CP. Despite offering less significant emission reductions, the lower cost alternatives to tarping, particularly irrigation with ATS solution, may offer substantial benefitwhere tarping is not economically viable.

Communication theoretic image restoration for binary-valued imagery.

We present a new image-restoration algorithm for binary-valued imagery. A trellis-based search method is described that exploits the finite alphabet of the target imagery. This algorithm seeks the maximum-likelihood solution to the image-restoration problem and is motivated by the Viterbi algorithm for traditional binary data detection in the presence of intersymbol interference and noise. We describe a blockwise method to restore two-dimensional imagery on a row-by-row basis and in which a priori knowledge of image pixel correlation structure can be included through a modification to the trellis transition probabilities. The performance of the new Viterbi-based algorithm is shown to be superior to Wiener filtering in terms of both bit error rate and visual quality. Algorithmic choices related to trellis state configuration, complexity reduction, and transition probability selection are investigated, and various trade-offs are discussed.

Information-based optical design for binary-valued imagery.

Applications such as optical data storage, optical computing, and optical interconnects require optical systems that manipulate binary-valued images. Such an optical system can be viewed as a two-dimensional array of binary communication channels. This perspective is used to motivate the use of pagewise mutual information as a metric for optical system analysis and design. Fresnel propagation and coherent imaging both are analyzed in terms of mutual-information transmission. An information-based space-bandwidth product is used to analyze the trade-off between the numerical aperture and the number of image pixels in a coherent 4f system. We propose a new merit function to facilitate information-based optical system design. Information maximization and bit-error-rate minimization both are possible with the new radially weighted encircled-energy merit function. We demonstrate the use of this new merit function through a design example and show that the information throughput is increased by 8% and the bit-error rate is reduced by 36% when compared with systems designed with traditional criteria.