The discovery of Arylex™ active and Rinskor™ active: Two novel auxin herbicides

Multiple classes of commercially important auxin herbicides have been discovered since the 1940s including the aryloxyacetates (2,4-D, MCPA, dichlorprop, mecoprop, triclopyr, and fluroxypyr), the benzoates (dicamba), the quinoline-2-carboxylates (quinclorac and quinmerac), the pyrimidine-4-carboxylates (aminocyclopyrachlor), and the pyridine-2-carboxylates (picloram, clopyralid, and aminopyralid). In the last 10 years, two novel pyridine-2-carboxylate (or picolinate) herbicides were discovered at Dow AgroSciences. This paper will describe the structure activity relationship study that led to the discovery of the 6-aryl-picolinate herbicides Arylex™ active (2005) and Rinskor™ active (2010). While Arylex was developed primarily for use in cereal crops and Rinskor is still in development primarily for use in rice crops, both herbicides will also be utilized in additional crops.     

Exploration of Perceptions of Dog Bites among YouTube™ Viewers and Attributions of Blame

Dog bites are a human public health and dog welfare problem. This qualitative study is the first to use YouTube^? to examine how viewers perceive risk of, and attribute blame for, dog bites. Comments underneath 10 videos, chosen to represent a diversity of dog-bite scenarios, were analyzed inductively using thematic analysis. Six themes emerged: 1) Commentators thought that dogs are inherently good-natured but wild animals and emphasized how dogs try to avoid biting people; 2) all recognized breeds of dogs were stereotyped and breed stereotypes were used to shift the blame away from the dog and onto a bite victim, unless the dog identified in a video was a pit bull type. The dog was often blamed in such case; 3) It was argued that a breed limits the extent to which a dog can be trained and controlled; 4) Owners/handlers were often blamed for bites due to their inability to control the dog, and commentators identified the need for appropriate training and socialization in order to control dogs and reduce bite risk; 5) Bite victims were also blamed for the bites when their behavior was perceived as provoking a dog. Although children's behavior was identified as causing a risk, parents of children bitten in the videos were blamed for bites instead due to their approach to child supervision; 6) Bites in a range of contexts, such as play or when viewers thought that the victim's behavior provoked a dog, were seen as well-de-served and normal. It was concluded that although comments on publicly available videos need to be interpreted with caution due to a self-selection bias, their analysis can help to identify attitudes and perceptions towards risk around dogs that could aid bite prevention interventions and policies.     

Pretreatment verification of dose calculation and delivery by means of measurements with PLEXITOM™ phantom

Aim

To validate a pretreatment verification method of dose calculation and dose delivery based on measurements with Metaplex PTW phantom.

Background

The dose-response relationships for local tumor control and radiosensitive tissue complications are strong. It is widely accepted that an accuracy of dose delivery of about 3.5% (one standard deviation) is required in modern radiotherapy. This goal is difficult to achieve. This paper describes our experience with the control of dose delivery and calculations at the ICRU reference point.

Materials and methods

The calculations of dose at the ICRU reference point performed with the treatment planning system CMS XiO were checked by measurements carried out in the PLEXITOM™ phantom.All measurements were performed with the ion chamber positioned in the phantom, at the central axis of the beam, at depth equivalent to the radiological depth (at gantry zero position). The source-to-phantom surface distance was always set to keep the source-to-detector distance equal to the reference point depth defined in the ICRU Report 50 (generally, 100 cm). The dose was measured according to IAEA TRS 398 report for measurements in solid phantoms. The measurement results were corrected with the actual accelerator''s output factor and for the non-full scatter conditions. Measurements were made for 111 patients and 327 fields.

Results

The average differences between measurements and calculations were 0.03% (SD = 1.4%), 0.3% (SD = 1.0%), 0.1% (SD = 1.1%), 0.6% (SD = 1.8%), 0.3% (SD = 1.5%) for all measurements, for total dose, for pelvis, thorax and H&N patients, respectively. Only in 15 cases (4.6%), the difference between the measured and the calculated dose was greater than 3%. For these fields, a detailed analysis was undertaken.

Conclusion

The verification method provides an instantaneous verification of dose calculations before the beginning of a patient''s treatment. It allows to detect differences smaller than 3.5%.     

Rapid Assessment of Primer Combinations and Recovery of AFLP™ Products using Ethidium Bromide Staining

AFLP is a novel high-resolution fingerprinting method that can be used to delineate intraspecific relationships among a large variety of fungi and plants. We demonstrate that with the appropriate technical modifications, ethidium bromide staining and non-denaturing polyacryalmide minigels can be an inexpensive and time saving alternative for screening DNA samples for suitable AFLP primer pairs. Furthermore, the recovery of ethidium bromide stained polymorphic DNA fragments is not as tedious as the recovery of isotopic DNA fragments.Abbreviations: EDTA, ethylene diamine tetraacetic acid; BSA, bovine serum albumin.     

Near-real-time acoustic monitoring of beaked whales and other cetaceans using a Seaglider™

In most areas, estimating the presence and distribution of cryptic marine mammal species, such as beaked whales, is extremely difficult using traditional observational techniques such as ship-based visual line transect surveys. Because acoustic methods permit detection of animals underwater, at night, and in poor weather conditions, passive acoustic observation has been used increasingly often over the last decade to study marine mammal distribution, abundance, and movements, as well as for mitigation of potentially harmful anthropogenic effects. However, there is demand for new, cost-effective tools that allow scientists to monitor areas of interest autonomously with high temporal and spatial resolution in near-real time. Here we describe an autonomous underwater vehicle--a glider--equipped with an acoustic sensor and onboard data processing capabilities to passively scan an area for marine mammals in near-real time. The glider was tested extensively off the west coast of the Island of Hawai'i, USA. The instrument covered approximately 390 km during three weeks at sea and collected a total of 194 h of acoustic data. Detections of beaked whales were successfully reported to shore in near-real time. Manual analysis of the recorded data revealed a high number of vocalizations of delphinids and sperm whales. Furthermore, the glider collected vocalizations of unknown origin very similar to those made by known species of beaked whales. The instrument developed here can be used to cost-effectively screen areas of interest for marine mammals for several months at a time. The near-real-time detection and reporting capabilities of the glider can help to protect marine mammals during potentially harmful anthropogenic activities such as seismic exploration for sub-sea fossil fuels or naval sonar exercises. Furthermore, the glider is capable of under-ice operation, allowing investigation of otherwise inaccessible polar environments that are critical habitats for many endangered marine mammal species.     

Effects of MagPro™ on muscle performance

Athletes are on an endless quest to enhance performance and are frequently barraged by products that purport to contribute to various components of athletic activity. The purpose of this study was to determine if MagPro? influenced muscle flexibility or muscle endurance. This was a double-blind, randomized, controlled study using a repeated-measures design. The Institutional Review Board approved consent was obtained. The participants were healthy, physically active adults (n = 38 for phase 1; n = 18 for phase 2). Two creams were used: MagPro? (Mg cream) and a placebo. In phase 1, each cream was applied to the gastroc-soleus muscles. A stretching protocol was completed, and ankle dorsiflexion was compared. In phase 2, 1 cream was applied to both quadriceps muscles. An endurance protocol using a Life Fitness bicycle was completed. The procedure was repeated with the other cream on the quadriceps muscle 1 week later. For the flexibility phase, an analysis of variance with repeated measures revealed no difference between the 2 creams (p = 0.50), but there was a change in the flexibility over time (p = 0.00). For the endurance phase, paired t-tests revealed that there was no significant difference between the first (p = 0.26) or second (p = 0.35) cycling bouts of either cream. Likewise, there were no differences between the first and second cycling bouts of both the creams (MagPro? p = 0.46; Placebo p = 0.08). Despite previous studies demonstrating improved performance with Mg supplements, MagPro? did not enhance the outcome measures of this study. Examination of alternative application techniques and other outcome measures would be appropriate.     

Monte carlo model and output factors of elekta infinity™ 6 and 10 MV photon beam

AimThis study aimed to commission the Elekta Infinity™ working in 6 and 10 MV photon beam installed in Concord International Hospital, Singapore, and compare the OFs between MC simulation and measurement using PTW semiflex and microDiamond detector for small field sizes.Material and MethodsThere are two main steps in this study: modelling of Linac 6 and 10 MV photon beam and analysis of the output factors for field size 2 × 2–10 × 10 cm². The EGSnrc/BEAMnrc-DOSXYZnrc code was used to model and characterize the Linac and to calculate the dose distributions in a water phantom. The dose distribution and OFs were compared to the measurement data in the same condition.ResultsThe commissioning process was only conducted for a 10 × 10 cm² field size. The PDD obtained from MC simulation showed a good agreement with the measurement. The local dose difference of PDDs was less than 2% for 6 and 10 MV. The initial electron energy was 5.2 and 9.4 MeV for 6 and 10 MV photon beam, respectively. This Linac model can be used for dose calculation in other situations and different field sizes because this Linac has been commissioned and validated using Monte Carlo simulation. The 10 MV Linac produces higher electron contamination than that of 6 MV.ConclusionsThe Linac model in this study was acceptable. The most important result in this work comes from OFs resulted from MC calculation. This value was more significant than the OFs from measurement using semiflex and microDiamond for all beam energy and field sizes because of the CPE phenomenon.     

DNA Isolation and AFLP™ Genetic Fingerprinting of shape Theobroma cacao (L.)

Accurate identification of parental plants and their hybrids is essential for an effective breeding programme. Traditional classification of cocoa varieties relies on the characterisation of agricultural traits at plant maturity. A rapid and reliable method is described, based on genotypic analysis. An efficient DNA isolation procedure was developed, yielding unsheared DNA of high purity. Two genetic fingerprinting techniques, RAPD and AFLP, were evaluated for their suitability in distinguishing cocoa varieties. RAPD analysis was unsatisfactory due to the low frequency of polymorphisms and poor reproducibility. AFLP was reliable in distinguishing phenotypically identical, known varieties of cocoa. Importantly, AFLP also revealed intra- and inter-varietal variation.Abbreviations: AFLP, amplified fragment length polymorphism; APS, ammonium persulphate; CTAB, hexadecyltrimethylammonium bromide; DEB, DNA extraction buffer; f.wt., fresh weight; NEB, nuclei extraction buffer; PMSF, phenylmethanesulphonyl fluoride; RAPD, random amplified polymorphic DNA; T4 PNK, Bacteriophage T4 polynucleotide kinase; Taq, Thermus aquaticus; TBE, tris-borate-EDTA; TEMED, NNNN tetramethylethylenediamine.     

Biosimilarity under stress: A forced degradation study of Remicade® and Remsima™

Remsima? (infliximab) is the first biosimilar monoclonal antibody (mAb) approved by the European Medical Agency and the US Food and Drug Administration. Remsima? is highly similar to its reference product, Remicade®, with identical formulation components. The 2 products, however, are not identical; Remsima? has higher levels of soluble aggregates, C-terminal lysine truncation, and fucosylated glycans. To understand if these attribute differences could be amplified during forced degradation, solutions and lyophilized powders of the 2 products were subjected to stress at elevated temperature (40–60°C) and humidity (dry-97% relative humidity). Stress-induced aggregation and degradation profiles were similar for the 2 products and resulted in loss of infliximab binding to tumor necrosis factor and FcγRIIIa. Appearances of protein aggregates and hydrolysis products were time- and humidity-dependent, with similar degradation rates observed for the reference and biosimilar products. Protein powder incubations at 40°C/97% relative humidity resulted in partial mAb unfolding and increased asparagine deamidation. Minor differences in heat capacity, fluorescence, levels of subvisible particulates, deamidation and protein fragments were observed in the 2 stressed products, but these differences were not statistically significant. The protein solution instability at 60°C, although quite significant, was also similar for both products. Despite the small initial analytical differences, Remicade® and Remsima? displayed similar degradation mechanisms and kinetics. Thus, our results show that the 2 products are highly similar and infliximab's primary sequence largely defines their protein instabilities compared with the limited influence of small initial purity and glycosylation differences in the 2 products.     

Matrix-m™ adjuvant induces local recruitment, activation and maturation of central immune cells in absence of antigen

Saponin-based adjuvants are widely used to enhance humoral and cellular immune responses towards vaccine antigens, although it is not yet completely known how they mediate their stimulatory effects. The aim of this study was to elucidate the mechanism of action of adjuvant Matrix-M™ without antigen and Alum was used as reference adjuvant. Adjuvant Matrix-M™ is comprised of 40 nm nanoparticles composed of Quillaja saponins, cholesterol and phospholipid. BALB/c mice were subcutaneously injected once with, 3, 12 or 30 µg of Matrix-M™, resulting in recruitment of leukocytes to draining lymph nodes (dLNs) and spleen 48 h post treatment. Flow cytometry analysis identified CD11b⁺ Gr-1^high granulocytes as the cell population increasing most in dLNs and spleen. Additionally, dendritic cells, F4/80^int cells, T-, B- and NK-cells were recruited to dLNs and in spleen the number of F4/80^int cells, and to some extent, B cells and dendritic cells, increased. Elevated levels of early activation marker CD69 were detected on T-, B- and NK-cells, CD11b⁺ Gr-1^high cells, F4/80^int cells and dendritic cells in dLNs. In spleen CD69 was mainly up-regulated on NK cells. B cells and dendritic cells in dLNs and spleen showed an increased expression of the co-stimulatory molecule CD86 and dendritic cells in dLNs expressed elevated levels of MHC class II. The high-dose (30 µg) of Matrix-M™ induced detectable serum levels of IL-6 and MIP-1β 4 h post administration, most likely representing spillover of locally produced cytokines. A lesser increase of IL-6 in serum after administration of 12 µg Matrix-M™ was also observed. In conclusion, early immunostimulatory properties were demonstrated by Matrix-M™ alone, as therapeutic doses resulted in a local transient immune response with recruitment and activation of central immune cells to dLNs. These effects may play a role in enhancing uptake and presentation of vaccine antigens to elicit a competent immune response.     

Efficient analysis and extraction of MS/MS result data from Mascot™ result files

Background  

Mascot™ is a commonly used protein identification program for MS as well as for tandem MS data. When analyzing huge shotgun proteomics datasets with Mascot™'s native tools, limits of computing resources are easily reached. Up to now no application has been available as open source that is capable of converting the full content of Mascot™ result files from the original MIME format into a database-compatible tabular format, allowing direct import into database management systems and efficient handling of huge datasets analyzed by Mascot™.     

Changes in physical activity and fitness after 3 months of home Wii Fit™ use

The purpose of this study was to examine changes in physical activity and fitness variables in members of 8 volunteer families after 3 months of home use of the Wii Fit? interactive video game. Pre and postintervention measurements were obtained from 21 subjects relative to physical activity (5 days of accelerometry), aerobic fitness (graded treadmill test), muscular fitness (push-ups), flexibility (sit-and-reach test), balance (composite equilibrium score), and body composition (body mass index and % body fat). Use characteristics of the Wii Fit? device were also determined. A series of 2 (age group) × 2 (time) repeated measures analyses of variance were conducted to assess changes over time and between adults and children. Three months of home Wii Fit? use revealed no significant age group × time interactions or main effects of group or time for daily physical activity, muscular fitness, flexibility, balance, or body composition. An age group × time interaction (p = 0.04) was observed in peak VO2 (ml·kg(-1)·min(-1)) with children displaying a significant (p = 0.03) increase after 3 months of Wii Fit? use, whereas adults showed no significant (p = 0.50) change. Daily Wii Fit? use per household declined by 82% (p < 0.01) from 21.5 ± 9.0 min·d(-1) during the first 6 weeks to 3.9 ± 4.0 min·d(-1) during the second 6 weeks. Most measures of health-related fitness in this exploratory study remained unchanged after 3 months of home use of the popular Wii Fit? whole-body movement interactive video game. Modest daily Wii Fit? use may have provided insufficient stimulus for fitness changes.     

Genotypic characterization of Neisseria meningitidis using pyrosequencing™

Pyrosequencing involves the synthesis of single-stranded deoxyribonucleic acid leading to rapid and accurate analysis of nucleotide sequences. This article describes the development of typing assays for the characterization of Neisseria meningitidis using Pyrosequencing. This involved developing methods for the nucleotide sequence analysis of important variable regions contained on a major capsule gene and on outer membrane protein genes that are used for grouping, typing, and subtyping meningococci. To achieve this, primers were designed for amplification of three genes, siaD, porB, and porA from the four main serogroups B, C, Y, and W135. To facilitate throughput and reproducibility, the method was also automated. Data from 717 isolates have shown that Pyrosequencing can be used for the single nucleotide polymorphism and sequence-analysis characterization of meningococci.     

Identification of bacteria in blood culture broths using matrix-assisted laser desorption-ionization Sepsityper™ and time of flight mass spectrometry

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) is a novel method for the direct identification of bacteria from blood culture broths. We evaluate for the first time, the performance of the MALDI Sepsityper? Kit and MS for the identification of bacteria compared to standard phenotypic methods using the manufacturer's specified bacterial identification criteria (spectral scores ≥1.700-1.999 and ≥2.000 indicated identification to genus and species level, respectively). Five hundred and seven positive blood culture broths were prospectively examined, of which 379 (74.8%; 358 monomicrobial, 21 polymicrobial) were identified by MALDI-TOF MS; 195 (100%) and 132 (67.7%) of 195 gram-positive; and 163 (100%) and 149 (91.4%) of 163 gram-negative organisms from monomicrobial blood cultures were correctly identified to genus and species level, respectively. Spectral scores <1.700 (no identification) were obtained in 128/507 (25.2%) positive blood culture broths, including 31.6% and 32.3% of gram-positive and polymicrobial blood cultures, respectively. Significantly more gram-negative organisms were identified compared to gram-positive organisms at species level (p<0.0001). Five blood cultures were misidentified, but at species level only; including four monomicrobial blood cultures with Streptococcus oralis/mitis that were misidentified as Streptococcus pneumoniae. Positive predictive values for the direct identification of both gram-positive and gram-negative bacteria from monomicrobial blood culture broths to genus level were 100%. A diagnostic algorithm for positive blood culture broths that incorporates gram staining and MALDI-TOF MS should identify the majority of pathogens, particularly to genus level.     

Pyrosequencing™

Nucleotide sequencing is an established method for gaining information relating to partial gene, whole gene, or whole genome sequence. Here we describe some of the background leading to the advent of modern nucleotide sequencing and how it has led to the development of Pyrosequencing™, a relatively new method for real-time nucleotide sequencing. In particular, we describe how this method can be used for typing bacterial pathogens.     

PIMWalker™

This article reports on PIMWalker, a free and interactive tool for visualising protein interaction networks. PIMWalker handles the unified molecular interaction (MI) format defined by members of the Proteomics Standards Initiative (the PSI MI format), and it is thus directly and easily usable by bench biologists. PIMWalker also comes with a documented, open-source Javatrade mark application programming interface allowing the bioinformatic programmer to easily extend the functions. AVAILABILITY: PIMWalker is available under a free license from http://pim.hybrigenics.com/pimwalker.     

Effects of Synbiotic2000™ Forte on the Intestinal Motility and Interstitial Cells of Cajal in TBI Mouse Model

The main objective of this study was to investigate the effects of Synbiotic2000? Forte on the intestinal motility and interstitial cells of Cajal (ICC) in traumatic brain injury (TBI) mouse model. Kunming mice were randomly divided into sham operation group (S group), enteral nutrition group with TBI (E group), and Synbiotic2000? Forte group with TBI (P group). The contractile activity of the intestinal smooth muscle, densities and ultrastructure of the ICC, kit protein concentration, weight, and defecation of mice were monitored and analyzed. TBI markedly suppressed contractile activity of the intestinal smooth muscle (P < 0.01), which led to a reduction of defecation (P < 0.01) and weight (P < 0.01). However, application of Synbiotic2000? Forte significantly improved contractile activity of the small intestine (P < 0.01), which may be related to protective effects to the interstitial cells of Cajal, smooth muscle cells, and enteric neurons. TBI impaired ICC networks and densities (P < 0.01), events that were protected by the application of Synbiotic2000? Forte. Synbiotic2000? Forte may attenuate TBI-mediated inhibition of the kit protein pathway. Synbiotic2000? Forte may improve intestinal motility and protect the ICC in the TBI mouse. These findings provide a novel support for the application of Synbiotic2000? Forte in intestinal motility disturbance after TBI.