BactMAP:An R package for integrating, analyzing and visualizing bacterial microscopy data

High-throughput analyses of single-cell microscopy data are a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP complies with standard practice in R which enables the use of advanced statistical analysis tools, and its graphic output is compatible with ggplot2, enabling adjustable plot graphics in every operating system. User feedback will be used to create a fully automated Graphical User Interface version of BactMAP in the future. Using BactMAP, we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z-ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap

Booster main magnet power supply, present operation and potential future upgrades

The Brookhaven Booster Main Magnet Power Supply (MMPS) is a 24 pulse thyristor control supply, rated at 5500 Amps, +/-2000 Volts, or 3000 Amps, +/-6000 Volts. The power supply is fed directly from the power utility and the peak magnet power is 18 MWatts. This peak power is seen directly at the incoming ac line. This power supply has been in operation for the last 18 years. This paper will describe the present topology and operation of the power supply, the feedback control system and the different modes of operation of the power supply. Since the power supply has been in operation for the last 18 years, upgrading this power supply is essential. A new power supply topology has been studied where energy is stored in capacitor banks. DC to DC converters are used to convert the dc voltage stored in the capacitor banks to pulsed DC voltage into the magnet load. This enables the average incoming power from the ac line to be constant while the peak magnet power is pulsed to +/- 18 MWatts. Simulations and waveforms of this power supply will be presented

Biomimetic Properties of Force-spun PHBV Membranes Functionalised with Collagen as Substrates for Biomedical Application

The force-spinning process parameters (i.e., spin speed, spinneret-collector distance, and polymer concentration), optimised and characterised in previous work by this group, allowed the rapid fabrication of large quantities of high surface area poly(3-hydroxybutyric acid-co-3-hydroxyvaleric acid) (PHBV) polymeric fibre membranes. This paper examined the potential application for force-spun PHBV fibres functionalised with type I collagen for tissue regeneration applications. PHBV fibre scaffolds provide a biologically suitable substrate to guide the regeneration of dermal tissues, however, have poor cellular adhesion properties. The grafting of collagen type-I to PHBV fibres demonstrated improved cell adhesion and growth in Neo-NHDF (neonatal human dermal fibroblasts) fibroblasts. The examination of fibre morphology, thermal properties, collagen content, and degradability was used to contrast the physicochemical properties of the PHBV and PHBV-Collagen fibres. Biodegradation models using phosphate buffered saline determined there was no appreciable change in mass over the course of 6 weeks; a Sirius Red assay was performed on degraded samples, showing no change in the quantity of collagen. Cell metabolism studies showed an increase in cell metabolism on conjugated samples after three and 7 days. In addition, in vitro cytocompatibility studies demonstrated superior cell activity and adhesion on conjugated samples over 7 days

Commissioning of the new AGS MMPS transformers

The Brookhaven AGS Main Magnet Power Supply (MMPS) is a thyristor control supply rated at 5500 Amps. +/-9000 Volts. The peak magnet power is 50 MWatts. The power supply is fed from a motor/generator manufactured by Siemens. During rectify and invert operation the P Bank power supplies are used. During the flattops the F Bank power supplies are used. The P Bank power supplies are fed from two 23 MVA transformers and the F Bank power supplies are fed from two 5.3 MYA transformers. The fundamental frequency of the F Bank power supplies is 1440 Hz, however the fundamental frequency of the P banks was 720 Hz. It was very important to reduce the ripple during rectify to improve polarized proton operations. For this reason and also because the original transformers were 45 years old we replaced these transformers with new ones and we made the fundamental frequency of both P and F banks 1440 Hz. This paper will highlight the major hurdles that were involved during the installation of the new transformers. It will present waveforms while running at different power levels up to 6MW full load. It will show the transition from the F-Bank power supplies to the P-Banks and also show the improvements in ripple made on the P-Bank power supplies

The NeST (Neoadjuvant systemic therapy in breast cancer) study: National Practice Questionnaire of United Kingdom multi-disciplinary decision making.

BACKGROUND: Neoadjuvant systemic therapy (NST) is increasingly used in the treatment of breast cancer, yet it is clear that there is significant geographical variation in its use in the UK. This study aimed to examine stated practice across UK breast units, in terms of indications for use, radiological monitoring, pathological reporting of treatment response, and post-treatment surgical management. METHODS: Multidisciplinary teams (MDTs) from all UK breast units were invited to participate in the NeST study. A detailed questionnaire assessing current stated practice was distributed to all participating units in December 2017 and data collated securely usingREDCap. Descriptive statistics were calculated for each questionnaire item. RESULTS: Thirty-nine MDTs from a diverse range of hospitals responded. All MDTs routinely offered neoadjuvant chemotherapy (NACT) to a median of 10% (range 5-60%) of patients. Neoadjuvant endocrine therapy (NET) was offered to a median of 4% (range 0-25%) of patients by 66% of MDTs. The principal indication given for use of neoadjuvant therapy was for surgical downstaging. There was no consensus on methods of radiological monitoring of response, and a wide variety of pathological reporting systems were used to assess tumour response. Twenty-five percent of centres reported resecting the original tumour footprint, irrespective of clinical/radiological response. Radiologically negative axillae at diagnosis routinely had post-NACT or post-NET sentinel lymph node biopsy (SLNB) in 73.0 and 84% of centres respectively, whereas 16% performed SLNB pre-NACT. Positive axillae at diagnosis would receive axillary node clearance at 60% of centres, regardless of response to NACT. DISCUSSION: There is wide variation in the stated use of neoadjuvant systemic therapy across the UK, with general low usage of NET. Surgical downstaging remains the most common indication of the use of NAC, although not all centres leverage the benefits of NAC for de-escalating surgery to the breast and/or axilla. There is a need for agreed multidisciplinary guidance for optimising selection and management of patients for NST. These findings will be corroborated in phase II of the NeST study which is a national collaborative prospective audit of NST utilisation and clinical outcomes