Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images

This paper describes an image-processing pipeline for the automatic segmentation of the nuclear envelope of HeLcells observed through Electron Microscopy. The pipeline was applied to a 3D stack of 300 images. The intermediate results of neighbouring slices are further combined to improve the final results. Comparison with a handsegmented ground truth reported Jaccard similarity values between 94-98% on the central slices with a decrease towards the edges of the cell where the structure was considerably more complex. The processing is unsupervised and each 2D slice is processed in about 5-10 seconds running on a MacBook Pro. No systematic attempt to make the code faster was made. These encouraging results could be further used to provide data for more complex segmentation techniques like Deep Learning, which require a considerable amount of data to train architectures like Convolutional Neural Networks. The code is freely available from https://github.com/reyesaldasoro/HeLa-Cell-Segmentatio

Local Signal Time-Series during Rest Used for Areal Boundary Mapping in Individual Human Brains

It is widely thought that resting state functional connectivity likely reflects functional interaction among brain areas and that different functional areas interact with different sets of brain areas. A method for mapping areal boundaries has been formulated based on the large-scale spatial characteristics of regional interaction revealed by resting state functional connectivity. In the present study, we present a novel analysis for areal boundary mapping that requires only the signal timecourses within a region of interest, without reference to the information from outside the region. The areal boundaries were generated by the novel analysis and were compared with those generated by the previously-established standard analysis. The boundaries were robust and reproducible across the two analyses, in two regions of interest tested. These results suggest that the information for areal boundaries is readily available inside the region of interest

Fructan and its relationship to abiotic stress tolerance in plants

Numerous studies have been published that attempted to correlate fructan concentrations with freezing and drought tolerance. Studies investigating the effect of fructan on liposomes indicated that a direct interaction between membranes and fructan was possible. This new area of research began to move fructan and its association with stress beyond mere correlation by confirming that fructan has the capacity to stabilize membranes during drying by inserting at least part of the polysaccharide into the lipid headgroup region of the membrane. This helps prevent leakage when water is removed from the system either during freezing or drought. When plants were transformed with the ability to synthesize fructan, a concomitant increase in drought and/or freezing tolerance was confirmed. These experiments indicate that besides an indirect effect of supplying tissues with hexose sugars, fructan has a direct protective effect that can be demonstrated by both model systems and genetic transformation

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

Hammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme class than were previously known, including the first representatives in fungi and archaea. Moreover, we have uncovered the first natural examples of “type II” hammerheads, and our findings reveal that this permuted form occurs in bacteria as frequently as type I and III architectures. We also identified a commonly occurring pseudoknot that forms a tertiary interaction critical for high-speed ribozyme activity. Genomic contexts of many hammerhead ribozymes indicate that they perform biological functions different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes. In rare instances, nucleotide variation occurs at positions within the catalytic core that are otherwise strictly conserved, suggesting that core mutations are occasionally tolerated or preferred

Modulating RNA structure and catalysis: lessons from small cleaving ribozymes

RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today’s knowledge in the field

Webometrics benefitting from web mining? An investigation of methods and applications of two research fields

Webometrics and web mining are two fields where research is focused on quantitative analyses of the web. This literature review outlines definitions of the fields, and then focuses on their methods and applications. It also discusses the potential of closer contact and collaboration between them. A key difference between the fields is that webometrics has focused on exploratory studies, whereas web mining has been dominated by studies focusing on development of methods and algorithms. Differences in type of data can also be seen, with webometrics more focused on analyses of the structure of the web and web mining more focused on web content and usage, even though both fields have been embracing the possibilities of user generated content. It is concluded that research problems where big data is needed can benefit from collaboration between webometricians, with their tradition of exploratory studies, and web miners, with their tradition of developing methods and algorithms

"Men's health--a little in the shadow": a formative evaluation of medical curriculum enhancement with men's health teaching and learning.

BACKGROUND: Enhancing a medical school curriculum with new men's health teaching and learning requires an understanding of the local capacity and the facilitators and barriers to implementing new content, and an approach that accommodates the systemic and cultural differences between medical schools. METHODS: A formative evaluation was undertaken to determine the perspectives of key informants (academics, curriculum developers) from four Australian medical schools about the strategies needed to enhance their curriculum with men's health teaching and learning. Through semi-structured questioning with 17 key informants, interviewees also described the contextual barriers and facilitators to incorporating new topic areas into existing curriculum. Interviews were recorded with consent, transcribed verbatim, and analysed by two researchers to identify key themes. RESULTS: Interviewees were enthusiastic about incorporating men's health content through a men's health curriculum framework but highlighted the need for systems to assist in identifying gaps in their current curriculum where the men's health topics could be integrated. The student experience was identified as a key driver for men's health teaching and learning. Furthermore, core men's health clinical outcomes needed to be defined and topic areas vertically integrated across the curricula. This would ensure that students were appropriately equipped with the skills and knowledge for subsequent clinical practice in a range of geographical settings. Interviewees consistently suggested that the best implementation strategy is to have someone 'on the ground' to work directly with medical school staff and champion the men's health discipline. Providing mechanisms for sharing knowledge and resources across medical schools was highlighted to facilitate implementation, particularly for those medical schools with limited men's health teaching resources. CONCLUSIONS: Despite the unanimous support for men's health teaching and learning, the evaluation highlighted that the student experience must be recognised as paramount when integrating new topic areas into an already packed curriculum. A community of practice, where medical schools share relevant resources and knowledge, could help to ensure a commonality of student experience with respect to men's health learning in medical schools across different geographical settings and with different levels of resourcing. Such an approach could also be adapted to other areas of curriculum enhancement