Synchronous nanoscale topographic and chemical mapping by differential-confocal controlled Raman microscopy

Confocal Raman microscopy is currently used for label-free optical sensing and imaging within the biological, engineering, and physical sciences as well as in industry. However, currently these methods have limitations, including their low spatial resolution and poor focus stability, that restrict the breadth of new applications. This paper now introduces differential-confocal controlled Raman microscopy as a technique that fuses differential confocal microscopy and Raman spectroscopy, enabling the point-to-point collection of three-dimensional nanoscale topographic information with the simultaneous reconstruction of corresponding chemical information. The microscope collects the scattered Raman light together with the Rayleigh light, both as Rayleigh scattered and reflected light (these are normally filtered out in conventional confocal Raman systems). Inherent in the design of the instrument is a significant improvement in the axial focusing resolution of topographical features in the image (to ∼1 nm), which, when coupled with super-resolution image restoration, gives a lateral resolution of 220 nm. By using differential confocal imaging for controlling the Raman imaging, the system presents a significant enhancement of the focusing and measurement accuracy, precision, and stability (with an antidrift capability), mitigating against both thermal and vibrational artefacts. We also demonstrate an improved scan speed, arising as a consequence of the nonaxial scanning mode

GCA in 2d

We make a detailed study of the infinite dimensional Galilean Conformal Algebra (GCA) in the case of two spacetime dimensions. Classically, this algebra is precisely obtained from a contraction of the generators of the relativistic conformal symmetry in 2d. Here we find quantum mechanical realisations of the (centrally extended) GCA by considering scaling limits of certain 2d CFTs. These parent CFTs are non-unitary and have their left and right central charges become large in magnitude and opposite in sign. We therefore develop, in parallel to the usual machinery for 2d CFT, many of the tools for the analysis of the quantum mechanical GCA. These include the representation theory based on GCA primaries, Ward identities for their correlation functions and a nonrelativistic Kac table. In particular, the null vectors of the GCA lead to differential equations for the four point function. The solution to these equations in the simplest case is explicitly obtained and checked to be consistent with various requirements.Comment: 45 pages; v2: 47 pages. Restructured introduction, minor corrections, added references. Journal versio

Does shear wave ultrasound independently predict axillary lymph node metastasis in women with invasive breast cancer?

Shear wave elastography (SWE) shows promise as an adjunct to greyscale ultrasound examination in assessing breast masses. In breast cancer, higher lesion stiffness on SWE has been shown to be associated with features of poor prognosis. The purpose of this study was to assess whether lesion stiffness at SWE is an independent predictor of lymph node involvement. Patients with invasive breast cancer treated by primary surgery, who had undergone SWE examination were eligible. Data were retrospectively analysed from 396 consecutive patients. The mean stiffness values were obtained using the Aixplorer(®) ultrasound machine from SuperSonic Imagine Ltd. Measurements were taken from a region of interest positioned over the stiffest part of the abnormality. The average of the mean stiffness value obtained from each of two orthogonal image planes was used for analysis. Associations between lymph node involvement and mean lesion stiffness, invasive cancer size, histologic grade, tumour type, ER expression, HER-2 status and vascular invasion were assessed using univariate and multivariate logistic regression. At univariate analysis, invasive size, histologic grade, HER-2 status, vascular invasion, tumour type and mean stiffness were significantly associated with nodal involvement. Nodal involvement rates ranged from 7 % for tumours with mean stiffness <50 kPa to 41 % for tumours with a mean stiffness of >150 kPa. At multivariate analysis, invasive size, tumour type, vascular invasion, and mean stiffness maintained independent significance. Mean stiffness at SWE is an independent predictor of lymph node metastasis and thus can confer prognostic information additional to that provided by conventional preoperative tumour assessment and staging

Anti-epileptic effect of Ganoderma lucidum polysaccharides by inhibition of intracellular calcium accumulation and stimulation of expression of CaMKII a in epileptic hippocampal neurons

Purpose: To investigate the mechanism of the anti-epileptic effect of Ganoderma lucidum polysaccharides (GLP), the changes of intracellular calcium and CaMK II a expression in a model of epileptic neurons were investigated. Method: Primary hippocampal neurons were divided into: 1) Control group, neurons were cultured with Neurobasal medium, for 3 hours; 2) Model group I: neurons were incubated with Mg2+ free medium for 3 hours; 3) Model group II: neurons were incubated with Mg2+ free medium for 3 hours then cultured with the normal medium for a further 3 hours; 4) GLP group I: neurons were incubated with Mg2+ free medium containing GLP (0.375 mg/ml) for 3 hours; 5) GLP group II: neurons were incubated with Mg2+ free medium for 3 hours then cultured with a normal culture medium containing GLP for a further 3 hours. The CaMK II a protein expression was assessed by Western-blot. Ca2+ turnover in neurons was assessed using Fluo-3/AM which was added into the replacement medium and Ca2+ turnover was observed under a laser scanning confocal microscope. Results: The CaMK II a expression in the model groups was less than in the control groups, however, in the GLP groups, it was higher than that observed in the model group. Ca2+ fluorescence intensity in GLP group I was significantly lower than that in model group I after 30 seconds, while in GLP group II, it was reduced significantly compared to model group II after 5 minutes. Conclusion: GLP may inhibit calcium overload and promote CaMK II a expression to protect epileptic neuron

Statistical colour models: an automated digital image analysis method for quantification of histological biomarkers

Background: Colour is the most important feature used in quantitative immunohisto- chemistry (IHC) image analysis; IHC is used to provide information relating to aetiology and to con rm malignancy. Methods: Statistical modelling is a technique widely used for colour detection in computer vision. We have developed a statistical model of colour detection applicable to detection of stain colour in digital IHC images. Model was rst trained by massive colour pixels collected semi-automatically. To speed up the training and detection processes, we removed luminance channel, Y channel of YCbCr colour space and chose 128 histogram bins which is the optimal number. A maximum likelihood classi- er is used to classify pixels in digital slides into positively or negatively stained pixels automatically. The model-based tool was developed within ImageJ to quantify targets identi ed using IHC and histochemistry. Results: The purpose of evaluation was to compare the computer model with human evaluation. Several large datasets were prepared and obtained from human oesopha- geal cancer, colon cancer and liver cirrhosis with di erent colour stains. Experimental results have demonstrated the model-based tool achieves more accurate results than colour deconvolution and CMYK model in the detection of brown colour, and is comparable to colour deconvolution in the detection of pink colour. We have also demostrated the proposed model has little inter-dataset variations. Conclusions: A robust and e ective statistical model is introduced in this paper. The model-based interactive tool in ImageJ, which can create a visual representation of the statistical model and detect a speci ed colour automatically, is easy to use and avail- able freely at http://rsb.info.nih.gov/ij/plugins/ihc-toolbox/index.html. Testing to the tool by di erent users showed only minor inter-observer variations in results

The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP

Temporal and Spatial Dynamics of Carbon Fixation by Moso Bamboo (Phyllostachys pubescens) in Subtropical China

To study the temporal and spatial dynamics of carbon fixation by Moso bamboo (Phyllostachys pubescens) in subtropical China, carbon fixation of leaves within the canopy of P. pubescens was measured with a LI-6400 portable photosynthesis system. The results showed that the capability of carbon fixation of P. pubescens leaves had obvious temporal and spatial dynamic variations. It was revealed that there were two peak periods and two low periods in the season variation of carbon fixation capability. Data also revealed that the capability of carbon fixation by five-year-old P. pubescens was more than that of one-year-old and three-year-old. Daily and seasonal carbon fixation showed a negative correlation with the CO2 concentration. The temporal and spatial dynamics of carbon fixation by P. pubescens described above provided a scientific basis for development of technologies in bamboo timber production

Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms.

Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies. Genome compaction and extensive gene losses distinguish the heterotrophic symbiosis of the bone-eating worm Osedax frankpressi from the chemoautotrophic symbiosis of deep-sea Vestimentifera. Osedax's endosymbionts complement many of the host's metabolic deficiencies, including the loss of pathways to recycle nitrogen and synthesise some amino acids. Osedax's endosymbionts possess the glyoxylate cycle, which could allow more efficient catabolism of bone-derived nutrients and the production of carbohydrates from fatty acids. Unlike in most Vestimentifera, innate immunity genes are reduced in O. frankpressi, which, however, has an expansion of matrix metalloproteases to digest collagen. Our study supports that distinct nutritional interactions influence host genome evolution differently in highly specialised symbioses

On the Temperature Dependence of the Shear Viscosity and Holography

We examine the structure of the shear viscosity to entropy density ratio eta/s in holographic theories of gravity coupled to a scalar field, in the presence of higher derivative corrections. Thanks to a non-trivial scalar field profile, eta/s in this setup generically runs as a function of temperature. In particular, its temperature behavior is dictated by the shape of the scalar potential and of the scalar couplings to the higher derivative terms. We consider a number of dilatonic setups, but focus mostly on phenomenological models that are QCD-like. We determine the geometric conditions needed to identify local and global minima for eta/s as a function of temperature, which translate to restrictions on the signs and ranges of the higher derivative couplings. Finally, such restrictions lead to an holographic argument for the existence of a global minimum for eta/s in these models, at or above the deconfinement transition.Comment: references adde

Drosophila muscleblind Codes for Proteins with One and Two Tandem Zinc Finger Motifs

Muscleblind-like proteins, Muscleblind (Mbl) in Drosophila and MBNL1-3 in vertebrates, are regulators of alternative splicing. Human MBNL1 is a key factor in the etiology of myotonic dystrophy (DM), a muscle wasting disease caused by the occurrence of toxic RNA molecules containing CUG/CCUG repeats. MBNL1 binds to these RNAs and is sequestered in nuclear foci preventing it from exerting its normal function, which ultimately leads to mis-spliced mRNAs, a major cause of the disease. Muscleblind-proteins bind to RNAs via N-terminal zinc fingers of the Cys3-His type. These zinc fingers are arranged in one (invertebrates) or two (vertebrates) tandem zinc finger (TZF) motifs with both fingers targeting GC steps in the RNA molecule. Here I show that mbl genes in Drosophila and in other insects also encode proteins with two TZF motifs, highly similar to vertebrate MBNL proteins. In Drosophila the different protein isoforms have overlapping but possibly divergent functions in vivo, evident by their unequal capacities to rescue the splicing defects observed in mbl mutant embryos. In addition, using whole transcriptome analysis, I identified several new splicing targets for Mbl in Drosophila embryos. Two of these novel targets, kkv (krotzkopf-verkehrt, coding for Chitin Synthase 1) and cora (coracle, coding for the Drosophila homolog of Protein 4.1), are not muscle-specific but expressed mainly in epidermal cells, indicating a function for mbl not only in muscles and the nervous system