Investigation of SHG in new scandium borate with three cations by the Kurtz-Perry method

This work is dedicated to study the optical properties of scandium borates with the general formula RExPrySc2+z(BO3)4 (x + y + z = 2, RE = Nd, Sm, Tb, Tm, Yb), grown by the TSSG method. The structure, absorption and luminescence of these crystals have been investigated

Linear and nonlinear optical properties of trigonal borate crystals K7MIn2-xYbx(B5O10)3 (M = Ca, Sr, Ba; x=0…2) with isolated B5O10 units

Noncentrosymmetric borates K7MIn2−xYbx(B5O10)3 (M = Ca, Sr, Ba; x = 0…2) were synthesized by the solid state reaction and the crystals were successfully grown by the top seeded solution growth method using the K2O-B2O3-MF2 flux. According to Rietveld refinement, the crystal structure belongs to the noncentrosymmetric R32 space group. Also, the octahedrally coordinated In atoms are located at wide ranges ∼8 Å which may be promising for phosphor and laser applications. Samples with ytterbium show a characteristic emission band in the range of 950–1050 nm related to the 2F5/2 → 2F7/2 transition of Yb3+ ions that is commonly used for laser generation. IR, Raman and absorption spectra were obtained for the samples as well. The short cut edge of UV absorption, SHG intensity comparable with KDP and low concentration quenching of luminescence suggest that the K7MIn2−xYbx(B5O10)3 borates are promising self-frequency doubling materials

UNCLES: Method for the identification of genes differentially consistently co-expressed in a specific subset of datasets

Background: Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently representative of real datasets. Results: Here, we propose an unsupervised method for the unification of clustering results from multiple datasets using external specifications (UNCLES). This method has the ability to identify the subsets of genes consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets, and to identify the subsets of genes consistently co-expressed in all given datasets. We also propose the M-N scatter plots validation technique and adopt it to set the parameters of UNCLES, such as the number of clusters, automatically. Additionally, we propose an approach for the synthesis of gene expression datasets using real data profiles in a way which combines the ground-truth-knowledge of synthetic data and the realistic expression values of real data, and therefore overcomes the problem of faithfulness of synthetic expression data modelling. By application to those datasets, we validate UNCLES while comparing it with other conventional clustering methods, and of particular relevance, biclustering methods. We further validate UNCLES by application to a set of 14 real genome-wide yeast datasets as it produces focused clusters that conform well to known biological facts. Furthermore, in-silico-based hypotheses regarding the function of a few previously unknown genes in those focused clusters are drawn. Conclusions: The UNCLES method, the M-N scatter plots technique, and the expression data synthesis approach will have wide application for the comprehensive analysis of genomic and other sources of multiple complex biological datasets. Moreover, the derived in-silico-based biological hypotheses represent subjects for future functional studies.The National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0310-1004)

Impact of optical coherence tomography on diagnostic decision-making by UK community optometrists: a clinical vignette study.

PURPOSE: In recent years, there has been widespread investment in imaging technologies by community optometrists in the UK, most notably optical coherence tomography (OCT). The aim of the current study was to determine the value of OCT in the diagnosis of posterior segment diseases in a representative sample of community optometrists using a clinical vignette methodology. METHODS: A group of community optometrists (n = 50) initially completed a standardised training package on OCT interpretation followed by a computer-based assessment featuring 52 clinical vignettes, containing images of healthy (n = 8) or glaucomatous (n = 18) discs or healthy (n = 8) or diseased (n = 18) fundi. Each vignette featured either a single fundus/disc photographic image, or a combination of a fundus/disc image with the corresponding OCT scan. An expert panel confirmed that the fundus images presented alone and those in combination with OCT data were of a similar level of difficulty and that the cases were typical of those seen in primary care. For each case, the optometrist selected their diagnosis from a pull-down list and reported their confidence in their decision using a 10-point Likert scale. Pairwise comparisons of the fundus image alone and fundus image/OCT combination were made for both diagnostic performance and confidence. RESULTS: The mean percentage of correct diagnoses using fundus imaging alone was 62% (95% CI 59-64%) and for the combination of fundus image/OCT was 80% (95% CI 77-82%). The mean false negative rate with fundus alone was 27% reducing to 13% with the OCT combination. Median confidence scores for fundus imaging alone was 8.0 (IQR 7.0-8.0) and 8.3 (IQR 8.0-9.0) for the combination. Improvements in performance and confidence were statistically significant (p < 0.001). CONCLUSION: The results from this vignette study suggests that OCT improves optometrists' diagnostic performance compared to fundus observation alone. These initial results suggest that OCT provides valuable additional data that could augment case-finding for glaucoma and retinal disease; however, further research is needed to assess its diagnostic performance in a routine clinical practice setting

Suprasellar cysts: clinical presentation, surgical indications, and optimal surgical treatment

<p>Abstract</p> <p>Background</p> <p>To describe the clinical presentation of suprasellar cysts (SSCs) and surgical indications, and compare the treatment methods of endoscopic ventriculocystostomy (VC) and ventriculocystocisternotomy (VCC).</p> <p>Methods</p> <p>We retrospectively reviewed the records of 73 consecutive patients with SSC who were treated between June 2002 and September 2009. Twenty-two patients were treated with VC and 51 with VCC. Outcome was assessed by clinical examination and magnetic resonance imaging.</p> <p>Results</p> <p>The patients were divided into five groups based on age at presentation: age less than 1 year (n = 6), 1-5 years (n = 36), 6-10 years (n = 15), 11-20 years (n = 11), and 21-53 years (n = 5). The main clinical presentations were macrocrania (100%), motor deficits (50%), and gaze disturbance (33.3%) in the age less than 1 year group; macrocrania (75%), motor deficits (63.9%), and gaze disturbance (27.8%) in the 1-5 years group; macrocrania (46.7%), symptoms of raised intracranial pressure (ICP) (40.0%), endocrine dysfunction (40%), and seizures (33.3%) in the 6-10 years group; symptoms of raised ICP (54.5%), endocrine dysfunction (54.5%), and reduced visual field or acuity (36.4%) in the 11-20 years group; and symptoms of raised ICP (80.0%) and reduced visual field or acuity (40.0%) in the 21-53 years group. The overall success rate of endoscopic fenestration was 90.4%. A Kaplan-Meier curve for long-term efficacy of the two treatment modalities showed better results for VCC than for VC (p = 0.008).</p> <p>Conclusions</p> <p>Different age groups with SSCs have different main clinical presentations. VCC appears to be more efficacious than VC.</p

In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer

© The Author(s), 2017. Background Hypoxia is a characteristic of breast tumours indicating poor prognosis. Based on the assumption that those genes which are up-regulated under hypoxia in cell-lines are expected to be predictors of poor prognosis in clinical data, many signatures of poor prognosis were identified. However, it was observed that cell line data do not always concur with clinical data, and therefore conclusions from cell line analysis should be considered with caution. As many transcriptomic cell-line datasets from hypoxia related contexts are available, integrative approaches which investigate these datasets collectively, while not ignoring clinical data, are required. Results We analyse sixteen heterogeneous breast cancer cell-line transcriptomic datasets in hypoxia-related conditions collectively by employing the unique capabilities of the method, UNCLES, which integrates clustering results from multiple datasets and can address questions that cannot be answered by existing methods. This has been demonstrated by comparison with the state-of-the-art iCluster method. From this collection of genome-wide datasets include 15,588 genes, UNCLES identified a relatively high number of genes (>1000 overall) which are consistently co-regulated over all of the datasets, and some of which are still poorly understood and represent new potential HIF targets, such as RSBN1 and KIAA0195. Two main, anti-correlated, clusters were identified; the first is enriched with MYC targets participating in growth and proliferation, while the other is enriched with HIF targets directly participating in the hypoxia response. Surprisingly, in six clinical datasets, some sub-clusters of growth genes are found consistently positively correlated with hypoxia response genes, unlike the observation in cell lines. Moreover, the ability to predict bad prognosis by a combined signature of one sub-cluster of growth genes and one sub-cluster of hypoxia-induced genes appears to be comparable and perhaps greater than that of known hypoxia signatures. Conclusions We present a clustering approach suitable to integrate data from diverse experimental set-ups. Its application to breast cancer cell line datasets reveals new hypoxia-regulated signatures of genes which behave differently when in vitro (cell-line) data is compared with in vivo (clinical) data, and are of a prognostic value comparable or exceeding the state-of-the-art hypoxia signatures.Dr. Abu-Jamous would like to acknowledge the financial assistance from Brunel University London. Professors Buffa and Harris acknowledge support from Cancer Research UK, EU framework 7, and the Oxford NIHR Biomedical Research Centre. Professor Harris acknowledges support from the Breast Cancer Research Foundation. Professor Nandi would like to acknowledge that this work was partly supported by the National Science Foundation of China grant number 61520106006 and the National Science Foundation of Shanghai grant number 16JC1401300. The funding bodies have no role in the design of the study, in the collection, analysis, and interpretation of data, or in writing the manuscript

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

BACKGROUND: Parasitic flatworms (Trematoda: Digenea) represent one of the most remarkable examples of drastic morphological diversity among the stages within a life cycle. Which genes are responsible for extreme differences in anatomy, physiology, behavior, and ecology among the stages? Here we report a comparative transcriptomic analysis of parthenogenetic and amphimictic generations in two evolutionary informative species of Digenea belonging to the family Psilostomatidae. METHODS: In this study the transcriptomes of rediae, cercariae and adult worm stages of Psilotrema simillimum and Sphaeridiotrema pseudoglobulus, were sequenced and analyzed. High-quality transcriptomes were generated, and the reference sets of protein-coding genes were used for differential expression analysis in order to identify stage-specific genes. Comparative analysis of gene sets, their expression dynamics and Gene Ontology enrichment analysis were performed for three life stages within each species and between the two species.RESULTS: Reference transcriptomes for P. simillimum and S. pseudoglobulus include 21,433 and 46,424 sequences, respectively. Among 14,051 orthologous groups (OGs), 1354 are common and specific for two analyzed psilostomatid species, whereas 13 and 43 OGs were unique for P. simillimum and S. pseudoglobulus, respectively. In contrast to P. simillimum, where more than 60% of analyzed genes were active in the redia, cercaria and adult worm stages, in S. pseudoglobulus less than 40% of genes had such a ubiquitous expression pattern. In general, 7805 (36.41%) and 30,622 (65.96%) of genes were preferentially expressed in one of the analyzed stages of P. simillimum and S. pseudoglobulus, respectively. In both species 12 clusters of co-expressed genes were identified, and more than a half of the genes belonging to the reference sets were included into these clusters. Functional specialization of the life cycle stages was clearly supported by Gene Ontology enrichment analysis.CONCLUSIONS: During the life cycles of the two species studied, most of the genes change their expression levels considerably, consequently the molecular signature of a stage is not only a unique set of expressed genes, but also the specific levels of their expression. Our results indicate unexpectedly high level of plasticity in gene regulation between closely related species. Transcriptomes of P. simillimum and S. pseudoglobulus provide high quality reference resource for future evolutionary studies and comparative analyses

Study of RBO3-ScBO3 phase diagrams and RSc3(BO3)4 orthoborates (R = La, Pr and Nd)

RBO3 – ScBO3 diagrams (R = La, Pr and Nd) were investigated by the solid state synthesis and DSC methods. In these systems the solid solutions based on RSc3(BO3)4, RBO3 and ScBO3 were identified. The single crystals of RSc3(BO3)4 were grown by spontaneous crystallization method from LiBO2-LiF flux. The borates containing Pr and Nd have typical luminescence in the red/IR range which correlated to Pr3+: 3P0 → 3H6, 1D2 → 3H4 (~ 620 nm), and 3P0 → 2F2, 1D2 → 3H5 (~ 655 nm) and Nd3+ electron transitions 4F3/2 → 4I9/2 (875 nm) and 4F3/2 → 4I11/2 (1055 nm). The luminescence intensity strongly depends on the concentration of the fluorophores. In addition the SHG efficiency (for radiation of Nd:YAG laser, 1064 nm) for grown PrSc3(BO3)4 crystals was found to be 1.85 times higher (deff) than for KDP revealing its high potential for various NLO application

Polymorphism in SmSc3(BO3)4: Crystal structure, luminescent and SHG properties

Low temperature C2/c and high temperature P321 modifications of SmxSc4-x (BO3)4 solid solutions were grown from LiBO2eLiF flux. These borates have typical luminescence for Sm3þ containing crystals with the two strongest peaks at 602 and 645 nm, which correspond to 4G5∕2 / 6H7∕2, 6H5∕2 electron transitions. In addition, the compounds were characterized by IR and Raman spectroscopy. SHG intensity for trigonal modification was found to be three times higher than that of KDP revealing its high potential for various NLO applications