Miracle-dz/UniFAR-FTUs huggingface dataset:
TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data

Tissue microarrays (TMAs) allow multiplexed analysis of tissue samples and are frequently used to estimate biomarker protein expression in tumour biopsies. TMA Navigator (www.tmanavigator.org) is an open access web application for analysis of TMA data and related information, accommodating categorical, semi-continuous and continuous expression scores. Non-biological variation, or batch effects, can hinder data analysis and may be mitigated using the ComBat algorithm, which is incorporated with enhancements for automated application to TMA data. Unsupervised grouping of samples (patients) is provided according to Gaussian mixture modelling of marker scores, with cardinality selected by Bayesian information criterion regularization. Kaplan–Meier survival analysis is available, including comparison of groups identified by mixture modelling using the Mantel-Cox log-rank test. TMA Navigator also supports network inference approaches useful for TMA datasets, which often constitute comparatively few markers. Tissue and cell-type specific networks derived from TMA expression data offer insights into the molecular logic underlying pathophenotypes, towards more effective and personalized medicine. Output is interactive, and results may be exported for use with external programs. Private anonymous access is available, and user accounts may be generated for easier data management.
Adherence in dental settings.

UNLABELLED Adherence is of central importance to promoting positive oral health behaviours. Understanding the processes involved in behaviour change and how change may be sustained is essential to support patients to change their behaviour successfully. We review the concept of adherence, the oral health behaviours of interest to the dental team and how change around these behaviours is currently managed. Theoretical models of behaviour change are reviewed and their possible implications for every day practice described. CLINICAL RELEVANCE This paper will help the dental team to understand the processes involved in behaviour change and support their patients to adopt and sustain positive oral health behaviours.
A Massively Parallel Fluorescence Assay to Characterize the Effects of Synonymous Mutations on TP53 Expression

Although synonymous mutations can affect gene expression, they have generally not been considered in genomic studies that focus on mutations that increase the risk of cancer. However, mounting evidence implicates some synonymous mutations as driver mutations in cancer. Here, a massively parallel assay, based on cell sorting of a reporter containing a segment of p53 fused to GFP, was used to measure the effects of nearly all synonymous mutations in exon 6 of TP53. In this reporter context, several mutations within the exon caused strong expression changes including mutations that may cause potential gain or loss of function. Further analysis indicates that these effects are largely attributed to errors in splicing, including exon skipping, intron inclusion, and exon truncation, resulting from mutations both at exon–intron junctions and within the body of the exon. These mutations are found at extremely low frequencies in healthy populations and are enriched a few-fold in cancer genomes, suggesting that some of them may be driver mutations in TP53. This assay provides a general framework to identify previously unknown detrimental synonymous mutations in cancer genes. Implications: Using a massively parallel assay, this study demonstrates that synonymous mutations in the TP53 gene affect protein expression, largely through their impact on splicing. Visual Overview: http://mcr.aacrjournals. org/content/molcanres/15/10/1301/F1.large. jpg. Mol Cancer Res; 15(10); 1301–7. ©2017 AACR. Visual Overview
Association between plasma trans‐fatty acid concentrations and diabetes in a nationally representative sample of US adults

A diet high in trans‐fatty acids (TFA) induces insulin resistance in rodent models and primates. However, previous epidemiological studies on the association between TFAs, based primarily on self‐reported intake from the diet, and diabetes in humans have yielded conflicting results. Herein we examined the associations of objectively measured plasma TFA concentrations with diabetes in a large population‐based study among US adults.
Mapping breast cancer blood flow index, composition, and metabolism in a human subject using combined diffuse optical spectroscopic imaging and diffuse correlation spectroscopy

Abstract. Diffuse optical spectroscopic imaging (DOSI) and diffuse correlation spectroscopy (DCS) are model-based near-infrared (NIR) methods that measure tissue optical properties (broadband absorption, μa, and reduced scattering, μs′) and blood flow (blood flow index, BFI), respectively. DOSI-derived μa values are used to determine composition by calculating the tissue concentration of oxy- and deoxyhemoglobin (HbO2, HbR), water, and lipid. We developed and evaluated a combined, coregistered DOSI/DCS handheld probe for mapping and imaging these parameters. We show that uncertainties of 0.3 mm−1 (37%) in μs′ and 0.003 mm−1 (33%) in μa lead to ∼53% and 9% errors in BFI, respectively. DOSI/DCS imaging of a solid tissue-simulating flow phantom and a breast cancer patient reveals well-defined spatial distributions of BFI and composition that clearly delineates both the flow channel and the tumor. BFI reconstructed with DOSI-corrected μa and μs′ values had a tumor/normal contrast of 2.7, 50% higher than the contrast using commonly assumed fixed optical properties. In conclusion, spatially coregistered imaging of DOSI and DCS enhances intrinsic tumor contrast and information content. This is particularly important for imaging diseased tissues where there are significant spatial variations in μa and μs′ as well as potential uncoupling between flow and metabolism.
Factors Associated With Metachronous Gastric Cancer Development After Endoscopic Submucosal Dissection for Early Gastric Cancer

Goals: To clarify the factors associated with metachronous gastric cancer development after endoscopic submucosal dissection (ESD) for early gastric cancer. Background: Patients who undergo ESD for early gastric cancer have an appreciable risk of developing metachronous gastric cancer. However, there have been few reports on the association between life style and the development of such cancer. Study: Patients with early gastric cancer who underwent ESD at our institution between 2003 and 2012 were enrolled. Metachronous gastric cancer was defined as secondary gastric cancer detected >1 year after initial ESD. Factors, including age, gender, body mass index, eradication of Helicobacter pylori, cigarette smoking, drinking, and continuous use of a proton pump inhibitor, associated with metachronous gastric cancer development were evaluated by Cox proportional hazard regression analysis. Results: A total of 539 patients with a mean 53.6-month follow-up period were analyzed. The 5-year cumulative incidence of secondary gastric cancer was 13.0%. Multivariate analysis exhibited that age of 60 years and above [hazard ratio (95% confidence interval)=4.05 (1.23-13.4)] and cigarette smoking [2.12 (1.19-3.78)] were independent risk factors for metachronous gastric cancer development. Furthermore, ≥20 pack-years of smoking [1.51 (1.03-2.24)] was a significant risk factor with a dose-response relationship (P for trend=0.042). There was no significant association between Helicobacter pylori eradication and metachronous gastric cancer development. Conclusions: This is the first study to demonstrate the detailed association between cigarette smoking and metachronous gastric cancer development.
Abundance of Hepatic Transporters in Caucasians: A Meta-Analysis

This study aimed to derive quantitative abundance values for key hepatic transporters suitable for in vitro–in vivo extrapolation within a physiologically based pharmacokinetic modeling framework. A meta-analysis was performed whereby data on abundance measurements, sample preparation methods, and donor demography were collated from the literature. To define values for a healthy Caucasian population, a subdatabase was created whereby exclusion criteria were applied to remove samples from non-Caucasian individuals, those with underlying disease, or those with subcellular fractions other than crude membrane. Where a clinically relevant active genotype was known, only samples from individuals with an extensive transporter phenotype were included. Authors were contacted directly when additional information was required. After removing duplicated samples, the weighted mean, geometric mean, standard deviation, coefficient of variation, and between-study homogeneity of transporter abundances were determined. From the complete database containing 24 transporters, suitable abundance data were available for 11 hepatic transporters from nine studies after exclusion criteria were applied. Organic anion transporting polypeptides OATP1B1 and OATP1B3 showed the highest population abundance in healthy adult Caucasians. For several transporters, the variability in abundance was reduced significantly once the exclusion criteria were applied. The highest variability was observed for OATP1B3 > OATP1B1 > multidrug resistance protein 2 > multidrug resistance gene 1. No relationship was found between transporter expression and donor age. To our knowledge, this study provides the first in-depth analysis of current quantitative abundance data for a wide range of hepatic transporters, with the aim of using these data for in vitro–in vivo extrapolation, and highlights the significance of investigating the background of tissue(s) used in quantitative transporter proteomic studies. Similar studies are now warranted for other ethnicities.
Towards the Improvement of Automatic Emotion Pre-annotation with Polarity and Subjective Information

Emotion detection has a high potential positive impact on the benefit of business, society, politics or education. Given this, the main objective of our research is to contribute to the resolution of one of the most important challenges in textual emotion detection: emotional corpora annotation. This will be tackled by proposing a semi-automatic methodology. It consists in two main phases: (1) an automatic process to pre-annotate the unlabelled sentences with a reduced number of emotional categories; and (2) a manual process of refinement where human annotators will determine which is the dominant emotion between the pre-defined set. Our objective in this paper is to show the pre-annotation process, as well as to evaluate the usability of subjective and polarity information in this process. The evaluation performed confirms clearly the benefits of employing the polarity and subjective information on emotion detection and thus endorses the relevance of our approach.
Cyberlindnera xishuangbannaensis f.a., sp. nov., a yeast isolated from rotting wood.

Three strains representing a novel species of yeast were isolated from samples of rotting wood collected from Xishuangbanna Tropical Rainforest in Yunnan Province, PR China. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) rRNA gene revealed that the novel species is a member of the genus Cyberlindnera, although the formation of ascospores was not observed. The novel species was related most closely to the type strain of the species Candida pattaniensis, but they had a 0.5 % sequence divergence (3 substitutions, 0 gap) in the D1/D2 domain and a 5.4 % sequence divergence (21 substitutions, 10 gaps) in the ITS region. The novel species could also be differentiated from the closely related species by some biochemical and physiological characteristics. The species name Cyberlindnera xishuangbannaensis f.a. , sp. nov. is proposed to accommodate these strains, with NYNU 16752T (=CICC 33163T=CBS 14692T) designated as the type strain. The MycoBank number is MB 822199.
The effect of composition on properties of blends from recylced rubber and polypropylene

Incorporation of waste (ethylene propylene diene rubber) EPDM into polyolefins has emerged as a new recycling technique that is eco-friendly and cost effective. The purpose of this study was to recycle EPDM, as well as to develop new impact modified blends. This study, which involved reactive blending of waste EPDM and polypropylene (PP) in a co-rotating twin screw extruder in the ratio range of 10/90 to 60/40, determined the effect of t-butyl hydroperoxide compatibilizer, low and high MFI grade of PP and ethylene-propylene impact copolymer on the mechanical properties of the blends. Formulations were injection molded and subsequently tested for tensile, flexural and impact properties. It was noted that the peroxide and the impact copolymer significantly improved the tensile elongation at break and impact resistance, but resulted in a decrease in the modulus. The approach of this investigation was to determine the optimum blending ratio of the components to achieve a balance in the flexural modulus and impact strength.
Engineered Nanocomposites for Additive Manufacturing of Microwave Electronics

Four types of high-permittivity and low-loss composite substrates based on a Polydimethylsiloxane (PDMS) elastomer host matrix, and Cyclo-Olefin Polymer (COP) reinforced by Ba0.55Sr0. 45TiO3 and MgCaTiO2 micro-fillers, with volume loading concentration up to 49%, have been prepared and characterized up to 20 GHz using cavity resonators. The high-k ceramic powders were sintered at temperatures up to 1500°C to further enhance the dielectric properties. The 49% loaded PDMS-Ba0.55Sr0. 45TiO3 composites with 1340°C sintered fillers have shown a relative permittivity er of ~23.51 and loss tangent tanδd < 0.047 at frequencies up to 20 GHz. Meanwhile the 39% loaded PDMS-Ba0.55Sr0. 45TiO3 composites with 1340°C sintered fillers have shown a relative permittivity er of ~15.02 and loss tangent tanδd < 0.042 at frequencies up to 16 GHz. On the other hand, the 37% loaded PDMS-MgCaTiO2 composites with 1100°C sintered fillers have exhibited relative permittivity er of ~12.19 and loss tangent tanδd < 0.021 at frequencies up.
Fabrication of the blazed convex grating by holographic ion beam etching

The blazed convex grating is one of the key elements in Offner imaging spectrometers. In this paper the diffraction characteristics of the blazed convex grating is investigated by using rigorous coupled-wave analysis. The results indicate that within the wavelength from 1 μm to 2.5 μm, the first-order diffraction efficiency can be over 40% through controlling the blazed angle of blazed grating. Furthermore, when the blazed angle is 3.9 degree, the first-order diffraction efficiency is still over 40% with the vertex angles between 120 degree and 150 degree. The blazed convex grating with the spatial frequency of 73 L/mm in the center will be fabricated by holographic lithography-ion beam etching.
Oscillatory Survival Probability: Analytical and Numerical Study of a Non-Poissonian Exit Time

We consider the escape of a planar diffusion process from the domain of attraction $\Omega$ of a stable focus of the drift in the limit of small diffusion. The boundary $\partial\Omega$ of $\Omega$ is an unstable limit cycle of the drift, and the focus is close to the limit cycle. A new phenomenon of oscillatory decay of the peaks of the survival probability of the process in $\Omega$ emerges for a specific distance of the focus to the boundary which depends on the amplitude of the diffusion coefficient. We show that the phenomenon is due to the complex-valued second eigenvalue $\lambda_2(\Omega)$ of the Fokker--Planck operator with Dirichlet boundary conditions. The dominant oscillation frequency, $1/\mathfrak{I}m\{\lambda_2(\Omega)\}$, is independent of the relative noise strength. The density of exit points on $\partial\Omega$ is concentrated in a small arc of $\partial\Omega$ closest to the focus. When the focus approaches the boundary, the principal eigenvalue, the reciprocal of which is the mean esc.
Non-autonomous crosstalk between the Jak/Stat and Egfr pathways mediates Apc1-driven intestinal stem cell hyperplasia in the Drosophila adult midgut

Inactivating mutations within adenomatous polyposis coli (APC), a negative regulator of Wnt signaling, are responsible for most sporadic and hereditary forms of colorectal cancer (CRC). Here, we use the adult Drosophila midgut as a model system to investigate the molecular events that mediate intestinal hyperplasia following loss of Apc in the intestine. Our results indicate that the conserved Wnt target Myc and its binding partner Max are required for the initiation and maintenance of intestinal stem cell (ISC) hyperproliferation following Apc1 loss. Importantly, we find that loss of Apc1 leads to the production of the interleukin-like ligands Upd2/3 and the EGF-like Spitz in a Myc-dependent manner. Loss of Apc1 or high Wg in ISCs results in non-cell-autonomous upregulation of upd3 in enterocytes and subsequent activation of Jak/Stat signaling in ISCs. Crucially, knocking down Jak/Stat or Spitz/Egfr signaling suppresses Apc1-dependent ISC hyperproliferation. In summary, our results uncover a novel non-cell-autonomous interplay between Wnt/Myc, Egfr and Jak/Stat signaling in the regulation of intestinal hyperproliferation. Furthermore, we present evidence suggesting potential conservation in mouse models and human CRC. Therefore, the Drosophila adult midgut proves to be a powerful genetic system to identify novel mediators of APC phenotypes in the intestine.
Information Extraction via Double Classification

Information Extraction is concerned with extracting relevant information from a (collection of) documents. We propose an approach consisting of two classification-based machine learning loops. In a first loop we look for the relevant sentences in a document. In the second loop, we perform a word-level classification. We test the system on the Software Jobs corpus and we do an extensive evaluation in which we discuss the influence of the different parameters. Furthermore we show that the type of evaluation method has an important influence on the results.
Unsupervised Speckle Level Estimation of SAR Images Using Texture Analysis and AR Model

In this paper, a new method is proposed for unsupervised speckle level estimation in synthetic aperture radar (SAR) images. It is assumed that fully developed speckle intensity has a Gamma distribution. Based on this assumption, estimation of the equivalent number of looks (ENL) is transformed into noise variance estimation in the logarithmic SAR image domain. In order to improve estimation accuracy, texture analysis is also applied to exclude areas where speckle is not fully developed (e.g., urban areas). Finally, the noise variance is estimated by a 2-dimensional autoregressive (AR) model. The effectiveness of the proposed method is verified with several SAR images from different SAR systems and simulated images. key words: AR model, equivalent number of looks (ENL), synthetic aperture radar (SAR), texture analysis.
Complete Genome Sequences of the Probiotic Lactic Acid Bacteria Lactobacillus helveticus D75 and D76

ABSTRACT Lactobacillus helveticus D75 and D76 were isolated from the intestinal tract of a healthy child. Both strains possess symbiotic, probiotic, and antagonistic activities. We have sequenced and annotated the whole genomes of L. helveticus D75 and D76 and have conducted a preliminary genome comparative analysis.
Experimental Study on RC Beams Strengthened with Externally Bonded FRP Sheets

In order to repair many structures damaged in Wenchuan earthquake,using carbon fiber reinforced polymer(CFRP) and glass fiber reinforced polymer(GFRP) to repair the reinforced concrete(RC) beams was studied.The failure types,stiffness change,crack developing characteristics and shear resistance were investigated.Beam size,stirrup ratio,FRP type and arrangements of sheets along the shear span were analyzed during experimental study.The test result indicated that CFRP or GFRP can increase the shear resistance and deformability greatly,and the rigidity of strengthened beams also increases obviously.Compared to strengthening with CFRP,the GFRP strengthening method increase the deformability and the utilization ratio of strengthening material.The shear resistance increases with the beam height,but not fit for the deformability.Increasing stirrup ratio can delay the crack appearing obviously,improve the cracking load and ultimate strength of strengthened beam,but reduce the ultimate deflection greatly.Finally,according to the analysis of test data,the theoretical and practical formula for calculating the bearing capacity of RC beams strengthened with FRP sheets was established.The results showed that the theoretical calculation is in accord with the experimental data.
Conserved Mosquito/Parasite Interactions Affect Development of Plasmodium falciparum in Africa

In much of sub-Saharan Africa, the mosquito Anopheles gambiae is the main vector of the major human malaria parasite, Plasmodium falciparum. Convenient laboratory studies have identified mosquito genes that affect positively or negatively the developmental cycle of the model rodent parasite, P. berghei. Here, we use transcription profiling and reverse genetics to explore whether five disparate mosquito gene regulators of P. berghei development are also pertinent to A. gambiae/P. falciparum interactions in semi-natural conditions, using field isolates of this parasite and geographically related mosquitoes. We detected broadly similar albeit not identical transcriptional responses of these genes to the two parasite species. Gene silencing established that two genes affect similarly both parasites: infections are hindered by the intracellular local activator of actin cytoskeleton dynamics, WASP, but promoted by the hemolymph lipid transporter, ApoII/I. Since P. berghei is not a natural parasite of A. gambiae, these data suggest that the effects of these genes have not been drastically altered by constant interaction and co-evolution of A. gambiae and P. falciparum; this conclusion allowed us to investigate further the mode of action of these two genes in the laboratory model system using a suite of genetic tools and infection assays. We showed that both genes act at the level of midgut invasion during the parasite's developmental transition from ookinete to oocyst. ApoII/I also affects the early stages of oocyst development. These are the first mosquito genes whose significant effects on P. falciparum field isolates have been established by direct experimentation. Importantly, they validate for semi-field human malaria transmission the concept of parasite antagonists and agonists.