Assisting classical paintings restoration : efficient paint loss detection and descriptor-based inpainting using shared pretraining

In the restoration process of classical paintings, one of the tasks is to map paint loss for documentation and analysing purposes. Because this is such a sizable and tedious job automatic techniques are highly on demand. The currently available tools allow only rough mapping of the paint loss areas while still requiring considerable manual work. We develop here a learning method for paint loss detection that makes use of multimodal image acquisitions and we apply it within the current restoration of the Ghent Altarpiece. Our neural network architecture is inspired by a multiscale convolutional neural network known as U-Net. In our proposed model, the downsampling of the pooling layers is omitted to enforce translation invariance and the convolutional layers are replaced with dilated convolutions. The dilated convolutions lead to denser computations and improved classification accuracy. Moreover, the proposed method is designed such to make use of multimodal data, which are nowadays routinely acquired during the restoration of master paintings, and which allow more accurate detection of features of interest, including paint losses. Our focus is on developing a robust approach with minimal user-interference. Adequate transfer learning is here crucial in order to extend the applicability of pre-trained models to the paintings that were not included in the training set, with only modest additional re-training. We introduce a pre-training strategy based on a multimodal, convolutional autoencoder and we fine-tune the model when applying it to other paintings. We evaluate the results by comparing the detected paint loss maps to manual expert annotations and also by running virtual inpainting based on the detected paint losses and comparing the virtually inpainted results with the actual physical restorations. The results indicate clearly the efficacy of the proposed method and its potential to assist in the art conservation and restoration processes

Cytosine Modifications and Distinct Functions of TET1 on Tumorigenesis

Vast emerging evidences are linking the base modifications and gene expression involved in essential metabolic pathways. Among the base modification markers extensively studied, 5-methylcytosine (5mC) and its oxidative derivatives (5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine (5-caC)) dynamically occur in DNA and RNA and have been acknowledged as the important epigenetic markers involved in regulation of cellular biological processes. The modification of C has been characterized biochemically, molecularly, and phenotypically, including elucidation of its methyltransferase complexes (writer), demethylases (eraser), 10-11 translocation proteins (TETs), and direct interaction proteins (readers). The levels and the landscapes of these epigenetic markers in the epitranscriptomes and epigenomes are precisely and dynamically regulated by the fine-tuned coordination of the writers and erasers in accordance with stages of the growth, development, and reproduction as naturally programmed during the life span. In mammalian genome, the TET family is consisted of three members, including TET1, TET2, and TET3. The link between aberrant modifications and diseases, such as cancers, neurodegenerative disorders, and heart diseases, has been appreciated. This review article will highlight the research advances in the writers and erasers for the modifications of cytosine in genome, as well as the dual function of TET1 in tumorigenesis as a tumor suppressor and a promoter. Additionally, the future research directions are addressed

Evaluation of Panoramic Radiographs in Relation to the Mandibular Third Molar and to Incidental Findings in an Adult Population

Objectives  The aim was to evaluate the characteristics of the mandibular third molars, especially in relation to the inferior alveolar nerve. Further aims were to investigate incidental findings in panoramic radiographs in an adult population, and to investigate image quality related to patient positioning. Materials and Methods  From a previous study with 451 randomly selected adult participants who lived in Sweden, 442 panoramic radiographs from four dental public health clinics were used. The third molars’ characteristics and relation to inferior alveolar nerve were evaluated. Incidental findings and patient positioning were recorded. Statistical Analysis  Frequency analysis was used to investigate the occurrence of all findings and their possible interconnections. Whether the patients’ age or gender had an impact or not was also analyzed. Results  The third molars were erupted in vertical position among 73% regardless of age. When retained or semi-retained, they were most commonly in mesioangular positions. The inferior alveolar nerve was located inferior to the roots in 52%, whereas an overlapped position was most common if the third molar was retained (90%), semi-retained (83%) or the age was less than 30 years (66%). Common incidental findings were apical radiolucencies, idiopathic osteosclerosis, and tooth fragments. Suboptimal patient positioning was found in one-third of the radiographs. Conclusions  Panoramic radiography is a useful method to evaluate third molar prior to surgical removal and may be the only image required. Most incidental findings on panoramic radiographs does not seem to require any further odontological management.publishedVersio

Non-coding RNA in Fragile X Syndrome and Converging Mechanisms Shared by Related Disorders

Fragile X syndrome (FXS) is one of the most common forms of hereditary intellectual disability. It is also a well-known monogenic cause of autism spectrum disorders (ASD). Repetitive trinucleotide expansion of CGG repeats in the 5′-UTR of FMR1 is the pathological mutation. Full mutation CGG repeats epigenetically silence FMR1 and thus lead to the absence of its product, fragile mental retardation protein (FMRP), which is an indispensable translational regulator at synapsis. Loss of FMRP causes abnormal neural morphology, dysregulated protein translation, and distorted synaptic plasticity, giving rise to FXS phenotypes. Non-coding RNAs, including siRNA, miRNA, and lncRNA, are transcribed from DNA but not meant for protein translation. They are not junk sequence but play indispensable roles in diverse cellular processes. FXS is the first neurological disorder being linked to miRNA pathway dysfunction. Since then, insightful knowledge has been gained in this field. In this review, we mainly focus on how non-coding RNAs, especially the siRNAs, miRNAs, and lncRNAs, are involved in FXS pathogenesis. We would also like to discuss several potential mechanisms mediated by non-coding RNAs that may be shared by FXS and other related disorders

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

The rise of multi-drug resistant (MDR) and extensively drug resistant (XDR) tuberculosis around the world, including in industrialized nations, poses a great threat to human health and defines a need to develop new, effective and inexpensive anti-tubercular agents. Previously we developed a chemical systems biology approach to identify off-targets of major pharmaceuticals on a proteome-wide scale. In this paper we further demonstrate the value of this approach through the discovery that existing commercially available drugs, prescribed for the treatment of Parkinson's disease, have the potential to treat MDR and XDR tuberculosis. These drugs, entacapone and tolcapone, are predicted to bind to the enzyme InhA and directly inhibit substrate binding. The prediction is validated by in vitro and InhA kinetic assays using tablets of Comtan, whose active component is entacapone. The minimal inhibition concentration (MIC99) of entacapone for Mycobacterium tuberculosis (M.tuberculosis) is approximately 260.0 µM, well below the toxicity concentration determined by an in vitro cytotoxicity model using a human neuroblastoma cell line. Moreover, kinetic assays indicate that Comtan inhibits InhA activity by 47.0% at an entacapone concentration of approximately 80 µM. Thus the active component in Comtan represents a promising lead compound for developing a new class of anti-tubercular therapeutics with excellent safety profiles. More generally, the protocol described in this paper can be included in a drug discovery pipeline in an effort to discover novel drug leads with desired safety profiles, and therefore accelerate the development of new drugs

Transcriptomic Dissection of Sexual Differences in \u3cem\u3eBemisia tabaci\u3c/em\u3e, an Invasive Agricultural Pest Worldwide

Sex difference involving chromosomes and gene expression has been extensively documented. In this study, the gender difference in the sweetpotato whitefly Bemisia tabaci was investigated using Illumina-based transcriptomic analysis. Gender-based RNAseq data produced 27 Gb reads, and subsequent de novo assembly generated 93,948 transcripts with a N50 of 1,853 bp. A total of 1,351 differentially expressed genes were identified between male and female B. tabaci, and majority of them were female-biased. Pathway and GO enrichment experiments exhibited a gender-specific expression, including enriched translation in females, and enhanced structural constituent of cuticle in male whiteflies. In addition, a putative transformer2 gene (tra2) was cloned, and the structural feature and expression profile of tra2 were investigated. Sexually dimorphic transcriptome is an uncharted territory for the agricultural insect pests. Molecular understanding of sex determination in B. tabaci, an emerging invasive insect pest worldwide, will provide potential molecular target(s) for genetic pest control alternatives

Induced Pluripotent Stem Cells: Generation Strategy and Epigenetic Mystery behind Reprogramming

Possessing the ability of self-renewal with immortalization and potential for differentiation into different cell types, stem cells, particularly embryonic stem cells (ESC), have attracted significant attention since their discovery. As ESC research has played an essential role in developing our understanding of the mechanisms underlying reproduction, development, and cell (de)differentiation, significant efforts have been made in the biomedical study of ESC in recent decades. However, such studies of ESC have been hampered by the ethical issues and technological challenges surrounding them, therefore dramatically inhibiting the potential applications of ESC in basic biomedical studies and clinical medicine. Induced pluripotent stem cells (iPSCs), generated from the reprogrammed somatic cells, share similar characteristics including but not limited to the morphology and growth of ESC, self-renewal, and potential differentiation into various cell types. The discovery of the iPSC, unhindered by the aforementioned limitations of ESC, introduces a viable alternative to ESC. More importantly, the applications of iPSC in the development of disease models such as neurodegenerative disorders greatly enhance our understanding of the pathogenesis of such diseases and also facilitate the development of clinical therapeutic strategies using iPSC generated from patient somatic cells to avoid an immune rejection. In this review, we highlight the advances in iPSCs generation methods as well as the mechanisms behind their reprogramming. We also discuss future perspectives for the development of iPSC generation methods with higher efficiency and safety

Reference Gene Selection for qRT-PCR Analysis in the Sweetpotato Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae)

BACKGROUND: Accurate evaluation of gene expression requires normalization relative to the expression of reliable reference genes. Expression levels of classical reference genes can differ, however, across experimental conditions. Although quantitative real-time PCR (qRT-PCR) has been used extensively to decipher gene function in the sweetpotato whitefly Bemisia tabaci, a world-wide pest in many agricultural systems, the stability of its reference genes has rarely been validated. RESULTS: In this study, 15 candidate reference genes from B. tabaci were evaluated using two Excel-based algorithms geNorm and Normfinder under a diverse set of biotic and abiotic conditions. At least two reference genes were selected to normalize gene expressions in B. tabaci under experimental conditions. Specifically, for biotic conditions including host plant, acquisition of a plant virus, developmental stage, tissue (body region of the adult), and whitefly biotype, ribosomal protein L29 was the most stable reference gene. In contrast, the expression of elongation factor 1 alpha, peptidylprolyl isomerase A, NADH dehydrogenase, succinate dehydrogenase complex subunit A and heat shock protein 40 were consistently stable across various abiotic conditions including photoperiod, temperature, and insecticide susceptibility. CONCLUSION: Our finding is the first step toward establishing a standardized quantitative real-time PCR procedure following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guideline in an agriculturally important insect pest, and provides a solid foundation for future RNA interference based functional study in B. tabaci

Transcriptomic and proteomic responses of sweetpotato whitefly, Bemisia tabaci, to thiamethoxam

BACKGROUND: The sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is one of the most widely distributed agricultural pests. Although it has developed resistance to many registered insecticides including the neonicotinoid insecticide thiamethoxam, the mechanisms that regulate the resistance are poorly understood. To understand the molecular basis of thiamethoxam resistance, omics analyses were carried out to examine differences between resistant and susceptible B. tabaci at both transcriptional and translational levels. RESULTS: A total of 1,338 mRNAs and 52 proteins were differentially expressed between resistant and susceptible B. tabaci. Among them, 11 transcripts had concurrent transcription and translation profiles. KEGG analysis mapped 318 and 35 differentially expressed genes and proteins, respectively, to 160 and 59 pathways (p CONCLUSIONS: This study demonstrates the applicability of high-throughput omics tools for identifying molecular candidates related to thiamethoxam resistance in an agricultural important insect pest. In addition, transcriptomic and proteomic analyses provide a solid foundation for future functional investigations into the complex molecular mechanisms governing the neonicotinoid resistance in whiteflies

Rapid spread of tomato yellow leaf curl virus in China is aided differentially by two invasive whiteflies

BACKGROUND: Tomato yellow leaf curl virus (TYLCV) was introduced into China in 2006, approximately 10 years after the introduction of an invasive whitefly, Bemisia tabaci (Genn.) B biotype. Even so the distribution and prevalence of TYLCV remained limited, and the economic damage was minimal. Following the introduction of Q biotype into China in 2003, the prevalence and spread of TYLCV started to accelerate. This has lead to the hypothesis that the two biotypes might not be equally competent vectors of TYLCV. METHODOLOGY/PRINCIPAL FINDINGS: The infection frequency of TYLCV in the field-collected B. tabaci populations was investigated, the acquisition and transmission capability of TYLCV by B and Q biotypes were compared under the laboratory conditions. Analysis of B. tabaci populations from 55 field sites revealed the existence of 12 B and 43 Q biotypes across 18 provinces in China. The acquisition and transmission experiments showed that both B and Q biotypes can acquire and transmit the virus, however, Q biotype demonstrated superior acquisition and transmission capability than its B counterparts. Specifically, Q biotype acquired significantly more viral DNA than the B biotype, and reached the maximum viral load in a substantially shorter period of time. Although TYLCV was shown to be transmitted horizontally by both biotypes, Q biotype exhibited significantly higher viral transmission frequency than B biotype. Vertical transmission result, on the other hand, indicated that TYLCV DNA can be detected in eggs and nymphs, but not in pupae and adults of the first generation progeny. CONCLUSIONS/SIGNIFICANCE: These combined results suggested that the epidemiology of TYLCV was aided differentially by the two invasive whiteflies (B and Q biotypes) through horizontal but not vertical transmission of the virus. This is consistent with the concomitant eruption of TYLCV in tomato fields following the recent rapid invasion of Q biotype whitefly in China