Miracle-dz/UniFAR-FTUs huggingface dataset:
EGFR mutations in non-small cell lung cancer: an audit from West China Hospital

ABSTRACT Objectives: To discover the incidence and characteristics of EGFR mutations in non-small cell lung cancer (NSCLC) in a single, large cohort as a part of routine diagnostic investigations. Methods: We reviewed EGFR mutations investigated by Amplification Refractory Mutation System (ARMS) PCR (covering 29 known mutations) using DNA samples from FFPE tissue or cell clot specimens in a total of 3894 cases of NSCLC analysed between 2012-2014. Results: EGFR mutations are preferentially associated with adenocarcinomaand adenosquamous histology, particularly those well to moderately differentiated, and were significantly more common in female than male patients irrespective of histological subtypes. Exon 19 deletion (45.7%) and exon 21 L858R (45.6%) accounted for the vast majority of the EGFR mutations detected, with the remaining mutations being infrequent (<2%). Compound mutations were seen in 51 (3%) of the mutant cases, the combination of these compound mutations could be classified into three subgroups according to the potential impact of individual mutations on EGFR TKI therapy. Accordingly, 7 cases had both sensitive mutations, 4 cases harboured one sensitive and one less responsive /uncertain mutation, 19 cases contained one sensitive and one resistant change, and a further 21 cases had two less responsive /uncertain mutations. Conclusion: Our data represents the largest EGFR mutation survey based on routine clinical diagnostic laboratory data from a single institution, it confirms the incidence and characteristics of EGFR mutations in NSCLC seen in Asian patients, and also unravels the combinatorial nature of rare compound EGFR mutations.
WebUml: reverse engineering of web applications

Web applications have become complex and crucial for many firms, especially when combined with areas such as CRM (Customer Relationship Management) and BPR (Business Process Reengineering). Since then the scientific community has focused attention to Web application design, development, analysis, testing, by studying and proposing methodologies and tools. This paper describes an automatic tool for the construction of UML models from existing Web applications. This tool, named WebUml, generates class and state diagrams by analysing source code and by interacting with the Web server. This reverse engineering tool is based on source code static analysis and also applies mutational techniques in order to exploit the server side execution engine to accomplish part of the dynamic analysis. This tool will be the core of a testing suite under construction at our laboratory. WebUml generated models (diagrams) will be used as a base for test case generation and coverage analysis.
Psychological Experience of Parents of Children With Type 1 Diabetes

Purpose The purpose of this review is to describe the prevalence of psychological distress in parents of children with type 1 diabetes (T1DM), the relationship between parental psychological distress and health outcomes, and parents’ psychological experience of having a child with T1DM. Clinical and research implications are presented. Method A systematic mixed-studies review was undertaken to review the quantitative and qualitative research on the parental experience of having a child with T1DM. A total of 34 articles met the inclusion criteria and were included in the review. Results The prevalence of parental psychological distress across all studies ranged from 10% to 74%, with an average of 33.5% of parents reporting distress at diagnosis and 19% of parents reporting distress 1 to 4 years after diagnosis. Parental psychological distress in parents of children with T1DM, regardless of how it was defined, was associated with higher child self-report of stress and depressive symptoms, more problematic child behavior, and lower child self-report of quality of life. Parental psychological distress also had negative effects on diabetes management. Themes of the qualitative synthesis indicated that parents perceived T1DM as a difficult diagnosis that contributed to significant family disruption. Adjustment occurred over time; however, ongoing stress was experienced. Conclusions Screening for psychological distress in parents of children with T1DM is indicated, and preventive interventions are needed.
Intelligent Algorithm for Maximum Power Tracking of Photovoltaic Energy System

the maximum power point (MPP) of a photovoltaic array is an essential operation for any PV system. Thus, changing the environmental conditions causes different maximum power point (MPP) driving for non-uniform power feeding for the load. So, researchers have developed many MPPT algorithms to maximize and stabilize the power derived for the load. But, these algorithms still suffer from some limitations such as high cost, complexity and sometime instability with rapid changes in the environmental conditions. The proposed system introduces integration between the artificial neural networks (ANN) and the fuzzy logic controller (FLC) for achieving MPPT. It can improve the performance of the MPPT algorithm for obtaining a stable maximum power derived for the loads. The proposed MPPT algorithm has been applied for a PV system feeds the power for a camp that exposes the radiation site. The results obtained from the suggested system have proved its significant success for the practical applications.
Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells

One of the great mysteries of the nucleolus surrounds its disappearance during mitosis and subsequent reassembly at late mitosis. Here, the relative dynamics of nucleolar disassembly and reformation were dissected using quantitative 4D microscopy with fluorescent protein-tagged proteins in human stable cell lines. The data provide a novel insight into the fates of the three distinct nucleolar subcompartments and their associated protein machineries in a single dividing cell. Before the onset of nuclear envelope (NE) breakdown, nucleolar disassembly started with the loss of RNA polymerase I subunits from the fibrillar centers. Dissociation of proteins from the other subcompartments occurred with faster kinetics but commenced later, coincident with the process of NE breakdown. The reformation pathway also follows a reproducible and defined temporal sequence but the order of reassembly is shown not to be dictated by the order in which individual nucleolar components reaccumulate within the nucleus after mitosis.
WebEye - Automated Collection of Malicious HTTP Traffic

With malware detection techniques increasingly adopting machine learning approaches, the creation of precise training sets becomes more and more important. Large data sets of realistic web traffic, correctly classified as benign or malicious are needed, not only to train classic and deep learning algorithms, but also to serve as evaluation benchmarks for existing malware detection products. Interestingly, despite the vast number and versatility of threats a user may encounter when browsing the web, actual malicious content is often hard to come by, since prerequisites such as browser and operating system type and version must be met in order to receive the payload from a malware distributing server. In combination with privacy constraints on data sets of actual user traffic, it is difficult for researchers and product developers to evaluate anti-malware solutions against large-scale data sets of realistic web traffic. In this paper we present WebEye, a framework that autonomously creates realistic HTTP traffic, enriches recorded traffic with additional information, and classifies records as malicious or benign, using different classifiers. We are using WebEye to collect malicious HTML and JavaScript and show how datasets created with WebEye can be used to train machine learning based malware detection algorithms. We regard WebEye and the data sets it creates as a tool for researchers and product developers to evaluate and improve their AI-based anti-malware solutions against large-scale benchmarks.
Concurrent separation logic

Concurrent Separation Logic (CSL) was originally advanced in papers of the authors published in Theoretical Computer Science for John Reynolds's 70th Birthday Festschrift (2007). Preliminary versions appeared as invited papers in the CONCUR'04 conference proceedings. Foundational work leading to these papers began in 2002. Since then there have been significant developments stemming from CSL, both in theoretical and practical research. In this retrospective paper we describe the main ideas that underpin CSL, placing these ideas into historical context by summarizing the prevailing tendencies in concurrency verification and programming language semantics when the logic was being invented in 2002-2003. We end with a snapshot of the state-of-the-art as of 2016. Along the way we describe some of the main developments in the intervening period, and we attempt to classify the work that has been done, along broad lines. While we do not intend an exhaustive survey, we do hope to provide some general perspective on what has been achieved in the field, what remains to be done, and directions for future work.
Model Support Algorithm in Powder Based Three Dimensional Printer

Generally, rapid prototype system, it bases on the operation principle to process layer by layer, and has several kinds of hardware already. The input of STL file format has become the de facto standard in rapid prototyping. With the application of complex material, the variety of product-type using RP technology will be dramatically extended and, no more, be limited in model production. However under the structure of 3D printing, large item production will be possible only if specific support were applied. This study proposes the hardware and software integrated method with the subject of the three-dimensional printing. The hardware utilizes ink-jet of general two-dimensional printer and combines with the traversing mechanism and the process controls and model material, and piles up in accordance with default layer thickness. As the supporting structure in STL-file format is generated through the concepts of the 3D-printing support generating method which is carried out by performing projection and displacement of selected triangular surfaces and then the generated 3D model is further constructed by Open GL and saved in STL-file format. As STL file is read, and then builds adjacency to store into the topology data structure. After the operation of direct slicing rule, hundreds of contours in each layer are obtained by using Visual C ++ programming language and OpenGL library to implement the algorithm above. It can confirm exactness that the software output and systematic feasibility of integrating the hardware through the result of system integration test on the 3D printer.
Protective effect of miconazole on rat myelin sheaths following premature infant cerebral white matter injury

The aim of the present study was to investigate the protective effects of miconazole on myelin sheaths following cerebral white matter damage (WMD) in premature infant rats. Sprague Dawley rats (3-days-old) were randomly divided into four groups (n=30 each) as follows: Sham surgery group, WMD model group, 10 mg/kg/day treatment group and 40 mg/kg/day treatment group. A cerebral white matter lesion model was created by ligating the right common carotid artery for 80 min. Treatment groups were administered with 10 or 40 mg/kg miconazole at 4–8 days following birth (early treatment group) or 5–11 days following birth (late treatment group). Rats in the model group received the same concentration of dimethylsulfoxide. Myelin basic protein (MBP) immunohistochemical staining and western blotting were used to detect the expression of cerebral white matter-specific MBP, and changes in myelin structure were observed using transmission electron microscopy. No swelling or necrosis was observed in the corpus callosum of the sham group rats, whereas rats in the model group demonstrated edema, loose structure, fiber disorder, inflammatory gliocytes and selective white matter lesions. Following treatment with miconazole, MBP expression in the corpus callosum was significantly higher compared with the model group. Furthermore, in the model group, myelin sheaths in the corpus callosum were loose with small vacuoles, there was a marked decrease in thickness and structural damage was observed. Conversely, a marked improvement in myelination was observed in the treatment group. The results of the present study suggest that miconazole is able to promote formation of the myelin sheath to ameliorate premature cerebral white matter lesions caused by ischemia or hypoxia in rats.
Cordyceps sinensis inhibits airway remodeling in rats with chronic obstructive pulmonary disease

Cordyceps sinensis is a traditional Chinese herbal medicine that has been used for centuries in Asia as a tonic to soothe the lung for the treatment of respiratory diseases. The aim of the present study was to determine the effects of C. sinensis on airway remodeling in chronic obstructive pulmonary disease (COPD) and investigate the underlying molecular mechanisms. Rats with COPD were orally administered C. sinensis at low, moderate or high doses (2.5, 5 or 7.5 g/kg/day, respectively) for 12 weeks. Airway tissue histopathology, lung inflammation and airway remodeling were evaluated. C. sinensis treatment significantly ameliorated airway wall thickening, involving collagen deposition, airway wall fibrosis, smooth muscle hypertrophy and epithelial hyperplasia in model rats with COPD. Additionally, C. sinensis administration in rats with COPD reduced inflammatory cell accumulation and decreased inflammatory cytokine production, including tumor necrosis factor-α, interleukin-8 and transforming growth factor (TGF)-β1 in bronchoalveolar lavage fluid. Meanwhile, the increased levels of α-smooth muscle actin and collagen I in the COPD group were also markedly decreased by C. sinensis treatment. Furthermore, compared with untreated rats with COPD, C. sinensis reduced the expression level of phosphorylated (p)-Smad2, p-Smad3, TGF-β1 and its receptors, with the concomitant increased expression of Smad7 in the lungs of rats with COPD. These results indicated that treatment with C. sinensis may be a useful approach for COPD therapy.
Tanks and temples

We present a benchmark for image-based 3D reconstruction. The benchmark sequences were acquired outside the lab, in realistic conditions. Ground-truth data was captured using an industrial laser scanner. The benchmark includes both outdoor scenes and indoor environments. High-resolution video sequences are provided as input, supporting the development of novel pipelines that take advantage of video input to increase reconstruction fidelity. We report the performance of many image-based 3D reconstruction pipelines on the new benchmark. The results point to exciting challenges and opportunities for future work.
MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis

Global warming is causing a negative impact on plant growth and adversely impacts on crop yield. MicroRNAs (miRNAs) are critical in regulating the expression of genes involved in plant development as well as defense responses. The effects of miRNAs on heat-stressed Arabidopsis warrants further investigation. Heat stress increased the expression of miR160 and its precursors but considerably reduced that of its targets, ARF10, ARF16, and ARF17. To study the roles of miR160 during heat stress, transgenic Arabidopsis plants overexpressing miR160 precursor a (160OE) and artificial miR160 (MIM160), which mimics an inhibitor of miR160, were created. T-DNA insertion mutants of miR160 targets were also used to examine their tolerances to heat stress. Results presented that overexpressing miR160 improved seed germination and seedling survival under heat stress. The lengths of hypocotyl elongation and rachis were also longer in 160OE than the wild-type (WT) plants under heat stress. Interestingly, MIM160 plants showed worse adaption to heat. In addition, arf10, arf16, and arf17 mutants presented similar phenotypes to 160OE under heat stress to advance abilities of thermotolerance. Moreover, transcriptome and qRT-PCR analyses revealed that HSP17.6A, HSP17.6II, HSP21, and HSP70B expression levels were regulated by heat in 160OE, MIM160, arf10, arf16, and arf17 plants. Hence, miR160 altered the expression of the heat shock proteins and plant development to allow plants to survive heat stress.
Association of Exclusive Breastfeeding Duration With Systemic Inflammation Markers in Adolescents: A Cross-Sectional Study

Background: Breastfeeding duration has been associated with less low-grade inflammation in healthy adolescents, but there is scarce information regarding obese subjects. This study aimed to evaluate whether exclusive breastfeeding is related to serum concentrations of inflammatory markers in a population of Spanish adolescents. Method: A cross-sectional study was performed on 1,001 adolescents (13.2 ± 1.2 years) randomly recruited from schools in southeast Spain. Data on breastfeeding duration were collected via a parental questionnaire. Interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) were determined by enzyme-linked immunosorbent assay. C-reactive protein (CRP) was determined by solid-phase chemiluminescent immunometric assay. Results: Nonadjusted and adjusted multivariate correlation analyses confirmed a strong association (p < .001, 95% confidence interval) between the three markers of inflammation and exclusive breastfeeding duration. No significant differences were observed for IL-6, TNF-α, and CRP serum concentrations among normal weight, overweight, and obese adolescents, except for IL-6 between normal weight and obese subjects. Likewise, no significant association was found between these markers of inflammation and body mass index (BMI) z-score. Conclusions: We found a possible association between inflammatory markers and exclusive breastfeeding duration in adolescents, regardless of their BMI. This finding suggests that increased body weight or obesity might not mediate the association between breastfeeding and inflammation. These results contribute to the understanding of the relationship between breastfeeding and inflammatory markers in adolescents.
An Approach to Determining Software Projects with Similar Functionality and Architecture Process Based on Artificial Intelligence Methods

Software engineers from all over the world solve independently a lot of similar problems. 1 In this condition the problem of code or even better architecture reusing becomes an issue of the 2 day. In this paper two phase approach to determining the functional and structural likenesses of 3 software projects is proposed. This approach combines two methods of artificial intelligence: natural 4 language processing techniques with a novel method for comparing software projects based on 5 ontological representation of their architecture automatically obtained from the projects source code. 6 Additionally several similarity metrics are proposed to estimate similarity between projects. 7
Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies.

BACKGROUND AND AIMS The genus Fritillaria (Liliaceae) comprises species with extremely large genomes (1C = 30 000-127 000 Mb) and a bicontinental distribution. Most North American species (subgenus Liliorhiza) differ from Eurasian Fritillaria species by their distinct phylogenetic position and increased amounts of heterochromatin. This study examined the contribution of major repetitive elements to the genome obesity found in Fritillaria and identified repeats contributing to the heterochromatin arrays in Liliorhiza species. METHODS Two Fritillaria species of similar genome size were selected for detailed analysis, one from each phylogeographical clade: F. affinis (1C = 45·6 pg, North America) and F. imperialis (1C = 43·0 pg, Eurasia). Fosmid libraries were constructed from their genomic DNAs and used for identification, sequence characterization, quantification and chromosome localization of clones containing highly repeated sequences. KEY RESULTS AND CONCLUSIONS Repeats corresponding to 6·7 and 4·7 % of the F. affinis and F. imperialis genome, respectively, were identified. Chromoviruses and the Tat lineage of Ty3/gypsy group long terminal repeat retrotransposons were identified as the predominant components of the highly repeated fractions in the F. affinis and F. imperialis genomes, respectively. In addition, a heterogeneous, extremely AT-rich satellite repeat was isolated from F. affinis. The FriSAT1 repeat localized in heterochromatic bands makes up approx. 26 % of the F. affinis genome and substantial genomic fractions in several other Liliorhiza species. However, no evidence of a relationship between heterochromatin content and genome size variation was observed. Also, this study was unable to reveal any predominant repeats which tracked the increasing/decreasing trends of genome size evolution in Fritillaria. Instead, the giant Fritillaria genomes seem to be composed of many diversified families of transposable elements. We hypothesize that the genome obesity may be partly determined by the failure of removal mechanisms to counterbalance effectively the retrotransposon amplification.
Ventral and Dorsal Pathways Relate Differently to Visual Awareness of Body Postures under Continuous Flash Suppression

Abstract Visual perception includes ventral and dorsal stream processes. However, it is still unclear whether the former is predominantly related to conscious and the latter to nonconscious visual perception as argued in the literature. In this study upright and inverted body postures were rendered either visible or invisible under continuous flash suppression (CFS), while brain activity of human participants was measured with functional MRI (fMRI). Activity in the ventral body-sensitive areas was higher during visible conditions. In comparison, activity in the posterior part of the bilateral intraparietal sulcus (IPS) showed a significant interaction of stimulus orientation and visibility. Our results provide evidence that dorsal stream areas are less associated with visual awareness.