Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensive translation of small ORFs revealed by polysomal ribo-Seq

Thousands of small Open Reading Frames (smORFs) encoding small peptides of fewer than 100 amino acids exist in our genomes. Examples of functional smORFs have been characterised in a few species but the actual number of translated smORFs, and their molecular, functional and evolutionary features are not known. Here we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions. This ‘polysomal ribo-Seq’ suggests that smORFs are translated at the same level and in the same relative numbers (80%) as normal proteins. The smORF peptides appear widely conserved, show activity in cells, and display a putative amino acid signature. These findings reinforce the idea that smORFs are an abundant and fundamental genome component, displaying features usually attributed to canonical proteins, including high translation levels, biological function, amino acid sequence specificity and cross-species conservation.
A revised 1.6 Å structure of the GTPase domain of the Parkinson’s disease-associated protein LRRK2 provides insights into mechanisms

Leucine-rich repeat kinase 2 (LRRK2) is a large 286 kDa multi-domain protein whose mutation is a common cause of Parkinson’s disease (PD). One of the common sites of familial PD-associated mutations occurs at residue Arg-1441 in the GTPase domain of LRRK2. Previously, we reported that the PD-associated mutation R1441H impairs the catalytic activity of the GTPase domain thereby traps it in a persistently "on" state. More recently, we reported that the GTPase domain of LRRK2 exists in a dynamic dimer-monomer equilibrium where GTP binding shifts it to the monomeric conformation while GDP binding shifts it back to the dimeric state. We also reported that all of the PD-associated mutations at Arg-1441, including R1441H, R1441C, and R1441G, impair the nucleotide-dependent dimer-monomer conformational dynamics of the GTPase domain. However, the mechanism of this nucleotide-dependent conformational dynamics and how it is impaired by the mutations at residue Arg-1441 remained unclear. Here, we report a 1.6 Å crystal structure of the GTPase domain of LRRK2. Our structure has revealed a dynamic switch region that can be differentially regulated by GTP and GDP binding. This nucleotide-dependent regulation is impaired when residue Arg-1441 is substituted with the PD-associated mutations due to the loss of its exquisite interactions consisting of two hydrogen bonds and a π-stacking interaction at the dimer interface. Significance Statement Mutations in LRRK2 are associated with familial Parkinson’s disease, so understanding its mechanism of actions and how they are changed by the disease-associated mutations is important for developing therapeutic strategies. This paper describes an atomic structure of the G-domain of LRRK2 revealing that the conformational dynamics of the switch regions are potentially important for its normal function. It further shows that a disease-associated mutation could lock the G domain in a persistently active-like conformation, thus perturbing its normal function.
Volume painting: incorporating volumetric rendering with line integral convolution (LIC)

Volume Painting: Incorporating Volumetric Rendering with Line Integral Convolution (LIC). (August 2005) Jaewook Lee, B.F. A. , Pusan National University Chair of Advisory Committee: Dr. Ergun Akleman This thesis presents an expressive (non-photorealistic) rendering approach created by combining volumetric rendering techniques with the Line Integral Convolution (LIC) in 3D space. Although some techniques that combine volume rendering with the LIC have been introduced in computer graphics, they are mainly used for the scientific visualization fields, such as the visualization of 3D fluid fields. Unlike earlier research, we will focus on artistic representation, which is significantly different than scientific visualization research. We will implement a brush-stroke effect on the implicit surfaces by using the LIC. The implicit surfaces are described as volume datasets that are created by the voxelization of triangular meshes. To acquire smearing effects on the surface we convolve along the vector fields with the densities of the voxels of the datasets. These vector fields are defined by users as texture maps. The final images are rendered with volume ray casting, integrating colors and densities of voxels with Perlin noise along vector fields. The Perlin noise provides randomness and allows us to generate scratches. Smearing effects on the surface of an object create the illusion of 3D brush-strokes as if a painter had created brush strokes on a canvas. The rendering system is implemented using standard C and C++ programming languages. 3D models are then created using Alias Maya TM and TopmodTM.
In Vitro Propagation of Hybrid Rice (Oryza sativa L.) 1. “Tissue-cultured” shoot primordial

An in vitro propagation system was developed for mass-production of hybrid rice by the multiplication of shoot primordial subjected to tissue culture (hereafter referred to as "tissue-cultured" shoot primordial). Shoot primordial were generated and maintained from mature embryos of hybrid rice (Oryza saliva L.). N6 modified medium (hormone 10·6M 2,4-dichlorophenoxyacetic acid (2,4-0) and 10·5 M cytokinin) was used. Shoot primordia maintained a high level of regeneration ability for more than one year. White bodies were formed synchronously from shoot primordia by keeping them in stationary culture at high temperature (30-35°C) in the dark. When shoot primordia and white bodies encapsulated in calcium alginate gel containing N6 modified media without hormones were sowed in soil, they germinated but did not grow. However they germinated and grew on a sterilized medium and ripened when transplanted to pots. Compared with plants grown from seeds, the majority of the plants derived from shoot primordia, which headed earlier, showed a shorter plant height, lighter grain weight and 1000 grain weight, and the percentage of fertility of some individuals was lower. Discipline: Biotechnology Additional key words: artificial seed, cultured seedling, micropropagation, tissue culture
A novel Tmem119-tdTomato reporter mouse model for studying microglia in the central nervous system

Microglia are resident immune cells of the central nervous system (CNS). The exact role of microglia in the physiopathology of CNS disorders is not clear due to lack of tools to discriminate between CNS resident and infiltrated innate immune cells. Here, we present a novel reporter mouse model targeting a microglia-specific marker (TMEM119) for studying the function of microglia in health and disease. By placing a reporter cassette (GSG-3xFlag-P2A-tdTomato) between the coding sequence of exon 2 and 3’UTR of the Tmem119 gene using CRISPR/Cas9 technology, we generated a Tmem119-tdTomato knock-in mouse strain. Gene expression assay showed no difference of endogenous Tmem119 mRNA level in the CNS of Tmem119tdTomato/+ relative to control Wild-type mice. The cells expressing tdTomato-were recognized by immunofluorescence staining using commercially available anti-TMEM119 antibodies. Using immunofluorescence and flow cytometry techniques, tdTomato+ cells were detected throughout the CNS, but not in peripheral tissues of adult Tmem119tdTomato/+ mice. In addition, aging does not seem to influence TMEM119 expression as tdTomato+ cells were detectable in the CNS of older mice (300 and 540 days old). Further immunofluorescence characterization shows that the tdTomato+ cells were highly colocalized with Iba1+ cells (microglia and macrophages) in the brain, but not with NeuN- (neurons), GFAP- (astrocytes) or Olig2- (oligodendrocytes) labeled cells. Moreover, flow cytometry analysis of brain tissues of adult mice demonstrates that the majority of microglial CD45lowCD11b+ cells (96.6%) are tdTomato positive. Functionally, using a laser-induced injury model, we measured time-lapse activation of tdTomato-labeled microglia by transcranial two-photon microscopy in live Tmem119tdTomato/+ mice. Taken together, the Tmem119-tdTomato reporter mouse model will serve as a valuable tool to specifically study the role of microglia in health and disease.
Characterization of Lysinibacillus Sphaericus C3-41 Strain Isolated from Northern Karnataka, India that is Toxic to Mosquito Larvae

One of the eco-friendly approaches to control mosquitoes is by the use of Lysinibacillus sphaericus . L. sphaericus (previous name Bacillus sphaericus ) C3-41 (CP000817) was isolated from Rabbanahalli village of Yadgir district, Karnataka, India and was identified by biochemical and molecular means. Biochemical tests established its identity as L. sphaericus . It is also clear from the phylogenetic analysis that 16S ribosomal RNA nucleotide sequence of L. sphaericus C3-41 (CP000817) showed 99.73 per cent similarity with reference strain. Bioassay of L. sphaericus against second instar larvae of Culex quinquefasciatus recorded significantly higher mortality of 100 per cent at 0.075 % CSM. When assayed against second instar larvae of Anopheles subpictus mortality was 83.33 per cent at 0.075 % CSM.This new strain of L. sphaericus isolated from Northern dry zone of Karnataka, where the temperature ranges from 38°C to 46°C, could be a better biological pesticide to tackle the Culex mosquito and prevent diseases transmitted by it, particularly in Northern Karnataka.
Improving the security of the heap through inter-process protection and intra-process temporal protection

In most current implementations, memory allocations and deallocations are performed by user-level library code which keeps heap meta-data (heap structure information) and the application's heap data stored in an interleaved fashion in the same address space. Such implementations are inherently unsafe: they allow attackers to use application's vulnerabilities (e.g. lack of heap-based buffer overflow checking) to corrupt its heap meta-data in order to execute malicious code or cause denial-of-service. In this dissertation, we propose an approach where heap meta-data and heap data are protected separately. Our first solution exploits existing inter-process protection mechanisms through Heap Server, a separate process that maintains heap meta-data on behalf of the application and runs in parallel with it. To perform memory allocations and deallocations, the application sends requests to the Server, which responds to the requests and updates the meta-data. Since the heap meta-data is kept in the Heap Server's address space, attacks on the application can no longer corrupt it. Heap Server is directly implementable in current systems because it does not require new hardware. To optimize Heap Server's performance, we explore non-blocking communication, bulk deallocation, and pre-allocation optimizations. Evaluated on a real system, a fully-optimized Heap Server performs almost identical to a Base heap management library with no protection mechanisms. As an alternative solution, we propose a new User-level Temporal Intra-Process Protection (UTIPP) mechanism in which a process protects itself from its own vulnerabilities by write-protecting its own heap meta-data, and only removing the protection for legitimate stores in the heap management library. Unlike existing kernel-level page protection which can only be modified in the privileged mode, UTIPP allows a process to modify the new write-protection bit with a single instruction without disrupting normal pipeline flow. Evaluated on a cycle-accurate simulator, UTIPP adds negligible overhead in most benchmarks. Another contribution of this dissertation is a new heap layout obfuscation technique which relies on randomizing the space between heap chunks and the order of chunks in the heap, making heap data attacks more difficult. This obfuscation is integrated with Heap Server and UTIPP.
Ventilation-Like Mechanical Strain Modulates the Inflammatory Response of BEAS2B Epithelial Cells

Protective mechanical ventilation is aimed at preventing ventilator-induced lung injury while ensuring sufficient gas exchange. A new approach focuses on the temporal profile of the mechanical ventilation. We hypothesized that the temporal mechanical strain profile modulates inflammatory signalling. We applied cyclic strain with various temporal profiles to human bronchial epithelial cells (BEAS2B) and assessed proinflammatory response. The cells were subjected to sinusoidal, rectangular, or triangular strain profile and rectangular strain profile with prestrain set to 0, 25, 50, or 75% of the maximum stain, static strain, and strain resembling a mechanical ventilation-like profile with or without flow-controlled expiration. The BEAS2B response to mechanical load included altered mitochondrial activity, increased superoxide radical levels, NF-kappaB translocation, and release of interleukin-8. The response to strain was substantially modulated by the dynamics of the stimulation pattern. The rate of dynamic changes of the strain profile correlates with the degree of mechanical stress-induced cell response.
Abundance of Aerially-Dispersing Spiders Declines with Increasing Road Traffic

ABSTRACT Roads and traffic have been implicated in population declines in a number of taxonomic groups. However, there is little research into the potential effects of roads or traffic on spiders. Here, we tested the prediction that there would be fewer aerially-dispersing (i.e., ballooning) spiders at high-traffic than low-traffic roads. We used custom-made sticky traps attached to a vehicle to collect ballooning spiders along 10 high-traffic–low-traffic rural road pairs in southeastern Ontario, Canada. We collected half as many spiders at high-traffic than low-traffic roads. This provides the first published evidence of negative traffic effects on ballooning spiders. Although consistent with our prediction that ballooning spiders are less abundant at high-traffic roads, there are several possible explanations for this finding. Further study is needed to investigate these explanations, including whether the observed traffic effect reflects reduced population sizes near high-traffic roads or reduced ballooning behaviour near high-traffic roads. If the former, then roads may represent a significant conservation concern for ballooning spider species.
A Review on Techniques for Generation of Knowledge in Scientific Database

At present, the stored information is increasing tremendously day by day. The sudden increase in the amount of texts on the web, it was almost impossible for people to keep upto-date information. Knowledge generation from textual database referred generally to the process of extracting interesting or non-retrieval patterns or knowledge from unstructured text documents. Using the technique such as information extraction, information retrieval, natural language processing, text mining and social network analysis can be easily found from the corpus of documents set. Knowledge generation in databases is the nontrivial process of identifying valid, novel, potentially useful, and ultimately understandable patterns in data. The development of proposed work is the acquirization or selection of target data set, integration and checking of data set, data cleaning, preprocessing and development of transformation model and selection of algorithm which gives generated knowledge as result interpretation, visualization, testing, verification and maintenance. Keywords—Knowledge generation, Corpus, Text mining, Social Network Analysis, Information Eextraction, Information Retrieval.
A framework for human-web interaction

Navigation is a critical issue in the World Wide Web and as such there is much interest in developing new navigation techniques and tools. Unfortunately, many of these new developments focus on technological innovation without considering other aspects of human-web interaction and underlying theories. Conceptual frameworks provide structure and guidance for design and research. This paper provides a comparative analysis of a number of conceptual frameworks particularly addressing the role of goals and navigational strategies. A schematic framework for human-web interaction is proposed providing interface designers and researchers with an insight into the various components and concepts in relation to web navigation.
DISCRIMINATIVE LEARNING APPROACHES FOR THE STATISTICAL PROCESSING OF CHINESE

We study discriminative approaches to statistical Chinese processing, including word segmentation, pos-tagging and parsing with constituent and dependency grammars. As the main approach of this thesis, we use a global linear model, trained by the generalized perceptron algorithm, together with beam-search decoding, to build our statistical systems. The combination of perceptron training and beam-search decoding leads to highly competitive accuracy and efficiency for all the tasks we investigate. For word segmentation, we propose a word-based approach that achieves competitive accuracy to the best character-based systems, without mapping segmentation into a sequence labeling problem. For pos-tagging, we built a joint system that performs word segmentation and tagging simultaneously, showing that it improves the accuracy over the traditional pipeline approach by enabling information interaction and avoiding error propagation. For constituent parsing, we develop our model based on a shift-reduce parsing algorithm, which currently provides state-of-the-art performance for Chinese, using a global model and beam-search, showing that it achieves comparable accuracy to the best scores in the literature. For dependency parsing, we combine the two predominant statistical methods into a single system using a global linear model, and achieve the current best accuracy for Chinese. One main advantage of the discriminative approach to statistical nlp is the freedom to define features that represent contextual information. For all the problems studied in this thesis, we achieve state-of-the-art accuracies by utilizing a wide range of information in a discriminative model. We conclude that the discriminative method is a competitive choice for the statistical processing of the Chinese language.
Carbon, nitrogen, and sulfur stable isotopic reconstruction of human diet in a mountainous woodland village in Sendaiji in premodern Japan

The reconstruction of everyday diets in villages is important for understanding the diversity of diets and commerce networks of food items in premodern Japan. However, premodern diets in villages have not been well studied compared with those in cities. In this study, stable isotope analyses were performed on 23 adult human skeletons excavated from Sendaiji, a mountainous woodland village of underground Christians in Osaka in premodern Japan. No significant isotopic differences was found between individuals identified as Buddhists and those identified as Christians or between females and males. The total mean carbon, nitrogen, and sulfur isotope ratios were –21.1 ± 0.4‰, 11.6 ± 1.0‰, and 8.9 ± 1.3‰, respectively. The carbon isotope ratios in Sendaiji were the lowest among the studied premodern populations probably because these individuals consumed woodland foods that are affected by the canopy effect. No significant correlation between sulfur and nitrogen isotope ratios was apparent, suggesting that there was little contribution from marine foods or marine fertilizers to the diet of individuals in premodern Sendaiji. The relatively high nitrogen isotope ratios in Sendaiji were possibly because of the denitrification in paddy rice fields, ammonium uptake by paddy rice, use of animal fertilizers, and/ or consumption of freshwater fish. To our knowledge, this is the first detailed bioarchaeological study of the premodern diet in a mountainous village in western Japan.
Phase compensation of rate limiters in JAS 39 Gripen

For a modern aerodynamically unstable fighter, like the JAS 39 Gripen, the flight control system (PCS) typically provides 45° phase margin. Therefore rate limiting of control surfaces is an important issue. Software rate limiters are placed on the control servo commands in order to prevent the hydraulic servos from rate limiting. When a rate limiter is saturated, the phase shift drastically reduces the stability margins of the closed loop and increases the risk for pilot-induced oscillation (PIO). This paper describes a novel method for compensating the phase shift of a rate limiter. In contrast to earlier phase compensation methods, this method uses feedback instead of logic or feedforward. Open loop and closed loop properties of the method are discussed. The method gives a drastic improvement on stability margins and reduces PIO tendencies. This is demonstrated on a JAS 39 Gripen example. Phase compensated rate limiters are now used in the JAS 39 Gripen PCS production software. Their effects on closed loop stability and flying qualities are discussed in the paper.
Automatic vehicle Detection and Tracking for Event Analysis in Intelligent Aerial Surveillance Using Dynamic Bayesian Networks

Prediction of vehicles is a challenging domain in the traffic control department. Many of the researches, academicians, scientists and intellectual minds so far applied many techniques but didn’t provide the accurate identifications of vehicle. So, in this paper we are highlighting Dynamic Back ground subtraction using colour histograms method based on Pixel wise classification. When applied this algorithm in the identification of vehicles, it is providing better accuracy when compared with previous approaches like sliding window method and region based method. In this paper we provided better identification of vehicles with the usage of pixel wise classification method.
Epidermal Growth Factor (EGF) single mutants highlighted by a homologs cross-conservation approach differentially affect the EGF Receptor (EGFR) downstream pathway

Molecular co-evolution is a key feature of biological systems. Molecular interactions (ligand-receptor, protein-protein, etc.) usually evolve simultaneously and independently to optimize binding. Frequently, these interactions involve one receptor that binds multiple ligands. Each ligand often leads to a different pathway activation intra-cellularly. Understanding single amino acid roles in evolving ligands and their contributions to downstream pathways of the receptor is still challenging. We developed a cross-conservation approach to identify functionally important EGF residues. Four EGF mutants (N32R, D46R, K48T, W50Y) have been selected and studied biochemically and at the cellular level. While these mutants retain binding affinities for EGFR similar to that of EGF, surprisingly the effects of two of them (D46R, K48T) at the cellular level changed, inducing higher proliferation levels in normal fibroblasts and reducing proliferation in skin cancer cells. These results lay the base to understand the basis of EGF signaling.