Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma

Development of head and neck squamous cell carcinoma (HNSCC) is characterized by accumulation of mutations in several oncogenes and tumor suppressor genes. We have formerly described the mutation pattern of HNSCC and described NOTCH signaling pathway alterations. Given the complexity of the HNSCC, here we extend the previous study to understand the overall HNSCC mutation context and to discover additional genetic alterations. We performed high depth targeted exon sequencing of 51 highly actionable cancer-related genes with a high frequency of mutation across many cancer types, including head and neck. DNA from primary tumor tissues and matched normal tissues was analyzed for 37 HNSCC patients. We identified 26 non-synonymous or stop-gained mutations targeting 11 of 51 selected genes. These genes were mutated in 17 out of 37 (46%) studied HNSCC patients. Smokers harbored 3.2-fold more mutations than non-smokers. Importantly, TP53 was mutated in 30%, NOTCH1 in 8% and FGFR3 in 5% of HNSCC. HPV negative patients harbored 4-fold more TP53 mutations than HPV positive patients. These data confirm prior reports of the HNSCC mutational profile. Additionally, we detected mutations in two new genes, CEBPA and FES, which have not been previously reported in HNSCC. These data extend the spectrum of HNSCC mutations and define novel mutation targets in HNSCC carcinogenesis, especially for smokers and HNSCC without HPV infection.
Spherical Image Processing for Accurate Visual Odometry with Omnidirectional Cameras

Due to their omnidirectional view, the use of catadioptric cameras is of great interest for robot localization and visual servoing. For simplicity, most vision-based algorithms use image processing tools (e.g. image smoothing) that were designed for perspective cameras. This can be a good approximation when the camera displacement is small with respect to the distance to the observed environment. Otherwise, perspective image processing tools are unable to accurately handle the signal distortion that is induced by the specific geometry of omnidirectional cameras. In this paper, we propose an appropriate spherical image processing for increasing the accuracy of visual odometry estimation. The omnidirectional images are mapped onto a unit sphere and treated in the spherical spectral domain. The spherical image processing take into account the specific geometry of omnidirectional cameras. For example we can design, a more accurate and more repeatable Harris interest point detector. The interest points can be matched between two images with a large baseline in order to accurately estimate the camera motion. We demonstrate with a real experiment the accuracy of the visual odometry obtained using the spherical image processing and the improvement with respect to the use of a standard perspective image processing.
Characterization of the Uptake of Organic Anion Transporter (OAT) 1 and OAT3 Substrates by Human Kidney Slices

The activities of renal multispecific organic anion transporters (OATs) 1 and 3 have not been fully evaluated in human kidneys. In the present study, the uptake of some organic anions was characterized in kidney slices from human intact renal cortical tissues: hOAT1 and hOAT3 substrates [p-aminohippurate (PAH) and 2,4-dichlorophenoxyacetate (2,4-D)] and hOAT3 substrates [benzylpenicillin (PCG), dehydroepiandrosterone sulfate (DHEAS), and estrone sulfate (ES)]. Despite large interbatch differences, hOAT1 and hOAT3 mRNA levels correlated well, and there was a good correlation between the uptake of PAH and PCG by kidney slices. The uptake of organic anions by kidney slices was saturable with Km values of 31 to 48 μM for PAH, 0.73 to 4.9 μM for 2,4-D, 14 to 90 μM for PCG, and 9.2 to 11 μM for ES. These parameters were comparable with those for hOAT1 and/or hOAT3. The uptake of DHEAS consists of two saturable components with Km values of 2.2 to 3.9 and 1300 μM, and the Km value of the high-affinity component was close to that for hOAT3. Furthermore, PAH more potently inhibited the uptake of 2,4-D than that of PCG and DHEAS. PCG had a weaker effect on the uptake of PAH and 2,4-D than expected from its Km value. Taken together, it is likely that the uptake of PAH and 2,4-D is due to OAT1, and the uptake of PCG and ES and part of DHEAS uptake are due to OAT3 in human kidney slices. Human kidney slices are useful tools for characterizing the renal uptake of drugs.
An Improvement of the Lovász Local Lemma via Cluster Expansion

An old result by Shearer relates the Lovász local lemma with the independent set polynomial on graphs, and consequently, as observed by Scott and Sokal, with the partition function of the hard-core lattice gas on graphs. We use this connection and a recent result on the analyticity of the logarithm of the partition function of the abstract polymer gas to get an improved version of the Lovász local lemma. As an application we obtain tighter bounds on conditions for the existence of Latin transversal matrices.
University of Washington System for 2015 KBP Cold Start Slot Filling

The University of Washington participated in Cold Start Slot Filling for TAC-KBP 2015 with a system that combines three methods: 1) its 2013 OPENIE-KBP system (Soderland et al., 2013); 2) a novel Implicit Relation Information Extractor (IMPLIE); and 3) MULTIR extractor (Hoffmann et al., 2011), trained on a combination of distant supervision and crowdsourced training instances. These three methods are complementary with little overlap in the resulting extractions. In particular, IMPLIE finds extractions that are beyond the scope of OPENIE-KBP.
Uniform sampling for multiple target tracking

A major problem in the application of particle filters to multiple target tracking is the loss of modes due to sample degeneracy. A particle filter based on the notion of uniform sampling is developed to address this issue. The proposed particle filter approximates uniform sampling in an auxiliary variable framework. Simulation results show that the proposed method provides significantly improved mode retention compared to a particle filter using the optimal importance density.
Dissolution of calcium pyrophosphate crystals by polyphosphates: an in vitro and ex vivo study

OBJECTIVE To determine the dissolving ability (DA) of linear pentasodium tripolyphosphate (PSTP), cyclic trisodium metaphosphate (TSMP), polymeric sodium metaphosphate (SMP) on synthetic crystals of calcium pyrophosphate dihydrate (CPPD) and on crystalline aggregates of menisci from patients with chondrocalcinosis (CC). METHODS Synthetic CPPD crystals were mixed with phosphate buffered saline (PBS), which contained the different polyphosphates, for one hour at 37°C. The calcified menisci were obtained from the knees of four female patients with CPPD disease who underwent total arthroscopic meniscectomy for degenerative meniscal lesions. Meniscal cryosections and fragments were incubated in SMP (15 mg/ml PBS) at 37°C for one hour and 24 hours, respectively. Histological evaluation on meniscal samples after polyphosphate incubation was carried out by ordinary transmitted light microscopy and polarised light microscopy. The dissolution of CPPD crystals by polyphosphates was assessed by atomic absorption spectroscopy, which determined the amount of calcium liberated from synthetic crystals and meniscal fragments. Cytotoxicity of SMP was evaluated by tetrazolium salt assay and by an ultrastructural study on cultured chondrocytes. RESULTS SMP and PSTP showed higher DA on CPPD crystals than TSMP. Analysis of the DA values at increasing concentrations of SMP showed that a concentration of 15 mg/ml completely dissolved 2.0 mg CPPD crystals. The solution of meniscal CPPD crystals showed a significant increase of calcium concentration after three hours and 24 hours of SMP incubation (p=0.0001; Kruskal-Wallis analysis of variance) compared with fragments incubated in PBS control solution. Macroscopic and microscopic evaluation of meniscal specimens showed a notable reduction of CPPD deposits. A 50% inhibitory dose on cultured chondrocytes was reached at the maximum concentration of SMP used in this work (15 mg/ml); ultrastructural analysis did not show morphological alterations in the treated cells. CONCLUSION The results of this study indicate that linear polyphosphates are effective in dissolving both synthetic and ex vivo CPPD crystal aggregates. This suggests a potential therapeutic use for these molecules in the treatment of symptomatic CC.
More rings to rule them all: fragmentation, 4D ↔ 5D and split-spectral flows

In this note we set-up an explicit 5D construction of AdS-fragmentation, whereby a single black ring splits-up into a multi-black ring configuration. Furthermore it is seen that these fragmented rings are equivalent to a direct 5D lift of 4D multi-center black holes. Along the way we also determine the 4D/5D transformations relevant for multi-center charges. It is seen that the physical charges involved in black ring fragmentation are Page charges arising due to 5D Chern-Simons terms. As an application of these methods, we reproduce the total angular momentum of concentric black rings, originally due to Gauntlett and Gutowski. Finally we provide a geometric interpretation of fragmented black rings using the idea of split-spectral flows, which seeks to study charge shifts of a given black ring due to fluxes generated in a multi-ring background.
Mechanical feasibility analysis of process optimized silicon microneedle for biomedical applications

In our previous work, we proposed a process optimized hollow silicon (Si) microneedle structure on a silicon chip, which had the highest aspect ratio (AR) reported so far. The 150 micrometer (µm) tall optimized microneedle structure with an AR of about 30∶1 was fabricated by reactive ion etch or RIE process on a p-type 500µm thick Si substrate for drug delivery applications. In this paper we have investigated mechanical properties of the process optimized hollow Si microneedle. More specifically, bending and buckling forces, Von Mises stress, tangential shear force, and effects of skin and/or tissue penetration pressure on the optimized microneedle have been analyzed by finite element method. Three dimensional solid stress and strain curves for the optimized structure have been reported. Both analytical and simulation results show that buckling force has the greatest influence on mechanical stability and that the force with the least mechanical impact is tangential shear force. The detailed analysis indicates that the optimized structure would be compatible with modern biomedical microsystems.
EVALUASI PROGRAM PEMBINAAN PRESTASI OLAHRAGA BOLA VOLI PADA SMK NEGERI DI KOTA BENGKULU

ABSTRAKPenelitian ini bertujuan untuk mendeskripsikan Evaluasi Program Pembinan Prestasi Olahraga Bola Voli pada SMK Negeri Di Kota Bengkulu. Subjek dalam penelitian ini adalah Pembina, Pelatih, Atlet SMK Negeri 1, SMK Negeri 3, SMK Negeri 5, SMK Negeri 7 Kota Bengkulu. Pengumpulan data dan Instrumen penelitian ini berupa kuesioner/angket yang sudah divalidasi oleh ahli. Analisis data dalam penelitian ini menggunakan analisis data kualitatif dan keabsahan data statistik yang menggunakan rumus persentase. Hasil penelitian dalam pembahasan menunjukan bahwa hasil Evaluasi Program Pembinaan Prestasi Olahraga Bola Voli Pada SMK Negeri Di Kota Bengkulu belum seluruhnya maksimal dalam pelaksanaannya dari 4 sekolah yang diteliti hanya 1 sekolah yang menjalankan program pembinaan dengan baik. Hal tersebut dilihat dari segi manajemen pengelolaan sarana dan prasaranan yang sangat minim, pengelolaan dana yang belum tersalurkan menyeluruh untuk kegiatan program pembinaan tersebut, serta kurangnya dukungan dari pihak sekolah. Kurang maksimalnya program latihan yang diberikan pelatih, membuat tujuan pencapaian prestasi puncak tidak dapat terlaksana dengan baik. Kesimpulan dari program pembinaan belum maksimal dari segi prasarana, pengelolaan dana, serta dukungan dari sekolah dari 4 sekolah yang di teliti hanya 25 % sekolah yang sudah melaksanakan program dengan baik.Kata Kunci: Evaluasi, Program Pembinaan Prestasi, Bola VoliABSTRACTThis study aimed to describe the Evaluation of the Achiefment Volley Ball Training Program at Vocational School in Bengkulu City. The subject of this study is trainerss, coachers, atlhetes of SMKN 1, SMKN 3, SMKN 5, SMKN 7 Bengkulu city. Dt colection and instrumen of the study is kuestionnaire which has been validated by expert. Data analisis oif this study used kualitative data analysis and statistic data validity used percentage the result of this study showed that the of grall result of the evaluation of the achievement volly ball training program at vocational school in Bengkulu city are not maximal yet in the implementation. from 4 school are studied, there is only one school which implement development program well. It can be seen from the lact of the good mnagement of facilities and infrastructure, the management of the found whish is not distributed yet for the development program, and the lact of support from school. Since the lack of training program from coachers, it makes the aim program of the peak achievement cannot be implemented well. The conclution of this study is dhat the development program is not running well in mangement of facility and infrastructures, management from school. From 4 schools are studied, there is only 25% which has implemented the development program well.Keywords: Evaluation, Achiefment Training Program, Volley Ball
Prevalence and Clonal Distribution of pcpA, psrP and Pilus-1 among Pediatric Isolates of Streptococcus pneumoniae

Streptococcus pneumoniae is the leading cause of vaccine-preventable deaths globally. The objective of this study was to determine the distribution and clonal type variability of three potential vaccine antigens: Pneumococcal serine-rich repeat protein (PsrP), Pilus-1, and Pneumococcal choline binding protein A (PcpA) among pneumococcal isolates from children with invasive pneumococcal disease and healthy nasopharyngeal carriers. We studied by Real-Time PCR a total of 458 invasive pneumococcal isolates and 89 nasopharyngeal pneumococcal isolates among children (total = 547 strains) collected in Barcelona, Spain, from January 2004 to July 2010. pcpA, psrP and pilus-1 were detected in 92.8%, 51.7% and 14.4% of invasive isolates and in 92.1%, 48.3% and 18% of carrier isolates, respectively. Within individual serotypes the prevalence of psrP and pilus-1 was highly dependent on the clonal type. pcpA was highly prevalent in all strains with the exception of those belonging to serotype 3 (33.3% in serotype 3 isolates vs. 95.1% in other serotypes; P<.001). psrP was significantly more frequent in those serotypes that are less apt to be detected in carriage than in disease; 58.7% vs. 39.1% P<. 001. Antibiotic resistance was associated with the presence of pilus-1 and showed a negative correlation with psrP. These results indicate that PcpA, and subsequently Psrp and Pilus-1 together might be good candidates to be used in a next-generation of multivalent pneumococcal protein vaccine.
Text Annotation for Political Science Research

Guest Editors’ Introduction Jo rnal of Information Technology & Politics Digitization is dramatically altering research demands and opportunities in political science, and in the social sciences more generally. To cite just a few examples, the advent of e-government has challenged governments to keep pace with rapidly expanding opportunities for public commenting via e-mail or Web portals during the development of government policy (Balla & Daniels, 2007); the creation of online media has dramatically increased the amount of accessible digital political content and altered the pace and dynamics of political campaigns (Hopkins & King, 2007); governments around the world now release huge volumes of digitized data on a daily basis (e.g., the U.S. Federal Register— http://www.gpoaccess.gov/fr/Index.html), while national projects are digitally scanning vast numbers of historical documents. For example, British parliamentary debates from the 17th century to the present are now accessible online, and ongoing research will extend their availability back to 1066. These developments in data accessibility are creating unprecedented opportunities both to reinvestigate longstanding questions in political science and to embark on the study of new questions. However, a central challenge of working with data of any sort is that it must be organized and classified so that the researcher can use it for the task at hand. In this volume, the data of interest is text. A government agency that receives tens of thousands of comments on a proposed regulation, for example, needs to be able to cull, categorize, and summarize the substantive information contained in those comments in a useful way. A scholar studying campaign coverage on the Internet needs to analyze and organize that coverage to test specific questions about its character. Manual approaches to extracting information from textual data can be challenging for large tasks where resources are limited (as they usually are). Computer-assisted approaches seem to be an attractive alternative: They can enable researchers to complete certain tasks with much greater speed. Nonetheless, it is also important to recognize that faster methods are not necessarily better methods. A computer program might be able to sort public comments by zip code more quickly than, and as accurately as, humans; but humans might be substantially better, albeit slower, at classifying public comments by topic. Ultimately, each manual, automated, or semi-automated method for analyzing textual data has its own set of benefits and costs that vary depending on the task at hand. This special volume of JITP includes eight articles investigating a diverse set of political science tasks, from e-government to political speeches to campaign coverage. The articles nicely illustrate a range of methodological challenges where extracting information from text is concerned. In the process, they also demonstrate the strengths and limitations of alternative text analysis methodologies. Text has always been an important source of data in political science. Text annotation
The Exploration Machine - a novel method for structure-preserving dimensionality reduction

We present a novel method for structure-preserving dimen- sionality reduction. The Exploration Machine (Exploratory Observation Machine, XOM) computes graphical representations of high-dimensional observations by a strategy of self-organized model adaptation. Although simple and computationally ecient, XOM enjoys a surprising flexibility to simultaneously contribute to several dierent domains of advanced ma- chine learning, scientific data analysis, and visualization, such as structure- preserving dimensionality reduction and data clustering. 1 Motivation The exceedingly growing amount of high-dimensional information stored in com- puter-accessible data bases and web resources raises the question of how to organize and extract useful knowledge from this abundant material. Here, a key issue is structure-preserving data reduction which has moved into the focus of interest as an issue of high-priority research eorts. Structure-preserving data reduction can frequently be accomplished by two alternative approaches, namely data partitioning in the sense of 'clustering' and dimensionality reduction often referred to as 'embedding'. In this paper, we introduce a novel algorithm called 'Exploration Machine' (Exploratory Observation Machine - XOM) that unexpectedly can approach both domains from a unified viewpoint within a single computational framework. Af- ter explaining the XOM algorithm, we present applications to the analysis of mul- tidimensional biomedical data from dierent real-world domains: whole-genome microarray gene expression experiments and functional MRI analysis. These two dierent examples convey XOM's capability to simultaneously contribute to the aforementioned dierent challenges of pattern recognition, namely structure- preserving dimensionality reduction and clustering.
Bioinformatics Applications Note Structural Bioinformatics Moderna Server: an Online Tool for Modeling Rna 3d Structures

The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program.
Activation of CD8 T Cells by Antigen Expressed in the Pituitary Gland

Ag expressed exclusively in the anterior pituitary gland and secreted locally by pituitary somatotrophs can gain access to the MHC class I presentation pathway and activate CD8 T cells. Influenza nucleoprotein (NP) was expressed as a transgene under the control of the human growth hormone (GH) locus control region. Activation of monoclonal F5 CD8 T cells specific for NP resulted in spontaneous autoimmune pathology of the pituitary gland in mice transgenic for both NP and the F5 TCR. Destruction of somatotrophs resulted in drastically reduced GH levels in adult mice and a dwarf phenotype. Adoptive transfer of F5 T cells into NP-transgenic hosts resulted in full T cell activation, first demonstrable in regional lymph nodes, followed by their migration to the pituitary gland. Despite the presence of activated, IFN-γ-producing CD8 T cells in the pituitary gland and a slight reduction in pituitary GH levels, no effect on growth was observed. Thus, CD8 T cells have access to the neuroendocrine system and get fully activated in the absence of CD4 help, but Ag recognition in this location causes autoimmune pathology only in the presence of excessive CD8 T cell numbers.
Parametric computation of the Legendre-Fenchel conjugate with application to the computation of the Moreau envelope

A new algorithm, named the Parametric Legendre Transform (PLT) algorithm, to compute the Legendre-Fenchel conjugate of a convex function of one variable is presented. It returns a parameterization of the graph of the conjugate except for some affine parts corresponding to nondifferentiable points of the function. The approach is extended to the computation of the Moreau envelope, resulting in a simple yet efficient algorithm. Theoretical results, the description (and extension) of the algorithm, its approximation error and the convergence, as well as the comparison with known algorithms are included.
KNOWLEDGE BASED ANALYSIS OF VARIOUS STATISTICAL TOOLS IN DETECTING BREAST CANCER

In this paper, we study the performance criterion of machine learning tools in classifying breast cancer. We compare the data mining tools such as Naïve Bayes, Support vector machines, Radial basis neural networks, Decision trees J48 and simple CART. We used both binary and multi class data sets namely WBC, WDBC and Breast tissue from UCI machine learning depositary. The experiments are conducted in WEKA. The aim of this research is to find out the best classifier with respect to accuracy, precision, sensitivity and specificity in detecting breast cancer.