Miracle-dz/UniFAR-FTUs huggingface dataset:
Role for RAD18 in Homologous Recombination in DT40 Cells

ABSTRACT RAD18 is an E3 ubiquitin ligase that catalyzes the monoubiquitination of PCNA, a modification central to DNA damage bypass and postreplication repair in both yeast and vertebrates. Although current evidence suggests that homologous recombination provides an essential backup in vertebrate rad18 mutants, we show that in chicken DT40 cells this is not the case and that RAD18 plays a role in the recombination reaction itself. Gene conversion tracts in the immunoglobulin locus of rad18 cells are shorter and are associated with an increased frequency of deletions and duplications. rad18 cells also exhibit reduced efficiency of gene conversion induced by targeted double-strand breaks in a reporter construct. Blocking an early stage of the recombination reaction by disruption of XRCC3 not only suppresses immunoglobulin gene conversion but also prevents the aberrant immunoglobulin gene rearrangements associated with RAD18 deficiency, reverses the elevated sister chromatid exchange of the rad18 mutant, and reduces its sensitivity to DNA damage. Together, these data suggest that homologous recombination is toxic in the absence of RAD18 and show that, in addition to its established role in postreplication repair, RAD18 is also required for the orderly completion of gene conversion.
Inhibition of Notch signaling reduces the stem-like population of breast cancer cells and prevents mammosphere formation.

BACKGROUND Cancer stem cells (CSCs) are believed to be responsible for breast cancer formation and recurrence; therefore, therapeutic strategies targeting CSCs must be developed. One approach may be targeting signaling pathways, like Notch, that are involved in stem cell self-renewal and survival. MATERIALS AND METHODS Breast cancer stem-like cells derived from cell lines and patient samples were examined for Notch expression and activation. The effect of Notch inhibition on sphere formation, proliferation, and colony formation was determined. RESULTS Breast cancer stem-like cells consistently expressed elevated Notch activation compared with bulk tumor cells. Blockade of Notch signaling using pharmacologic and genomic approaches prevented sphere formation, proliferation, and/or colony formation in soft agar. Interestingly, a gamma-secretase inhibitor, MRK003, induced apoptosis in these cells. CONCLUSION Our findings support a crucial role for Notch signaling in maintenance of breast cancer stem-like cells, and suggest Notch inhibition may have clinical benefits in targeting CSCs.
A neural network for unsupervised categorization of multivalued input patterns: an application to satellite imaee clustering

This article presents an implementation of an artificial neural network (ANN) which performs unsupervised detection of recognition categories from arbitrary sequences of multivalued input patterns. The proposed ANN is called Simplified Adaptive Resonance Theory Neural Network (SARTNN). First, an Improved Adaptive Resonance Theory 1 (IARTl)-based neural network for binary pattern analysis is discussed and a Simplified ARTl (SART1) model is proposed. Second, the SARTl model is extended to multivalued input pattern clustering and SART” is presented. A normalized coefficient which measures the degree of match between two multivalued vectors, the Vector Degree of Match (VDM), provides SARTNN with the metric needed to perform clustering. Every ART architecture guarantees both plasticity and stability to the unsupervised learning stage. The SARTNN plasticity requirement is satisfied by implementing its attentional subsystem as a self-organized, feed-forward, flat Kohonen’s ANN (KANN). The SARTNN stability requirement is properly driven by its orienting subsystem. SARTNN processes multivalued input vectors while featuring a simplified architectural and mathematical model with respect to both the ARTl and the AkT2 models, the latter being the ART model fitted to multivalued input pattern categorization. While the ART2 model exploits ten user-defined parameters, SARTNN requires only two user-defined parameters to be run: the first parameter is the vigilance threshold, p, that affects the network’s sensibility in detecting new output categories, whereas the second parameter, T, is related to the network's learning rate. Both parameters have an intuitive physical meaning and allow the user to choose easily the proper discriminating power of the category extraction algorithm. The SARTNN performance is tested as a satellite image clustering algorithm. A chromatic component extractor is recommended in a satellite image preprocessing stage, in order to pursue SARTNN invariant pattern recognition. In comparison with classical clustering algorithms like ISODATA, the implemented system gives good results in terms of ease of use, parameter robustness and computation time. SARTNN should improve the performance of a Constraint Satisfaction Neural Network (CSNN) for image segmentation. SARTNN, exploited as a self-organizing first layer, should also improve the performance of both the Counter Propagation Neural Network (CPNN) and the Reduced connectivity Coulomb Energy Neural Network (RCENN).
THE PLANT HOMEODOMAIN ( PHD ) FINGERS OF CHD 4 ARE HISTONE H 3-BINDING MODULES WITH PREFERENCE FOR UNMODIFIED H 3 K 4 AND METHYLATED H 3 K 9

BINDING MODULES WITH PREFERENCE FOR UNMODIFIED H3K4 AND METHYLATED H3K9 Robyn E. Mansfield, Catherine A. Musselman, Ann H. Kwan, Adam L. Garske, Foteini Davrazou, John M. Denu, Tatiana G. Kutateladze and Joel P. Mackay From School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia Department of Pharmacology, School of Medicine, University of Colorado Denver, Aurora, CO 80045, USA Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA Running head: CHD4 PHD fingers each bind histone H3 Correspondence should be addressed to JPM (joel.mackay@sydney.edu.au, +61-2-9351-3906, fax +61-2-9351-4726).
Random Feature-based Online Multi-kernel Learning in Environments with Unknown Dynamics

Kernel-based methods exhibit well-documented performance in various nonlinear learning tasks. Most of them rely on a preselected kernel, whose prudent choice presumes task-specific prior information. Especially when the latter is not available, multi-kernel learning has gained popularity thanks to its flexibility in choosing kernels from a prescribed kernel dictionary. Leveraging the random feature approximation and its recent orthogonality-promoting variant, the present contribution develops a scalable multi-kernel learning scheme (termed Raker) to obtain the sought nonlinear learning function `on the fly,' first for static environments. To further boost performance in dynamic environments, an adaptive multi-kernel learning scheme (termed AdaRaker) is developed using weighted combinations of advices from hierarchical ensembles of experts. The weights account not only for each kernel's contribution to the learning, but also for the unknown dynamics. Performance is analyzed in terms of both static and dynamic regrets. AdaRaker is uniquely capable of tracking nonlinear learning functions in environments with unknown dynamics, with analytic performance guarantees. Tests with synthetic and real datasets are carried out to showcase the effectiveness of the novel algorithms, and their performance.
Pharmacokinetics of ambroxol and clenbuterol tablets in healthy Chinese volunteers.

OBJECTIVE To investigate the pharmacokinetics of Ambroxol and Clenbuterol Tablets in Chinese healthy volunteers after a single or multiple dosages oral administration. METHODS A total of 9 healthy adult subjects were given Ambroxol and Clenbuterol Tablets in a single dosage or multiple dosages respectively. LC/MS/MS were used for the determination of Ambroxol and Clenbuterol of in plasma. The important pharmacokinetic parameters were calculated by DAS 2.0 software (compartment model). RESULTS Single and multiple dosage groups of Ambroxol and Clenbuterol were all fitted two-compartment model. The pharmacokinetics fitted first order kinetics process. No difference in pharmacokinetics of Ambroxol in single and multiple dosage groups volunteers was observed, Which showed no marked changes, suggesting that multiple dosing did not influence the velocity of drug metabolism. Moreover, parameters of Clenbuterol had significant difference between the single and multiple dosage groups (P<0.05), showing there was accumulation in the body. 9 subjects had completed single or multiple dosages oral administration test, with no adverse drug reactions appeared during the test. CONCLUSION There was no obvious accumulation of Ambroxol after repeated dosing. But obvious accumulation of Clenbuterol was noted in multiple-dose administration. The established method is sensitive, accurate, reliable and specific, and it can meet the requirement of clinical pharmacokinetic trial.
Secured User Authentication using Encrypted Palmprint

Securing personal privacy and deterring identity theft are national priorities. Biometrics, an emerging set of technologies, provides an effective solution. Foremost examples of are biometric technologies that identify and authenticate faces, hands, palmprints, fingers, signatures, irises, voices, and fingerprints. The biometric data whenever transmitted across the network can be stolen and misused, which provides a fear over the personal privacy. In order to provide personal privacy over palmprints we propose an idea using encryption scheme over the image. In this paper, the palmprint images are obtained from the user, then encrypted and stored in the database server thereby the personal privacy of palmprints can be provided.
Removing Eye‐movement Artifacts from the EEG during the Intracarotid Amobarbital Procedure

Summary: Purpose: The EEG is often recorded during the intracarotid amobarbital procedure (IAP) to help in the assessment of the spatial extent and the duration of the effect of the drug. In scalp recordings, the EEG is always heavily contaminated with eye movement artifacts as the patient actively performs visual tasks.
Development of an earlobe crease identification system to support diagnosis of arteriosclerosis

It is well known that an earlobe crease (ELC) is related with cardiovascular disease. However evaluation of ELC has been carried out subjectively. We propose a novel system for objective and quantitative evaluation of ELC characteristics. The outline of earlobe was detected using the Canny edge detector. The number of ELCs and the ratio of the ELC length for the lobule from photographs of bilateral earlobes were calculated from the extracted outline of earlobes. Our system's validity for ELCs detection was compared with doctors' diagnosis using sensitivity and specificity analysis. The result showed that the validity of our system was equal to the diagnosis of the medical doctors (kappa coefficient: 0.93). It was thus concluded that the proposed system is useful to predict atherosclerotic disease.
Characterization of an Extracellular Virulence FactorMade by Group A Streptococcus with Homology to theListeria monocytogenes Internalin Family ofProteins

ABSTRACT Leucine-rich repeats (LRR) characterize a diverse array of proteins and function to provide a versatile framework for protein-protein interactions. Importantly, each of the bacterial LRR proteins that have been well described, including those of Listeria monocytogenes, Yersinia pestis, and Shigella flexneri, have been implicated in virulence. Here we describe an 87.4-kDa group A Streptococcus (GAS) protein (designated Slr, for streptococcal leucine-rich) containing 10 1/2 sequential units of a 22-amino-acid C-terminal LRR homologous to the LRR of the L. monocytogenes internalin family of proteins. In addition to the LRR domain, slr encodes a gram-positive signal secretion sequence characteristic of a lipoprotein and a putative N-terminal domain with a repeated histidine triad motif (HxxHxH). Real-time reverse transcriptase PCR assays indicated that slr is transcribed abundantly in vitro in the exponential phase of growth. Flow cytometry confirmed that Slr was attached to the GAS cell surface. Western immunoblot analysis of sera obtained from 80 patients with invasive infections, noninvasive soft tissue infections, pharyngitis, and rheumatic fever indicated that Slr is produced in vivo. An isogenic mutant strain lacking slr was significantly less virulent in an intraperitoneal mouse model of GAS infection and was significantly more susceptible to phagocytosis by human polymorphonuclear leukocytes. These studies characterize the first GAS LRR protein as an extracellular virulence factor that contributes to pathogenesis and may participate in evasion of the innate host defense.
Glycolipid changes in murine myelogenous leukemias: neutral glycolipids as markers for specific populations of leukemias.

We have studied the glycolipid composition of six different murine myelogenous leukemias as well as that of T-cell leukemias and normal spleen cells. Neutral and acidic lipid fractions were isolated by column chromatography on DEAE-Sephadex and analyzed by high-performance thin-layer chromatography (HPTLC) and an HPTLC overlay method. Murine myelogenous leukemias were found to contain globo- and ganglio-series neutral glycolipids, e.g., glucosylceramide (Glc-cer), lactosylceramide (Lac-cer), globotriaosylceramide (Gb3), globoside (Gb4), Forssman glycolipid (Gb5), and asialo-GM1 (GA1). Monoblastic leukemia cells contained increased proportions of Gb3, Gb4, Gb5, and GA1. Monocytic and myelomonocytic leukemia cells contained increased proportions of Glc-cer and Lac-cer. Especially, Glc-cer accounted for approximately 60% of the total neutral glycolipids in monocytic leukemia cells. Gb3 was the major neutral glycolipid in reticulum cell neoplasm type A, and it accounted for approximately 75% of the neutral glycolipids. GA1 was the major neutral glycolipid in myeloblastic and granulocytic leukemia cells as well as T-cell leukemias. Especially, granulocytic leukemia cells contained predominantly GA1, and it accounted for approximately 80% of the total neutral glycolipids. The pattern of gangliosides in myelogenous leukemias was more complex when compared with that of the neutral glycolipids; murine myelogenous leukemias contained at least 13 gangliosides, including such major gangliosides as GM1, GM1b containing N-acetyl neuraminic acid and N-glycolyl neuraminic acid, and Ga1NAc-GM1b. Alterations of glycolipid composition in murine myeloid leukemias may be associated with cellular differentiation and maturation, and therefore these characteristic glycolipid species may be regarded as markers for specific populations of leukemia cells.
International Conference in Knowledge Based and Intelligent Information and Engineering Systems-KES 2013 The Prediction of Ellipses Using Topic Model for Japanese Colloquial Inquiry Text

Generally inquiries through Web forms and e-mails are increasing. These inquiry texts usually include many informal expressions use of the colloquial style and many omitted words. An omitted word causes the meaning of a sentence to become ambiguous and makes the reader misread and misunderstand a context. In this paper we propose a method to predict omitted words from context and knowledge using topic information. From the results of evaluation experiment, we have confirmed that some of our methods can predict omitted words at the accuracy rate more than 40% for the expression that we used in the experiment. c © 2013 The Authors. Published by Elsevier B.V. Selection and peer-review under responsibility of KES International.
External beam irradiation and the combination of cisplatin and carmustine followed by carmustine alone for the treatment of high‐grade glioma

The poor prognosis reported for patients with high‒grade glial neoplasms indicates a need for the development of multimodality therapeutic approaches. The addition of chemotherapy has contributed variably to increased survival. The objective of the current study (Southwest Oncology Group [SWOG] 9016) was to determine whether concurrent radiotherapy and chemotherapy with the combination of carmustine and cisplatin could be given safely in a cooperative group setting. Additional objectives included the estimation of response rate, the rate of disease stabilization, and the probability of 1‐year survival.
Non-Destructive Visual-Statistical Approach to Detect Leaks in Water Mains

— In this paper, an effective non-destructive, non-invasive approach for leak detection was proposed. The process relies on analyzing thermal images collected by an IR viewer device that captures thermo-grams. In this study a statistical analysis of the collected thermal images of the ground surface along the expected leak location followed by a visual inspection of the thermo-grams was performed in order to locate the leak. In order to verify the applicability of the proposed approach the predicted leak location from the developed approach was compared with the real leak location. The results showed that the expected leak location was successfully identified with an accuracy of more than 95%.
Automatic Spontaneous Speech Recognition for Punjabi Language Interview Speech Corpus

Automatic Speech Recognition presents natural phenomena for the communication among man and machine. The purpose of Speech Recognition speech system is to convert the sequence of sound units in the form of text description. The main objective of the research work is to develop the automatic spontaneous speech model for the Punjabi language. Punjabi is categorized as a constituent of the Indo-Aryan subgroup of the Indo-European family of languages. So far no work has been done in the field of spontaneous Punjabi speech recognition system. In spontaneous speech system, the sounds are usually unprompted and non- designed and are commonly described by repetitions, repairs, false start, partial words and non-planned words, silence gap etc. In this paper, the focus is on the development of the spontaneous speech model for the recognition of the Punjabi language. The GUI for Punjabi speech model also has been created and tested for the live Punjabi interview speech corpus. The recognition accuracy is 98.6% for Punjabi sentences and 98.8% for Punjabi words. The sphinx toolkit and java programming are used to build a spontaneous speech model for Punjabi live speech.
Adaptive optics imaging of inherited retinal diseases

Adaptive optics (AO) ophthalmoscopy allows for non-invasive retinal phenotyping on a microscopic scale, thereby helping to improve our understanding of retinal diseases. An increasing number of natural history studies and ongoing/planned interventional clinical trials exploit AO ophthalmoscopy both for participant selection, stratification and monitoring treatment safety and efficacy. In this review, we briefly discuss the evolution of AO ophthalmoscopy, recent developments and its application to a broad range of inherited retinal diseases, including Stargardt disease, retinitis pigmentosa and achromatopsia. Finally, we describe the impact of this in vivo microscopic imaging on our understanding of disease pathogenesis, clinical trial design and outcome metrics, while recognising the limitation of the small cohorts reported to date.
Representation of the solar capacity value in the ReEDS capacity expansion model

An important emerging issue is the estimation of renewables' contributions to reliably meeting system demand, or their capacity value. While the capacity value of thermal generation can be estimated easily, assessment of wind and solar requires a more nuanced approach due to resource variability. Reliability-based methods, particularly, effective load-carrying capacity (ELCC), are considered to be the most robust techniques for addressing this resource variability. The Regional Energy Deployment System (ReEDS) capacity expansion model and other long-term electricity capacity planning models require an approach to estimating CV for generalized PV and system configurations with low computational and data requirements. In this paper we validate treatment of solar photovoltaic (PV) capacity value by ReEDS capacity expansion model by comparing model results to literature for a range of energy penetration levels. Results from the ReEDS model are found to compare well with both comparisons-despite not being resolved at an hourly scale.
Evaluation of hearthstone game states with neural networks and sparse autoencoding

In this paper, an approach to evaluating game states of a collectible card game Hearthstone is described. A deep neural network is employed to predict the probability of winning associated with a given game state. Encoding the game state as an input vector is based on another neural network, an autoencoder with a sparsity-inducing loss. The autoencoder encodes minion information in a sparse-like fashion so that it can be efficiently aggregated. Additionally, the model is regularized by decorrelation of hidden layer neuron activations, a concept derived from an existing regularizing method DeCov. The approach was developed for AAIA'17 data mining competition “Helping AI to play Hearthstone” and achieved 5th place out of 188 submissions.
ATP‐activated channels gate calcium entry in single smooth muscle cells dissociated from rabbit ear artery.

1. A combination of the techniques of microspectrofluorimetry and whole‐cell patch clamp was used to investigate changes in cytoplasmic Ca2+ concentration (Cai2+) in single arterial smooth muscle cells on external application of ATP. 2. ATP applied to cells held under voltage clamp at ‐‐60 mV evoked an inward current and an associated rise in Cai2+. In the absence of extracellular Ca2+. ATP‐activated inward currents were observed but there was no rise in Cai2+. 3. Pre‐treatment of cells with noradrenaline or caffeine did not prevent the rise in Cai2+ on subsequent application of ATP. 4. The ATP‐activated rise in Cai2+ was voltage dependent as outward currents evoked by ATP at positive membrane potentials were not associated with a change in Cai2+. 5. At ‐‐60 mV, the rise in Cai2+ due to ATP application was dependent on the magnitude of the ATP current response, such that Cai2+ increased by about 0.5 nM/pC charge transferred through ATP‐gated channels. 6. The results suggest that ATP‐gated channels in these cells admit sufficient Ca2+ in a physiological Ca2+ gradient to significantly elevate Cai2+. About 10% of the ATP‐gated current may be carried by Ca2+ ions. Thus the ATP‐activated channels have a dual excitatory function: depolarization due to Na+ entry promotes action potential discharge and voltage‐gated Ca2+ entry, and also direct entry of Ca2+ through the ATP‐activated channels.
Project in Visual Computing

During the internship at ShapeDiver GmbH [1] the visual quality of an existing WebGL [2] platform had to be improved. This platform is used as an online 3D configurator, in which customers can modify the properties of parametric models. This includes the modification of properties like shape, size and materials. The difficulty for this project was to contemplate the fact that the product can be customized by the user in real-time. 1 Contract Requirements The contract requirements that were specified for this project were separated into three different categories: 1. Methods for the improvement of the overall quality of the renderer. Specifically, improvements for illumination, shadows and reflections. 2. Creation of 5 optimized materials. (Wood, Gold, Fabric, Steel and Plastic) 3. The application of points 1. and 2. in 3 scenes that must be defined by the employer.