Miracle-dz/UniFAR-FTUs huggingface dataset:
SWI/SNF and Asf1 Independently Promote Derepression of the DNA Damage Response Genes under Conditions of Replication Stress

The histone chaperone Asf1 and the chromatin remodeler SWI/SNF have been separately implicated in derepression of the DNA damage response (DDR) genes in yeast cells treated with genotoxins that cause replication interference. Using genetic and biochemical approaches, we have tested if derepression of the DDR genes in budding yeast involves functional interplay between Asf1 and SWI/SNF. We find that Asf1 and SWI/SNF are both recruited to DDR genes under replication stress triggered by hydroxyurea, and have detected a soluble complex that contains Asf1 and the Snf2 subunit of SWI/SNF. SWI/SNF recruitment to DDR genes however does not require Asf1, and deletion of Snf2 does not affect Asf1 occupancy of DDR gene promoters. A checkpoint engagement defect is sufficient to explain the synthetic effect of deletion of ASF1 and SNF2 on derepression of the DDR genes in hydroxyurea-treated cells. Collectively, our results show that the DDR genes fall into a class in which Asf1 and SWI/SNF independently control transcriptional induction.
Photodegradation Mechanisms on Poly(ε-caprolactone) (PCL)

Photodegradation of PCL was performed exposing injected specimens to ultraviolet radiation (UVB) up to 9 weeks. Photodegradated PCL specimens were tested by Differential Scanning Calorimetry (DSC), Infrared Spectroscopy (FTIR), mechanical properties, Optical Microscopy (MO) and Scanning Electron Microscopy (SEM). Upon exposure decrease in elongation at break and increase of elastic modulus were verified, higher degree of crystallinity was observed for longer exposure what can be due to the chemi-crystallization mechanism. From IR spectra new carbonyl group (C=O) peaks were observed. Presence of micro cracks on specimens’ surface was identified by MO. From morphological analyses is suggested that the photodegradation in PCL takes place by bulk erosion mechanism.
A fiber-optic evanescent field absorption sensor

Waveguide evanescent field absorption has been measured as a function of cladding refractive index and bulk absorption coefficient. A simple theory for interpreting these results has been developed. An all-fiber species concentration sensor has been constructed and its performance characterized.Waveguide evanescent field absorption has been measured as a function of cladding refractive index and bulk absorption coefficient. A simple theory for interpreting these results has been developed. An all-fiber species concentration sensor has been constructed and its performance characterized.
Bayesian Inference in Incomplete Multi-Way Tables

Summary We describe and illustrate approaches to Bayesian inference in multi-way contingency ta-bles for which partial information, in the form of subsets of marginal totals, is available.In such problems, interest lies in questions of inference about the parameters of modelsunderlying the table together with imputation for the individual cell entries. We discussquestions of structure related to the implications for inference on cell counts arising fromassumptions about log-linear model forms, and a class of simple and useful prior distribu-tions on the parameters of log-linear models. We then discuss \local move" and \globalmove" Metropolis-Hastings simulation methods for exploring the posterior distributions forparameters and cell counts, focusing particularly on higher-dimensional problems. As a by-product, we note potential uses of the \global move" approach for inference about numbersof tables consistent with a prescribed subset of marginal counts. Illustration and compar-ison of MCMC approaches is given, and we conclude with discussion of areas for furtherdevelopments and current open issues.Some key words: Bayesian inference; Disclosure limitation; Fixed margins problem; Imputation; Log-linear models; Markov basis; Markov chain Monte Carlo; Missing data.2
Text Extraction from Visiting Card

This paper describe the one of the method of text extraction from visiting card images with fanciful design containing complicated color background and reverse contrast regions. The proposed method is based on edge detection followed by grouping of edges based on size, orientation and color attributes. After detecting edges of text from card we can apply image processing steps such as noise removal, segmentation to extract text from complex image. This text image can be recognized using OCR . We can design OCR using Artificial Neural Network. Some post processing like color identification and binarization will be helpful to get a pure binary text image for OCR. Keywords— OCR (Optical Character Recognition), Binarization, Segmentation
Providing a High Level Abstraction for SDN Networks in GENI

Software Defined Networks make it possible to decouple routing from forwarding, allowing the routing decisions to be made by a (logically)centralized controller which are then communicated to the switches in the network (for example, via the Open Flow protocol). One problem facing end users is the need to map high level abstractions - like the path a flow should take - to a set of low level forwarding rules tailored to, and installed at, every switch along the path. Installing such rules manually is tedious and error prone, and writing a controller program to do it is equally, if not more, challenging. In this paper, we propose a new set of tools that allow users (experimenters)to easily map their high level routing policies to low level Open Flow rules, and to help users reverse engineer high level policies from the installed set of low level flow rules. The tools provide users with the abstraction of end-to-end flows that users can install, list, and delete. The tools automatically handle the details of computing and installing all the rules needed to implement end-to-end flows, and are also capable of identifying flows and, if desired, removing flows that already exist. The tools have been implemented as modules in the GENI Desktop providing users with a graphical interface to their flows. In addition, we have implemented a module to monitor the performance of flows that have been installed. We describe our prototype implementation and present performance numbers obtained via the service.
SWARMORPH: Multirobot Morphogenesis Using Directional Self-Assembly

In this paper, we propose SWARMORPH: a distributed morphology generation mechanism for autonomous self-assembling mobile robots. Self-organized growth of global morphological structures emerges through the repeated application of local morphology extension rules. We present details of the directional self-assembly mechanism that provides control over the orientation of interrobot connections. We conduct real-world experiments to validate the low-level directional self-assembly mechanism and the growth of global morphologies. We demonstrate the scalability of the approach with large numbers of robots in simulation-based experiments.
Inference of Phrase-Based Translation Models via Minimum Description Length

We present an unsupervised inference procedure for phrase-based translation models based on the minimum description length principle. In comparison to current inference techniques that rely on long pipelines of training heuristics, this procedure represents a theoretically wellfounded approach to directly infer phrase lexicons. Empirical results show that the proposed inference procedure has the potential to overcome many of the problems inherent to the current inference approaches for phrase-based models.
Design and Analysis of Hip Joint Parallel Rehabilitation Mechanism

This paper presents a 3-UPU spatial parallel mechanism for the rehabilitation of hip joint which can be broadly used in the rehabilitation robot, although the hip medical rehabilitation robot is rarely usage today. This parallel mechanism has three rotational DOFs, and the rotation axes intersect at one point, so it's very suitable to implement the rehabilitation of the hip joint where has three rotational DOFs. This paper analysis the characteristics and movement mechanism based on the screw theory, provides a new method to research the parallel mechanism.
Model-driven Java code refactoring

Refactoring is an important technique for restructuring code to improve its design and increase programmer productivity and code reuse. Performing refactorings manually, however, is tedious, time consuming and error-prone. Thus, providing an automated support for them is necessary. Unfortunately even in our days, such automation is still not easily achieved and requires formal specifications of the refactoring process. Moreover, extensibility and tool development automation are factors that should be taken into consideration when designing and implementing automated refactorings. In this paper, we introduce a model-driven approach where refactoring features, such as code representation, analysis and transformation adopt models as first-class artifacts. We aim at exploring the value of model transformation and code generation when formalizing refactorings and developing tool support. The presented approach is applied to the refactoring of Java code using a prototypical implementation based on the Eclipse Modeling Framework, a language workbench, a Java metamodel and a set of OMG standards.
PI3K/AKT regulates aggrecan gene expression by modulating Sox9 expression and activity in nucleus pulposus cells of the intervertebral disc

The goal of the investigation was to test the hypothesis that the phosphoinositide‐3 kinase (PI3K)/AKT signaling pathway regulates the expression of the major extracellular matrix component of the intervertebral disc, aggrecan, in nucleus pulposus cells. Primary rat nucleus pulposus cells were treated with PI3K inhibitor to measure changes in gene and protein expression. In addition, cells were transfected with various luciferase reporter plasmids to investigate mechanisms of regulation of aggrecan gene expression. We found that treatment of nucleus pulposus cells with a PI3K inhibitor, LY294002 resulted in decreased expression of aggrecan and a reduction in deposition of sulfated glycosaminoglycans. Moreover, pharmacological suppression or co‐expression of dominant negative (DN)‐PI3K or DN‐AKT resulted in downregulation of aggrecan promoter activity. Expression of constitutively active (CA)‐PI3K significantly induced aggrecan promoter activity. We observed that PI3K maintained Sox9 gene expression and activity: inhibition of PI3K/AKT resulted in decreased Sox9 expression, lowered promoter activity, and mediated a reduction in Sox9 transcriptional activity. PI3K effects were independent of phosphorylation status of C‐terminus transactivation domain (TAD) of Sox9. Finally, we noted that in nucleus pulposus cells, PI3K signaling controlled transactivation of p300 (p300‐TAD activity), an important transcriptional co‐activator of Sox9. Results of these studies demonstrate for the first time that PI3K/AKT signaling controls aggrecan gene expression, in part by modulating Sox9 expression and activity in cells of the nucleus pulposus. J. Cell. Physiol. 221: 668–676, 2009. © 2009 Wiley‐Liss, Inc.
A Robust Beamforming Approach to Guarantee Instantaneous Secrecy Rate

We consider a well-known beamforming approach that induces jamming signals to avoid eavesdropping from a transmitter equipped with an antenna array in this paper. With this beamforming, which is called masked beamforming, in order to guarantee a certain instantaneous secrecy rate, we formulate robust beamforming problems with a constraint that deals with the eavesdropper channel's uncertainty and find the solutions. Unlike a guaranteed ergodic secrecy rate, this guaranteed instantaneous secrecy rate allows us to use codes of short codewords for secure communications with masked beamforming over slow-fading channels. In addition, since the optimal solutions are found in closed form, we do not need to resort to any convex optimization solvers.
Prolonged neoadjuvant chemotherapy with GM-CSF in locally advanced breast cancer.

BACKGROUND Neoadjuvant chemotherapy improves survival in patients with locally advanced breast cancer (LABC). Usually three to four cycles of conventional-dose neoadjuvant chemotherapy are administered prior to local therapy, and another three cycles thereafter. In an attempt to improve results, we increased the dosages and applied GM-CSF, which, besides being a hematopoietic growth factor, has become increasingly known for its immunostimulatory effects, which might enhance the antitumor effect. METHODS Forty-two patients with stage IIIA or IIIB breast cancer were treated with doxorubicin (A) (90 mg/m2) and cyclophosphamide (C) (1,000 mg/m2) at three-weekly intervals. In the second and fourth cycle a 10% dose reduction of both agents was applied. On the second day GM-CSF 250 micrograms/m2/day was started and given for 10 days. Initially, some patients were treated with < or = four cycles, but as the study progressed and toxicity appeared tolerable, six cycles were given whenever possible. After the chemotherapy, patients underwent surgery and postoperative radiotherapy. RESULTS The response rate for the whole group to AC was 98% (95% confidence interval 94%-100%), with a clinical complete response rate of 50% (95% confidence interval 35%-65%). Six patients had a pathological complete response. Median follow-up from the start of chemotherapy is 49 months (range 10-100). The disease-free survival (DFS) at three years is 57% and the overall survival (OS) at three years is 79%. There is a significant trend for improved DFS (p = 0.0000) and OS (p = 0.0002) with increasing number of cycles. CONCLUSION The results of the present study with neoadjuvant dose-intensive AC chemotherapy and GM-CSF compare favorably with previous studies in patients with LABC. This is most apparent in patients who received six cycles of neoadjuvant chemotherapy. We hypothesize that these encouraging results are probably related to the prolonged presence of the primary tumor, and to the long-term administration of GM-CSF with the primary tumor and axillary lymph nodes in situ. Therefore, a randomized study is warranted. We already initiated an international randomized trial in patients with LABC in order to answer two questions. First, does prolonged neoadjuvant chemotherapy result in an improved DFS and OS in comparison with the conventional approach, and secondly, what is the effect of GM-CSF in this approach in comparison with G-CSF?
Bayesian Poisson process partition calculus with an application to Bayesian Lévy moving averages

This article develops, and describes how to use, results concerning disintegrations of Poisson random measures. These results are fashioned as simple tools that can be tailor-made to address inferential questions arising in a wide range of Bayesian nonparametric and spatial statistical models. The Poisson disintegration method is based on the formal statement of two results concerning a Laplace functional change of measure and a Poisson Palm/Fubini calculus in terms of random partitions of the integers (1,.,n). The techniques are analogous to, but much more general than, techniques for the Dirichlet process and weighted gamma process developed in {Ann. Statist. 12 (1984) 351-3571 and [Ann. Inst. Statist. Math. 41 (1989) 227-245]. In order to illustrate the flexibility of the approach, large classes of random probability measures and random hazards or intensities which can be expressed as functionals of Poisson random measures are described. We describe a unified posterior analysis of classes of discrete random probability which identifies and exploits features common to all these models. The analysis circumvents many of the difficult issues involved in Bayesian nonparametric calculus, including a combinatorial component. This allows one to focus on the unique features of each process which are characterized via real valued functions h. The applicability of the technique is further illustrated by obtaining explicit posterior expressions for Levy-Cox moving average processes within the general setting of multiplicative intensity models. In addition, novel computational procedures, similar to efficient procedures developed for the Dirichlet process, are briefly discussed for these models.
The analysis on the determinants of mobile VIP customer churn: a logistic regression approach

According to 20/80 principle, retaining VIP customers is one of the most critical challenges in the maturing mobile telecommunications service market. However, there are little literatures to explain why the VIP customers churn. Using mobile VIP customers’ huge transaction and billing database, this study investigates determinants of mobile VIP customer churn. The results indicate that the switching cost: virtual private mobile network (VPMN) and family package are the most important factors in VIP customers churn. However, some marketing tools on ordinary users such as accumulated loyalty points, terminal bound contract do not work on VIP customers, which raise the questions about this marketing programme effectiveness. This study provides implications for the competition policies of mobile telephony market.
UbiRockMachine: a multimodal music voting service for shared urban spaces

In this paper we suggest a conceptual architecture for music systems, designed to shift the control over a shared urban space to the users themselves, and also to encourage social interaction between co-located friends and strangers alike. We present UbiRockMachine, a prototype application designed to bring the communities of local, un-signed music producers and music consumers together. The application provides a two-way communications channel where the music producers make their creative content available to people occupying a shared social space. These people then democratically choose the music played in the shared public space and provide valuable feedback to the musicians by downloading and rating their content. We present findings from empirical user testing carried out in three separate locations, and outline directions for future work and further experiments.
Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM 9152T

ABSTRACT Here, we report the draft genome sequences of the type strains of three cellulolytic or hemicellulolytic alkaliphilic Bacillus species: Bacillus wakoensis, Bacillus akibai, and Bacillus hemicellulosilyticus. The genome information for these three strains will be useful for studies of alkaliphilic Bacillus species, their evolution, and biotechnological applications for their enzymes.
Toward biomaterial-based implantable photonic devices

Abstract Optical technologies are essential for the rapid and efficient delivery of health care to patients. Efforts have begun to implement these technologies in miniature devices that are implantable in patients for continuous or chronic uses. In this review, we discuss guidelines for biomaterials suitable for use in vivo. Basic optical functions such as focusing, reflection, and diffraction have been realized with biopolymers. Biocompatible optical fibers can deliver sensing or therapeutic-inducing light into tissues and enable optical communications with implanted photonic devices. Wirelessly powered, light-emitting diodes (LEDs) and miniature lasers made of biocompatible materials may offer new approaches in optical sensing and therapy. Advances in biotechnologies, such as optogenetics, enable more sophisticated photonic devices with a high level of integration with neurological or physiological circuits. With further innovations and translational development, implantable photonic devices offer a pathway to improve health monitoring, diagnostics, and light-activated therapies.
Effects of crowding on ornithine–urea cycle enzyme mRNA expression and activity in gulf toadfish (Opsanus beta)

SUMMARY The gulf toadfish (Opsanus beta) is a facultatively ureotelic fish that excretes primarily urea under conditions of crowding or confinement. To examine the relationship between ammonia production, urea production and the ornithine–urea cycle (O–UC) enzyme activity and mRNA expression, we subjected toadfish to two-day and seven-day crowding regimes. Plasma cortisol levels were measured and liver tissue was assayed for ammonia and urea concentrations. Liver glutamine synthetase (GS), carbamoyl phosphate synthetase III (CPS), ornithine carbamoyl transferase (OCT) and arginase (ARG) activities were also measured. Quantitative PCR was utilized to determine liver GS, CPS, OCT, ARG, argininosuccinate synthetase (ASS) and argininosuccinate lyase (ASL) mRNA expression. Hepatic ammonia concentrations decreased with increased duration of crowding whereas liver urea and circulating cortisol levels increased. An elevation in enzyme activity with increased duration of crowding was observed for all four O-UC enzymes examined. By contrast, mRNA expression was variable for the O–UC enzymes and only CPS and ASS had mRNA expression levels that were elevated in crowded fish. These results suggest that the activities of O–UC enzymes are better predictors for urea production than O–UC enzyme mRNA expression levels.
Reliable and energy-efficient routing protocol for mobile sink groups in wireless sensor networks

To support a group of mobile sinks in wireless sensor networks, region-based routing protocols by using a single entity nature have been proposed. They periodically register the region location information of the mobile sink group and exploit flooding for the data delivery within the region. However, they have a data delivery failure problem for some sinks due to the asynchrony between the registered region and the actual region of the mobile sink group due to its mobility. They also have an excessive energy consumption problem due to flooding data within the region. Thus, to solve the data delivery failure and the excessive energy consumption problems, we propose a routing protocol for a mobile sink group by utilizing its movement pattern which has a slow variance and continuous stream i.e. moving properties. In the proposed protocol, a source sends its data only to sensor nodes on a line that a mobile sink group potentially passes, and mobile sinks get the data from the line when they pass it. Simulation results show that the proposed protocol has better performance than the existing protocols.
Semantic Search in Tabular Structures

Keywords: tabular structures, ontology learning, semantic web, query answeringReceived: November 18, 2005The Semantic Web search aims to overcome the bottleneck of ﬁnding relevant information using formalknowledge models, e.g. ontologies. The focus of this paper is to extend a typical search engine withsemantic search over tabular structures. We categorize HTML documents into topics and genres. Using theTARTAR system, tabular structures in the documents are then automatically transformed into ontologiesand annotated to build a knowledge base. When posting queries, users receive responses not just as lists oflinks and description extracts, but also enhanced with replies in the form of detailed structured data.Povzetek: Razvili smo metode semanticnega spleta za iskanje informacij v tabelah. ˇ