Miracle-dz/UniFAR-FTUs huggingface dataset:
A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum

ABSTRACT While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.
Modified 2-D Cepstrum Using Soft-Computing

We proposed a method which can solve the low speech recognition rate problem under noisy environment. in our system, the method is GAS-based Speech Recognition using Two Dimensional cepstrum. Two dimensional cepstrum (TDC) can simultaneously represent several kinds of information contained in the speech waveform: static and dynamic features, as well as global and fine frequency structures. from analysis, an utterance only some TDC coefficients will be selected to form a feature vector. Hence, it has the advantages of soft computation and less storage space. However, it is quite sensitive to background noise. in order to solve this problem, we propose the GAS-based M-TDC method in our system to improve the performance of TDC under noisy condition. from the experiments with five noise types, we found that the GAS-based M-TDC have better recognition results than the TDC under the noisy environments.
Auditory Interpretation and Application of Warped Linear Prediction

This paper presents a study on a specific signal processing technique, the warped linear prediction (WLP), interpreted here from an auditory perception point of view. WLP is a signal modeling technique that can approximate the frequency resolution properties of the human ear. WLP is shown in this paper to have system-level similarities with signal analysis found in the peripheral auditory system. Several phenomena in auditory modeling are addressed where WLP-based spectral modeling and residual processing are useful. Pitch analysis, including multipitch analysis, segregation of harmonic signals by pitch-predictive means, and other processing techniques (synthesis, recognition) are shortly discussed.
Prognoses and Prognostic Factors of Carcinosarcoma, Endometrial Stromal Sarcoma and Uterine Leiomyosarcoma: A Comparison with Uterine Endometrial Adenocarcinoma

Aims: The aims of this study were to evaluate the factors affecting prognosis in patients with uterine sarcomas and to demonstrate that carcinosarcoma bears a similarity to high-grade endometrial carcinoma in terms of its prognosis and clinicopathological parameters. Methods: In June 2004, 17 Japanese institutions received questionnaires regarding uterine sarcomas. Study patients had uterine sarcomas initially treated at each institution between January 1990 and May 2004. Survival analyses and comparisons were performed by univariate methods. Patient data of 921 cases of endometrial adenocarcinoma were also analyzed and compared to the data with the uterine sarcomas. Results: One hundred twenty-one patients with uterine sarcomas were identified who met study eligibility criteria. In uterine sarcomas, carcinosarcoma had a worse prognosis than other sarcomas, but the difference was not significant (p = 0.302). In carcinosarcoma, significant differences were observed with age (p = 0.0388), stage (p < 0.01) and surgical procedure (with or without pelvic lymphadenectomy, p = 0.0316). In carcinosarcoma and G3 adenocarcinoma, no significant difference was identified with regard to overall survival in univariate (p = 0.191) and multivariate (p = 0.168) analyses. Conclusion: Our results demonstrate that the clinical behavior of carcinosarcoma strongly resembles that of G3 endometrial adenocarcinoma, setting it apart from other ‘pure’ uterine sarcomas.
Synchrotron X-ray PIV of blood flow in an optically opaque bifurcation model

Particle image velocimetry (PIV) of biological flows is commonly conducted on in vitro models using planar PIV. This requires optical access to the model and is restricted to obtaining two components of velocity for a single plane of the domain. X-ray PIV provides the ability not only to image opaque specimens, such as ex vivo blood vessels, but also to acquire the velocity field within the entire domain. This paper investigates the fluid dynamics of blood flow in an optically opaque in vitro model, chosen to be consistent with that of a healthy human carotid bifurcation. The velocity profile of the internal carotid artery (ICA) is seen to develop a region of low wall shear stress identified on the outside wall of the ICA. Additionally, the use of gas micro-bubbles has proven successful in providing a stronger signal for X-ray PIV experiments.
Controlling Inference: Avoiding P-level Reduction During Analysis

This paper presents a concept hierarchy-based approach to privacy preserving data collection for data mining called the P-level model. The P-level model allows data providers to divulge information at any chosen privacy level (P-level), on any attribute. Data collected at a high P-level signifies divulgence at a higher conceptual level and thus ensures more privacy. Providing guarantees prior to release, such as satisfying k-anonymity (Samarati 2001; Sweeney 2002), can further protect the collected data set from privacy breaches due to linking the released data set with external data sets. However, the data mining process, which involves the integration of various data values, can constitute a privacy breach if combinations of attributes at certain P-levels result in the inference of knowledge that exists at a lower P-level. This paper describes the P-level reduction phenomenon and proposes methods to identify and control the occurrence of this privacy breach.
HVDC Cable Systems—Highlighting Extruded Technology

HVDC cable systems are growing in number. This is a result of globally defined targets leading to an increase of investments in renewables. The HVDC cable systems enable us to integrate these new energy sources in a manner that reduces losses and stabilizes operations. In this paper, the focus is on extruded HVDC cables. Starting from a general description of the forces that drive us toward more cables, this paper quantifies the push for higher voltages. The extruded cable system on a product level is described followed by design aspects. Particularly, the effect of thermal runaway is highlighted. The accessories, joints, and terminations are described. The advantages of the concept nonlinear field grading are described. This paper ends with some words on realized commercial projects and future trends.
AMPol: Adaptive Messaging Policy

Interoperability in a large-scale distributed system is challenged by the diversity of node policies. We introduce AMPol (adaptive messaging policy), a service-oriented architecture that facilitates policy-aware, end-to-end adaptive messaging between multiple parties. AMPol provides services for expressing non-functional QoS policies, finding them, and carrying out system extensions to adapt to them. We implement this approach with a Web service middleware that allows parties to use policies for features like attachments, payment, encryption, and signatures. Our implementation demonstrates how AMPol can enhance the function of email messaging by enabling automatic deployment and use of features like cycle exhaustion puzzles, reverse Turing tests and identity based encryption without the need for global deployment or changes to the baseline messaging system
Barriers to women achieving their entrepreneurial potential: Women and risk

Purpose – This paper provides a comprehensive summary of the academic literature with regard to risk and its role in the entrepreneurial experience of women. Entrepreneurial risk has an under-developed conceptual basis and distilling gender-specific aspects is difficult. Various academic disciplines have contributed to the topic of risk, e.g., economics, and often decision making is used to contextualise the topic. Though the literature does not always prove an association between the different facets of risk and entrepreneurship, there is general agreement that a number of factors, e.g., personal, political and social inter-relate to influence risk and subsequent behaviour. Design/methodology/approach – Uses a desk-based approach to data collection. An overview of the main issues concerning risk and entrepreneurship is given to contexualise the gender aspects to be discussed, drawing on the extant literature. Findings – The paper posits that an understanding of the gender aspects of risk is required if policy measures are to be constructive and help women overcome barriers and achieve their entrepreneurial potential. The conclusions drawn from the literature provide the foundations for a discussion of the likely policy measures that are required to encourage women entrepreneurs. Research limitations/implications – A summary is provided of the research and information gaps that remain in terms of women entrepreneurship and risk with the aim of encouraging further research in the area. Originality/value – Provides a comprehensive summary of the literature with regard to risk and the entrepreneurial experience of women, and discusses the likely policy measures required to encourage women entrepreneurs.
Efficient duck hepatitis B virus production by an avian liver tumor cell line

Duck hepatitis B virus (DHBV) is produced in small amounts following transfection of human hepatoma or hepatoblastoma cell lines with cloned viral DNA. In a search for better hosts for DHBV replication, two avian liver cell lines were investigated. One of these cell lines, LMH, produced 5 to 10 times more DNA replicative intermediates and 10 to 20 times more infectious DHBV than did either of the two human cell lines, HuH-7 and Hep G2. Utilization of cell lines in genetic analyses of virus replication is often dependent upon obtaining efficient complementation between cotransfected viral genomes. We assayed transcomplementation of a viral polymerase (pol) gene mutant, which is rather inefficient in transfected human cells, and found that viral DNA synthesis was at least 20 times more efficient following cotransfection of LMH cells than in similarly transfected HuH-7 cells. Recombination, a potential interpretation problem in complementation assays, occurred at low levels in the cotransfected cultures but was substantially reduced or eliminated by creation of an LMH subline stably expressing the viral polymerase. This cell line, pol-7, supported the replication of DHBV pol mutants at ca. 10 to 15% of the level of virus replication obtained following transfection with wild-type viral DNA. By transcomplementation of a pol gene mutant in LMH cells, we were able to produce sufficient virus with the mutant genome to investigate the role of polymerase in covalently closed circular DNA amplification. Our results substantiate the hypothesis that covalently closed circular DNA is synthesized by the viral reverse transcriptase.
Discrete-event simulation optimization using ranking, selection, and multiple comparison procedures: A survey

An important use for discrete-event simulation models lies in comparing and contrasting competing design alternatives without incurring any physical costs. This article presents a survey of the literature for two widely used classes of statistical methods for selecting the best design from among a finite set of k alternatives: ranking and selection (R&S) and multiple comparison procedures (MCPs). A comprehensive survey of each topic is presented along with a summary of recent unified R&S-MCP approaches. Procedures are recommended based on their statistical efficiency and ease of application; guidelines for procedure application are offered.
Hiding Information in Multiple Level-line Moirés

Secure documents often comprise an information layer that is hard to reproduce. Moiré techniques for the prevention of counterfeiting rely on the superposition of an array of transparent lines or microlenses on top of a base layer containing hidden information. Level-line moirés consist of shapes that appear to be beating upon relative translation of a revealing grating on top of a base, in which the desired information is encoded. Usually, the base only contains the information corresponding to one moiré. In order to increase the difficulty of counterfeiting, we use tessellations to incorporate two or more moirés within the same layer. With the method we propose, the information corresponding to up to seven level-line moirés can be embedded within a single base layer. The moirés are recovered with a revealer printed on a transparency or with an array of cylindrical lenses. This method is general and can be extended to other fabrication technologies.
A TECHNIQUE FOR ORTHOTOPIC LIVER TRANSPLANTATION IN THE RAT

This report describes in detail the technique of orthotopic liver transplantation in syngeneic rats which are relatively inexpensive and readily available. We also report the long-term survival and function of these grafts. The technique involves the use of a miniaturized extracorporeal portal to jugular shunt. The donor liver is perfused and cooled. Implantation is accomplished using standard microvascular suture techniques. Successful orthotopic liver transplants were performed in 47 of 64 rats. Long-term survival up to 14 months was achieved in seven animals. Liver function was measured by serial determination of bilirubin, serum glutamic oxaloacetic transaminase (SGOT), and alkaline phosphatase. Elevations in bilirubin and SGOT in the immediate postoperative period returned to normal by the second postoperative week. Marked variations were seen in alkaline phosphatase values, and there was slow return to normal levels. Open liver biopsies were performed on long-term survivors at 3, 5, and 7 months and revealed essentially normal liver parenchyma, with slight mononuclear infiltration of the portal spaces and some sinusoidal dilatation. The practicability of the transplant and organ preservation, and the advantages of using the inbred rat as the experimental animal are discussed.
Models for Composing Heterogeneous Software Architectures

A persistent problem in software engineering is the problem of software composition. The emergence of software architectures and architectural styles has focused attention on a new set of abstractions with which we can create and compose software systems. We examine the problem of providing a model for the composition of different architectural styles within software systems, i.e. the problem of composing heterogeneous architectures. We describe a model of pure styles that is based on a uniform representation. We provide a disciplined approach for analyzing some key aspects of architectural composition, and show the conditions under which systems will fail to be composed. INTRODUCTION A persistent problem in computer science is how to put software systems together out of smaller subsystems, the problem of software composition. There are many levels of granularity at which this problem can be tackled. For example, some of the earliest software engineers dealt with systems at the machine language or assembly language level of granularity. Succeeding engineers addressed the composition problem at a coarser level of granularity using higher level programming languages. The emergence of software architectures and architectural styles ([8]) has introduced a still coarser level of granularity (and higher level of abstraction) at which we can reason about the creation and composition of software systems.
The State of Qatar Informative Web Portal

This paper describes the electronic government project in the state of Qatar known as Qatar Central Government Portal (Hukoomi e-Gov). It highlights the main online services that are offered to Qataris citizens and residents. The main objective of the e-Gov portal, as claimed by its project manager, is to achieve the highest performance in executing governmental transactions electronically, through streamlined business processes and integrated information technology solutions. Although this web portal offers an important range of online services, it lacks however, in information about the state of Qatar like schools and education, entertainment, tourism and monuments, banking, malls and shopping centers, hospitals and health care centers, etc. Thus, an informative web portal about the country is needed. It should be the main point of access to information about Qatar and complement its e-Gov portal, Hukoomi. New visitors and potential residents can then get the necessary information about the previous facilities through this informative portal. Many modern countries have developed their business and informative portals. We discuss in this work the design and characteristics of our proposed informative web portal about the state of Qatar and we propose a disambiguation algorithm to retrieve the main documents related to the user query.
Multi-Loop Feedback Hierarchy Involving Human Workers in Manufacturing Processes

In manufacturing environments today, automated machinery works alongside human workers. In many cases computers and humans oversee different aspects of the same manufacturing steps, sub-processes, and processes. This paper identifies and describes four feedback loops in manufacturing and organises them in terms of their time horizon and degree of automation versus human involvement. The data flow in the feedback loops is further characterised by features commonly associated with Big Data. Velocity, volume, variety, and veracity are used to establish, describe and compare differences in the data flows.
The Effects of Bilingualism on Examination Scores : A Different Setting

In Papua New Guinea the three external examinations that primary school students take in their final year are important for their possible entry into the secondary level of the school system. Sixty per cent of students leave the system at this point. This study investigated whether the level of competencies in both a student's first language and in English, the language of schooling, influenced final scores on the external examinations. The results show that indeed there is such an influence. Implications are suggested for both the Papua New Guinea school system and general language theory.
Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s-1·MBq-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.
THE USE OF SANDWICH-CULTURED RAT HEPATOCYTES TO DETERMINE THE INTRINSIC CLEARANCE OF COMPOUNDS WITH DIFFERENT EXTRACTION RATIOS: 7-ETHOXYCOUMARIN AND WARFARIN

The application of sandwich-cultured rat hepatocytes for the identification of the hepatic intrinsic clearance of compounds with widely varying extraction ratios was investigated. We previously showed the applicability of this in vitro system, in combination with a model describing molecular diffusion, hepatocyte/medium partition, and nonsaturated metabolism, which resulted in a successful identification of this parameter for tolbutamide. This approach is further validated using the compounds 7-ethoxycoumarin and warfarin, covering a 100-fold range of extraction ratios. Clearance of these two substrates could be reliably determined, but only if the depletion of the parent compound in medium as well as in the hepatocyte sandwich was measured. Sensitivity analyses showed that the time course of depletion of the parent compound in medium, especially for warfarin, is insensitive to the partition and diffusion parameter values, whereas depletion in the hepatocyte sandwich was far more sensitive. When varying the volumes of collagen in the sandwich culture, it appears that the most reliable kinetic parameters could be obtained by fitting the data with the smaller collagen volume and that these parameters obtained from fitting to data of the larger volumes generally cannot be verified satisfactorily with the data of the smaller volumes. The values of hepatic clearance that were obtained after extrapolation of the intrinsic clearance to the hepatic clearance from blood were comparable within a factor of 2 to hepatic clearance data in the literature. This indicates that this sandwich culture and modeling system can be applied for the identification of the hepatic intrinsic clearance rate of the total range from low to high clearance compounds.