Miracle-dz/UniFAR-FTUs huggingface dataset:
Change Management and Software Reuse Supportive 'Genetic Information System Development and Maintenance' Model

The aim of the present research work is to develop an information system development process and a model for the development of new generation information systems. New age information systems are those information systems that are capable of fulfilling the demand of highly dynamic information requirements derived from the competitive environments of business organizations and support controlling the complexity involved in their maintenance and software configuration management. Present research work analyzes the theoretical, financial, technical and practical problems related to the information system development, maintenance and change management to propose an appropriate system development process and a model for the development as well as maintenance of information systems with maximum software reuse. The proposed system development process and model provide inherent support to the business organizations in having total control over information system development, maintenance and software configuration management.
Building‐block approach for determining low‐frequency normal modes of macromolecules

Normal mode analysis of proteins of various sizes, ranging from 46 (crambin) up to 858 residues (dimeric citrate synthase) were performed, by using standard approaches, as well as a recently proposed method that rests on the hypothesis that low‐frequency normal modes of proteins can be described as pure rigid‐body motions of blocks of consecutive amino‐acid residues. Such a hypothesis is strongly supported by our results, because we show that the latter method, named RTB, yields very accurate approximations for the low‐frequency normal modes of all proteins considered. Moreover, the quality of the normal modes thus obtained depends very little on the way the polypeptidic chain is split into blocks. Noteworthy, with six amino‐acids per block, the normal modes are almost as accurate as with a single amino‐acid per block. In this case, for a protein of n residues and N atoms, the RTB method requires the diagonalization of an n × n matrix, whereas standard procedures require the diagonalization of a 3N × 3N matrix. Being a fast method, our approach can be useful for normal mode analyses of large systems, paving the way for further developments and applications in contexts for which the normal modes are needed frequently, as for example during molecular dynamics calculations. Proteins 2000;41:1–7. © 2000 Wiley‐Liss, Inc.
Optimal design of a CMOS op-amp via geometric programming

We describe a new method for determining component values and transistor dimensions for CMOS operational amplifiers (op-amps). We observe that a wide variety of design objectives and constraints have a special form, i.e., they are posynomial functions of the design variables. As a result, the amplifier design problem can be expressed as a special form of optimization problem called geometric programming, for which very efficient global optimization methods have been developed. As a consequence we can efficiently determine globally optimal amplifier designs or globally optimal tradeoffs among competing performance measures such as power, open-loop gain, and bandwidth. Our method, therefore, yields completely automated sizing of (globally) optimal CMOS amplifiers, directly from specifications. In this paper, we apply this method to a specific widely used operational amplifier architecture, showing in detail how to formulate the design problem as a geometric program. We compute globally optimal tradeoff curves relating performance measures such as power dissipation, unity-gain bandwidth, and open-loop gain. We show how the method can he used to size robust designs, i.e., designs guaranteed to meet the specifications for a variety of process conditions and parameters.
Regulation and Function of TRPM7 in Human Endothelial Cells: TRPM7 as a Potential Novel Regulator of Endothelial Function

TRPM7, a cation channel of the transient receptor potential channel family, has been identified as a ubiquitous magnesium transporter. We here show that TRPM7 is expressed in endothelial cells isolated from the umbilical vein (HUVEC), widely used as a model of macrovascular endothelium. Quiescence and senescence do not modulate TRPM7 amounts, whereas oxidative stress generated by the addition of hydrogen peroxide increases TRPM7 levels. Moreover, high extracellular magnesium decreases the levels of TRPM7 by activating calpains, while low extracellular magnesium, known to promote endothelial dysfunction, stimulates TRPM7 accumulation partly through the action of free radicals. Indeed, the antioxidant trolox prevents TRPM7 increase by low magnesium. We also demonstrate the unique behaviour of HUVEC in responding to pharmacological and genetic inhibition of TRPM7 with an increase of cell growth and migration. Our results indicate that TRPM7 modulates endothelial behavior and that any condition leading to TRPM7 upregulation might impair endothelial function.
A novel ensemble classifier approach using weak classifier learning on overlapping clusters

This paper presents a novel approach for creating and training of an ensemble classifier. The approach is based on creating atomic and non-atomic clusters at different levels, training of weak classifiers on overlapping clusters and fusion of their decisions. The subsets of data are obtained by clustering of original training data sets into multiple partitions. As each partition represents highly correlated patterns from different classes, the proposed approach trains weak classifiers on difficult-to-classify patterns and combines the decision at various levels. The approach is tested on six benchmark datasets from UCI machine learning repository. The results show that the proposed approach achieves better classification accuracy than the existing approaches.
Cognitive Human Factors for Telemedicine Systems

The recent integration of telephony systems with information and communication technology (ICT) enables the development of innovative tools for telemedicine. The dissemination and widespread acceptance of telephone-based care monitoring systems challenge the researcher to deal with the cognitive factors involved in the patient-physician interaction, and the way they should be to shape up the technological solutions. This paper proposes a model that describes the impact of socio-cognitive factors in the complex process of health care management. The model has been used to design and develop a telephone system for the management of hypertensive patient within the EU funded Homey project. The knowledge existed in a widely accepted guideline for the care of hypertension has been represented and augmented through the proposed cognitive model. The final product is an intelligent system able to manage an adaptive dialogue. It monitors patients' adherence and increases their involvement by promoting self-care through frequent virtual visits, which is complementary to the traditional face-to-face encounters with their primary care physicians.
PriC-mediated DNA Replication Restart Requires PriC Complex Formation with the Single-stranded DNA-binding Protein*

Background: PriC can reload the DnaB helicase onto single-stranded DNA-binding protein (SSB)-coated DNA, which is the first step in DNA replication restart. Results: PriC directly interacts with SSB and alters its mode of DNA binding. Conclusion: PriC/SSB complex formation is essential for PriC-mediated DnaB loading. Significance: Learning how DNA replication restart occurs is critical for understanding bacterial genome maintenance mechanisms. Frequent collisions between cellular DNA replication complexes (replisomes) and obstacles such as damaged DNA or frozen protein complexes make DNA replication fork progression surprisingly sporadic. These collisions can lead to the ejection of replisomes prior to completion of replication, which, if left unrepaired, results in bacterial cell death. As such, bacteria have evolved DNA replication restart mechanisms that function to reload replisomes onto abandoned DNA replication forks. Here, we define a direct interaction between PriC, a key Escherichia coli DNA replication restart protein, and the single-stranded DNA-binding protein (SSB), a protein that is ubiquitously associated with DNA replication forks. PriC/SSB complex formation requires evolutionarily conserved residues from both proteins, including a pair of Arg residues from PriC and the C terminus of SSB. In vitro, disruption of the PriC/SSB interface by sequence changes in either protein blocks the first step of DNA replication restart, reloading of the replicative DnaB helicase onto an abandoned replication fork. Consistent with the critical role of PriC/SSB complex formation in DNA replication restart, PriC variants that cannot bind SSB are non-functional in vivo. Single-molecule experiments demonstrate that PriC binding to SSB alters SSB/DNA complexes, exposing single-stranded DNA and creating a platform for other proteins to bind. These data lead to a model in which PriC interaction with SSB remodels SSB/DNA structures at abandoned DNA replication forks to create a DNA structure that is competent for DnaB loading.
SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity

Identifying protein surface regions preferentially recognizable by antibodies (antigenic epitopes) is at the heart of new immuno-diagnostic reagent discovery and vaccine design, and computational methods for antigenic epitope prediction provide crucial means to serve this purpose. Many linear B-cell epitope prediction methods were developed, such as BepiPred, ABCPred, AAP, BCPred, BayesB, BEOracle/BROracle, and BEST, towards this goal. However, effective immunological research demands more robust performance of the prediction method than what the current algorithms could provide. In this work, a new method to predict linear antigenic epitopes is developed; Support Vector Machine has been utilized by combining the Tri-peptide similarity and Propensity scores (SVMTriP). Applied to non-redundant B-cell linear epitopes extracted from IEDB, SVMTriP achieves a sensitivity of 80.1% and a precision of 55.2% with a five-fold cross-validation. The AUC value is 0.702. The combination of similarity and propensity of tri-peptide subsequences can improve the prediction performance for linear B-cell epitopes. Moreover, SVMTriP is capable of recognizing viral peptides from a human protein sequence background. A web server based on our method is constructed for public use. The server and all datasets used in the current study are available at http://sysbio.unl. edu/SVMTriP.
The Epidemiology of District Surgery in Malawi: a Two Year Study of Surgical Rates and Indices in Rural Africa

Background: The true surgical requirement of a rural African population is also not precisely known. Methods: Data gathered over a 2-year period from 1993 to 1995 on surgical and anaesthetic activities in 18 District Hospitals in Malawi are presented. Results: Theatre records showed that 45,032 operations were carried out at District Hospitals in the study area which had a catchment population of 6,100,000 giving an average annual rate of 369 operations per 100,000 population (range 151-1337). Of the total, 11,466 operations were classed as major, giving an average annual rate of 94 per 100,000 population (range 31-242 / 100,000). Comparable rates for total and major operations carried out in the central referral hospital were 865 and 269 per 100,000, respectively, allowing for referrals. A total of 7,288 caesarean sections (CS) were carried out, constituting 65.6% of all major operations. The rural CS rate was 60 per 100,000 compared to the central hospital rate of 151 per 100,000. In the district hospitals, 75% of all surgery, including most major operations, was carried out by paramedical cadres (Clinical Officers or Medical Assistants), 8.2% by the resident District Health Officer and 0.8% by visiting specialists. All general and regional anaesthesia was given by paramedical cadres. The ratios of CS to all major operations and laparotomy to all major operations showed a different pattern of surgery between district hospitals and between district and central hospitals. The value of these indices in identifying deficiencies in the surgical services is discussed. East and Central African Journal of Surgery . 2011 Nov/ December;16 (3)
Pixel lensing as a way to detect extrasolar planets in M31

We study the possibility to detect extrasolar planets in M31 through pixel-lensing observations. Using a Monte Carlo approach, we select the physical parameters of the binary lens system, a star hosting a planet, and we calculate the pixel-lensing light curve taking into account the finite source effects. Indeed, their inclusion is crucial since the sources in M31 microlensing events are mainly giant stars. Light curves with detectable planetary features are selected by looking for significant deviations from the corresponding Paczy´ nski shapes. We find that the timescale of planetary deviations in light curves increase (up to 3–4 d) as the source size increases. This means that only few exposures per day, depending also on the required accuracy, may be sufficient to reveal in the light curve a planetary companion. Although the mean planet mass for the selected events is about 2 MJupiter, even small mass planets (M P < 20 M⊕) can cause significant deviations, at least in the observations with large telescopes. However, even in the former case, the probability to find detectable planetary features in pixel-lensing light curves is at most a few per cent of the detectable events, and therefore many events have to be collected in order to detect an extrasolar planet in M31. Our analysis also supports the claim that the anomaly found in the candidate event PA-99-N2 towards M31 can be explained by a companion object orbiting the lens star.
Perception of social context and activity following participation in a physical fitness intervention during residential adolescent addiction treatment.

The aim of this study was to assess perception of activity and social context scales1 of adolescent substance abusers following participation in a physical activity intervention during residential drug treatment. The sample was assessed on entry to treatment, on completion of treatment; six weeks postresidential treatment and six months after treatment using mean, standard deviation, and t-tests. In general, the overall mean scores for perception of social context increased from entry to completion of the treatment program, decreased six weeks post–treatment, and increased when six months in aftercare. Some significant difference was recorded between entry to treatment and six weeks post-treatment (p = 0.04). The results relating to perception of activity increased from entry to completion of the treatment program, increased at six weeks post-treatment, and decreased to six months in aftercare. Some significant differences were recorded between entry and six weeks post-treatment (p = 0.02), between completion of treatment and six months in aftercare (p = 0.03), and between six weeks post-treatment and six months in aftercare (p = 0.05). This research hoped to illustrate the potential of physical activity as alternative leisure pursuit following addiction treatment to help prevent relapse for adolescent substance abusers by reducing contact with other users and providing a healthy and positive social outlet.
Just-In-Time Manufacturing System: From Introduction to Implement

JIT production system identifies the hidden problems in the value chain and reduces the production waste of the system while increasing the throughout (Sales-Raw Material Cost). Even though the JIT system seems to be interesting and less complicated it requires lot of coordination with supply chain to avoid delays in the production schedule. This article discusses in depth the implementation of JIT manufacturing. The objectives are twofold. The first objective is to acquaint the reader with the overall JIT concept and the factors necessary for its implementation; the concepts presented here represent the ideal principles and methods of implementation.
Estimating the weight of metric minimum spanning trees in sublinear-time

In this paper we present a sublinear time (1 + ε)-approximation randomized algorithm to estimate the <i>weight</i> of the minimum spanning tree of an <i>n</i>-point metric space. The running time of the algorithm is <i>Û</i>(<i>n</i>/ε<sup>O(1)</sup>). Since the full description of an <i>n</i>-point metric space is of size Θ(<i>n</i><sup>2</sup>), the complexity of our algorithm is <i>sublinear</i> with respect to the input size. Our algorithm is almost optimal as it is not possible to approximate in <i>o</i>(<i>n</i>) time the weight of the minimum spanning tree to within any factor. Furthermore, it has been previously shown that no <i>o</i>(<i>n</i><sup>2</sup>) algorithm exists that <i>returns a spanning tree</i> whose weight is within a constant times the optimum.
Supervised Recurrent Hashing for Large Scale Video Retrieval

Hashing for large-scale multimedia is a popular research topic, attracting much attention in computer vision and visual information retrieval. Previous works mostly focus on hashing the images and texts while the approaches designed for videos are limited. In this paper, we propose a \textit{Supervised Recurrent Hashing} (SRH) that explores the discriminative representation obtained by deep neural networks to design hashing approaches. The long-short term memory (LSTM) network is deployed to model the structure of video samples. The max-pooling mechanism is introduced to embedding the frames into fixed-length representations that are fed into supervised hashing loss. Experiments on UCF-101 dataset demonstrate that the proposed method can significantly outperforms several state-of-the-art methods.
3-D Reconstruction for Diverging X-Ray Beams

It is shown here that the fast digital convolution technique used for parallel x-ray beams can be used also to reconstruct a density function for diverging x-ray beams. This technique when combined with what was called previously a generalized ¿¿¿-filter yields good accuracy, a flexibility to cope with noise and a substantial reduction in the x-ray dosage. Finite field transforms and zero-order interpolation can be used also to improve the speed of the x-ray reconstruction process. Tests based on these methods are performed on an ideal phantom. A detailed comparison is made between a system using diverging beams, and a system using parallel beams with simulated data.
Rao-blackwellized particle filter for turn rate estimation

A Rao-Blackwellized particle filter is developed for single target turn rate estimation from noisy position measurements. Missing measurements and false alarms are handled via incorporation of Probabilistic Data Association (PDA) in the particle filter. The performance of the proposed filter is compared to an Extended Kalman Filter (EKF) through Monte Carlo simulations. When assuming perfect data association, it is found that the proposed filter is comparable to the EKF in terms of RMS errors but that it outperforms the EKF in terms of covariance consistency. Simulations including missing measurements and false alarms show that the proposed filter clearly outperforms the EKF with respect to RMSE and track divergence.
Biological nano-functionalization of titanium-based biomaterial surfaces: a flexible toolbox

Surface functionalization with bioactive molecules (BAMs) on a nanometre scale is a main field in current biomaterial research. The immobilization of a vast number of substances and molecules, ranging from inorganic calcium phosphate phases up to peptides and proteins, has been investigated throughout recent decades. However, in vitro and in vivo results are heterogeneous. This may be at least partially attributed to the limits of the applied immobilization methods. Therefore, this paper highlights, in the first part, advantages and limits of the currently applied methods for the biological nano-functionalization of titanium-based biomaterial surfaces. The second part describes a new immobilization system recently developed in our groups. It uses the nanomechanical fixation of at least partially single-stranded nucleic acids (NAs) into an anodic titanium oxide layer as an immobilization principle and their hybridization ability for the functionalization of the surface with BAMs conjugated to the respective complementary NA strands.
System-level process variability compensation on memory organizations. On the scalability of multi-mode memories

Process variation and the dynamism of modern applications can degrade the expected performance of a system. Execution time can be severely affected by both factors, resulting in deadline violations and energy consumption overheads. Memory organizations, which account for a large part of the system energy and the time budgets, are especially vulnerable to process variation. Configurable - multimode - memories are a promising technology to deal with these problems, but they also introduce new issues that need to be solved. Essentially, adding configuration capabilities to the memories comes with a cost, both in memory area and control complexity; hence, we need to evaluate what is the minimum amount of re-configurability to satisfy system's constraints. In this paper, we analyze the scalability of configurable memories and highlight the relationship among mode allocation, memory mapping and data allocation.
Role of Fluid-Attenuated Inversion Recovery in the Diagnosis of Meningitis: Comparison with Contrast-Enhanced Magnetic Resonance Imaging

Objective: Fluid-attenuated inversion recovery (FLAIR) has shown promise in the detection of subarachnoid space disease. The exact role of FLAIR in the diagnosis of meningitis has not been established. The purpose of this study was to evaluate FLAIR in the detection of meningitis in comparison with contrast-enhanced T1-weighted images (T1WI) in a blinded-reader study. We describe hyperintense sulci (HS) on FLAIR sequence in meningitis in relation to cerebrospinal fluid (CSF) protein and effective echo time (TE). Methods: Two observers blinded to clinical information reviewed magnetic resonance (MR) images of patients with the diagnosis of meningitis and those of age-matched controls. The diagnosis was confirmed from chart review and CSF results. FLAIR images were obtained with 2 different TE values of 120 milliseconds and 150 milliseconds. FLAIR changes were correlated with CSF protein concentration and contrast-enhanced T1WI. Results: Twenty-eight MR images of meningitis patients were reviewed. There were 23 abnormal MR images including 16 abnormal FLAIR scans with hyperintense sulci and 23 with leptomeningeal enhancement on contrast-enhanced T1WI. HS on FLAIR correlated with leptomeningeal enhancement on contrast-enhanced T1WI. Four viral and 1 bacterial meningitis had normal MR images (FLAIR and postcontrast TIWI). Two different TE values were used: 120 milliseconds (n = 15) and 150 milliseconds (n = 13). All patients with effective TE of 150 milliseconds. and CSF protein of more than 132 mg/dL had hyperintense sulci whereas patients with effective TE of 120 milliseconds and CSF protein of 257 mg/dL or more had HS. Conclusions: The sensitivity of contrast-enhanced T1WI was higher than FLAIR. HS on FLAIR correlated with contrast enhancement on T1WI. However, the sensitivity of FLAIR depends on CSF protein concentration threshold for (CSF hyperintensity) for a given effective TE. FLAIR cannot replace contrast-enhanced T1WI in diagnosing meningitis.