Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence in Mexico, 1998–2008, of Vibrio cholerae CTX+ El Tor carrying an additional truncated CTX prophage

Significance Vibrio cholerae classical (CL) biotype was isolated, along with biotype El Tor (ET) and altered ET carrying the cholera toxin (CTX) gene of CL biotype, during the 1991 cholera epidemic in Mexico, subsequently becoming endemic until 1997. Microbiological, molecular, and phylogenetic analyses of V. cholerae isolated from both clinical and environmental samples during 1998–2008 confirm important genetic events, namely predominance of ET over CL and altered ET in Mexico. Although altered ET is predominantly associated with cholera globally, progression of CTX+ V. cholerae ET with truncated CTX prophage to the predominant pathogen causing endemic cholera in Mexico may prove to be yet another key historical point in the global epidemiology of cholera. The seventh cholera pandemic caused by Vibrio cholerae O1 El Tor (ET) has been superseded in Asia and Africa by altered ET possessing the cholera toxin (CTX) gene of classical (CL) biotype. The CL biotype of V. cholerae was isolated, along with prototypic and altered ET, during the 1991 cholera epidemic in Mexico and subsequently remained endemic until 1997. Microbiological, molecular, and phylogenetic analyses of clinical and environmental V. cholerae isolated in Mexico between 1998 and 2008 revealed important genetic events favoring predominance of ET over CL and altered ET. V. cholerae altered ET was predominant after 1991 but not after 2000. V. cholerae strains isolated between 2001 and 2003 and a majority isolated in 2004 lacked CTX prophage (Φ) genes encoding CTX subunits A and B and repeat sequence transcriptional regulators of ET and CL biotypes: i.e., CTXΦ−. Most CTXΦ− V. cholerae isolated in Mexico between 2001 and 2003 also lacked toxin coregulated pili tcpA whereas some carried either tcpAET or a variant tcpA with noticeable sequence dissimilarity from tcpACL. The tcpA variants were not detected in 2005 after CTXΦ+ ET became dominant. All clinical and environmental V. cholerae O1 strains isolated during 2005–2008 in Mexico were CTXΦ+ ET, carrying an additional truncated CTXΦ instead of RS1 satellite phage. Despite V. cholerae CTXΦ− ET exhibiting heterogeneity in pulsed-field gel electrophoresis patterns, CTXΦ+ ET isolated during 2004–2008 displayed homogeneity and clonal relationship with V. cholerae ET N16961 and V. cholerae ET isolated in Peru.
Failure analysis for model-based organ segmentation using outlier detection

During the last years Model-Based Segmentation (MBS) techniques have been used in a broad range of medical applications. In clinical practice, such techniques are increasingly employed for diagnostic purposes and treatment decisions. However, it is not guaranteed that a segmentation algorithm will converge towards the desired solution. In specific situations as in the presence of rare anatomical variants (which cannot be represented) or for images with an extremely low quality, a meaningful segmentation might not be feasible. At the same time, an automated estimation of the segmentation reliability is commonly not available. In this paper we present an approach for the identification of segmentation failures using concepts from the field of outlier detection. The approach is validated on a comprehensive set of Computed Tomography Angiography (CTA) images by means of Receiver Operating Characteristic (ROC) analysis. Encouraging results in terms of an Area Under the ROC Curve (AUC) of up to 0.965 were achieved.
A path‐analytic strategy to analyze psychoanalytic treatment effects

This paper introduces a path‐analytic strategy to analyze psychoanalytic treatment effects. A simple causal model is used to analyze a well‐known case study by Charles Brenner. Application of even this simple model to the case study sharpens causal inferences that may be validly made, highlights important aspects of the psychoanalytic process and builds a foundation for further model development.
A VLSI implementation of an SM4 algorithm resistant to power analysis

SM4 is a block cipher proposed by the Chinese government. Strengthening the research and extension of SM4 is significant to the development and promotion of Chinese cryptography standards. To date, research relevant to SM4 is rare. Thus, we propose the implementation of an SM4 algorithm resistant to power analysis. Ideally, a secure masking scheme is used for the SM4 cipher, which is particularly suited for implementation in the application specific integrated circuit. Moreover, the mask scheme in our chip implementation process is improved to make SM4 safer. Simulation results confirm that the use of counteractive measures resistant to power analysis is credible.
Observer design methodology for stochastic and deterministic robustness

A unified observer with stochastic and deterministic robustness is developed in this paper so that an observer is less sensitive to both stochastic and deterministic uncertainties. For stochastic robustness, the norm of the observer gain and the lower bound of the observer decay rate are shown to be design factors which can minimize the upper bound of the estimation error variance. For deterministic robustness, the L 2 norm-based condition number of the observer eigenvector matrix is utilized to address robust estimation performance against deterministic uncertainties. In order to justify the proposed method, a graphical approach is first introduced, and then a multi-objective optimization problem including linear matrix inequality constraints is formulated to provide the unified robustness.
Visual saliency and potential field data enhancements: Where is your attention drawn?

Interpretation of gravity and magnetic data for exploration applications may be based on pattern recognition in which geophysical signatures of geologic features associated with localized characteristics are sought within data. A crucial control on what comprises noticeable and comparable characteristics in a data set is how images displaying those data are enhanced. Interpreters are provided with various image enhancement and display tools to assist their interpretation, although the effectiveness of these tools to improve geologic feature detection is difficult to measure. We addressed this challenge by analyzing how image enhancement methods impact the interpreter’s visual attention when interpreting the data because features that are more salient to the human visual system are more likely to be noticed. We used geologic target-spotting exercises within images generated from magnetic data to assess commonly used magnetic data visualization methods for their visual saliency. Our aim was achieved in two stages. In the first stage, we identified a suitable saliency detection algorithm that can computationally predict visual attention of magnetic data interpreters. The computer vision community has developed various image saliency detection algorithms, and we assessed which algorithm best matches the interpreter’s data observation patterns for magnetic target-spotting exercises. In the second stage, we applied this saliency detection algorithm to understand potential visual biases for commonly used magnetic data enhancement methods. We developed a guide to choosing image enhancement methods, based on saliency maps that minimize unintended visual biases in magnetic data interpretation, and some recommendations for identifying exploration targets in different types of magnetic data.
AFM study of glucagon fibrillation via oligomeric structures resulting in interwoven fibrils

Glucagon is a 29-residue amphiphatic hormone involved in the regulation of blood glucose levels in conjunction with insulin. In concentrated aqueous solutions, glucagon spontaneously aggregates to form amyloid fibrils, destroying its biological activity. In this study we utilize the atomic force microscope (AFM) to elucidate the fibrillation mechanism of glucagon at the nanoscale under acidic conditions (pH 2.0) by visualizing the nanostructures of fibrils formed at different stages of the incubation. Hollow disc-shaped oligomers form at an early stage in the process and subsequently rearrange to more solid oligomers. These oligomers co-exist with, and most likely act as precursors for, protofibrils, which subsequently associate to form at least three different classes of higher-order fibrils of different heights. A repeat unit of around 50 nm along the main fibril axis suggests a helical arrangement of interwoven protofibrils. The diversity of oligomeric and fibrillar arrangements formed at pH 2.0 complements previous spectroscopic analyses that revealed that fibrils formed under different conditions can differ substantially in stability and secondary structure.
The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer

Muscle creatine kinase (MCK) is induced to high levels during skeletal muscle differentiation. We have examined the upstream regulatory elements of the mouse MCK gene which specify its activation during myogenesis in culture. Fusion genes containing up to 3,300 nucleotides (nt) of MCK 5' flanking DNA in various positions and orientations relative to the bacterial chloramphenicol acetyltransferase (CAT) structural gene were transfected into cultured cells. Transient expression of CAT was compared between proliferating and differentiated MM14 mouse myoblasts and with nonmyogenic mouse L cells. The major effector of high-level expression was found to have the properties of a transcriptional enhancer. This element, located between 1,050 and 1,256 nt upstream of the transcription start site, was also found to have a major influence on the tissue and differentiation specificity of MCK expression; it activated either the MCK promoter or heterologous promoters only in differentiated muscle cells. Comparisons of viral and cellular enhancer sequences with the MCK enhancer revealed some similarities to essential regions of the simian virus 40 enhancer as well as to a region of the immunoglobulin heavy-chain enhancer, which has been implicated in tissue-specific protein binding. Even in the absence of the enhancer, low-level expression from a 776-nt MCK promoter retained differentiation specificity. In addition to positive regulatory elements, our data provide some evidence for negative regulatory elements with activity in myoblasts. These may contribute to the cell type and differentiation specificity of MCK expression.
Improved Quantization Error Compensation Method for Fixed-Width Booth Multipliers

A novel quantization error (QE) compensation method is proposed in design of high accuracy fixed-width radix-4 Booth multipliers, which will effectively reduce the QE and save the area of multipliers when they are employed in cognitive radio (CR) detector and digital signal processor (DSP). The truncated partial-products of the proposed multipliers are finely divided into three sections: reserved section, adaptive compensation section, and constant compensation section. The QE compensation carries of the multipliers are generated by applying probability estimation based on a shrunken minor truncated sectionwhich is a combination of the constant compensation and adaptive compensation. The proposed compensation method not only reduces the QE of the fixed width Booth multipliers, but also avoids the exhaustive computing resources (time and memory) during getting the compensation carries by statistical simulation. The proposed method can achieve higher accuracy than the existing works under the same area and power budgets. Simulation and experiment results show that the improved compensation method has the minimum power-delay products compared with the existing methods under the same area and can save up to 30% area for realization of full-width radix-4 Booth multipliers.
Toward a Metadata Generation Framework

In the June 2003 issue of D-Lib Magazine, Kenney et al. (2003) discuss a comparative study between Cornell's email reference staff and Google's Answers service. This interesting study provided insights on the potential impact of "computing and simple algorithms combined with human intelligence" for library reference services. As mentioned in the Kenney et al. article, Bill Arms (2000) had discussed the possibilities of automated digital libraries in an even earlier D-Lib article. Arms discusses not only automating reference services, but also another library function that seems to inspire lively debates about automation—metadata creation. While intended to illuminate, these debates sometimes generate more heat than light.
World Population & Human Capital in the Twenty-first Century: An Overview

This book addresses systematically and quantitatively the role of educational attainment in global population trends and models. Seven background chapters summarize past trends in fertility, mortality, migration, and education; examine relevant theories and identify key determining factors; and set the assumptions that are subsequently translated into alternative scenario projections to 2100. These assumptions derive from a global survey of hundreds of experts and five expert meetings on as many continents. Another chapter details their translation into multi-dimensional projections by age, sex, and level of education. The book's final chapters analyse the results, emphasizing alternative trends in human capital, new ways of studying ageing and the quantification of alternative population, and education pathways in the context of global sustainable development. An appendix and associated web link present detailed results for all countries. The book shows that adding education to age and sex substantially alters the way we see the future.
ASIS-based code analysis automation

The Ada Semantic Interface Specification (ASIS) is an interface between an Ada environment and any tool requiring information from it. An Ada environment comprises valuable semantic and syntactic information that can be exploited for automated code analysis. ASIS provides an open and published callable interface that gives access to this information; further, ASIS has been designed to be independent of underlying Ada environment implementations, thus supporting portability of code analysis tools while relieving tool developers from needing to understand the complexities of an Ada environment's proprietary and evolving internal representation.
Barriers to Evidence-Based Care in Nursing: Historical Legacies and Conflicting Cultures

The British National Health Service (NHS) has witnessed many fundamental changes over the last decade, one of the most significant of which is the imperative for health-care professionals to ensure that their clinical practice can be supported by research evidence. This move from intuition and historical ritual to scientific justification has not been fully successful in either the medical or non-medical professions, with the result that a great deal of research has been sponsored at both the national and local levels to investigate the reasons underlying the research/practice divide. Within nursing the problem has been particularly exacerbated by its ideological framework, the culture and tradition of the profession itself and the recent reforms that were intended to raise its professional status and autonomy. This paper considers the impact of nursing traditions and stereotypes and the bureaucratic structures of the NHS on the introduction of evidence-based nursing care. It is suggested that the essential nature of nursing, its legacy and philosophy, together with the health service's hidden agendas, have conspired to keep nursing in a subordinated, quasi-professional role as one means by which the workforce can be controlled. Because the nursing profession has colluded with this, albeit inadvertently, it now needs to re-establish its complementary functions, in order to salvage its position and truly establish nursing as a profession in its own right.
Role of Yeast Insulin-Degrading Enzyme Homologs in Propheromone Processing and Bud Site Selection

The Saccharomyces cerevisiae AXL1 gene product Axl1p shares homology with the insulin-degrading enzyme family of endoproteases. Yeast axl1 mutants showed a defect in a-factor pheromone secretion, and a probable site of processing by Axl1p was identified within the a-factor precursor. In addition, Axl1p appears to function as a morphogenetic determinant for axial bud site selection. Amino acid substitutions within the presumptive active site of Axl1p caused defects in propheromone processing but failed to perturb bud site selection. Thus, Axl1p has been shown to participate in the dual regulation of distinct signaling pathways, and a member of the insulinase family has been implicated in propeptide processing.
The effect of intradialytic food intake on the urea reduction ratio and single-pool Kt/V values in patients followed-up at a hemodialysis center*

This study was conducted to determine the effect of intradialytic food intake on the urea reduction rate (URR) and single-pool Kt/V (spKt/V) values in hemodialysis (HD) patients. Materials and methods: The study was designed as a quasiexperiment. Twenty-five patients were enrolled in this study. The patients' mean age was 56.5 ± 13.0 years and median time on HD was 63 months. In the first stage of the study, patients were given a standard meal after the first hour of the treatment. The same study group underwent HD without intradialytic food intake 1 week later. Predialysis and postdialysis blood samples for measurement of blood urea nitrogen levels were drawn at the HD sessions with and without food intake. The URR and spKt/V values were calculated. Descriptive statistics, the paired samples t-test, repeated measures analysis of variance, and power analysis were used for the analysis of data. Results: The mean URR and spKt/V values of the patients were higher in the session without food ingestion compared to the other session. Statistically significant differences were found between the sessions with and without food intake for URR and spKt/V values (P < 0.001). Conclusion: Intradialytic food intake seems to cause a decrease in the URR and spKt/V values.
Meshless reconstruction method for fluorescence molecular tomography based on compactly supported radial basis function

Abstract. Fluorescence molecular tomography (FMT) is a promising tool in the study of cancer, drug discovery, and disease diagnosis, enabling noninvasive and quantitative imaging of the biodistribution of fluorophores in deep tissues via image reconstruction techniques. Conventional reconstruction methods based on the finite-element method (FEM) have achieved acceptable stability and efficiency. However, some inherent shortcomings in FEM meshes, such as time consumption in mesh generation and a large discretization error, limit further biomedical application. In this paper, we propose a meshless method for reconstruction of FMT (MM-FMT) using compactly supported radial basis functions (CSRBFs). With CSRBFs, the image domain can be accurately expressed by continuous CSRBFs, avoiding the discretization error to a certain degree. After direct collocation with CSRBFs, the conventional optimization techniques, including Tikhonov, L1-norm iteration shrinkage (L1-IS), and sparsity adaptive matching pursuit, were adopted to solve the meshless reconstruction. To evaluate the performance of the proposed MM-FMT, we performed numerical heterogeneous mouse experiments and in vivo bead-implanted mouse experiments. The results suggest that the proposed MM-FMT method can reduce the position error of the reconstruction result to smaller than 0.4 mm for the double-source case, which is a significant improvement for FMT.
Space-Frequency-Coded MIMO OFDM Receivers Based on Gaussian Message Passing

Forney-style factor graphs are used for modeling space-frequency-coded MIMO OFDM systems over frequency-selective fading channels. We analyze the Gaussian message passing mechanism for the Alamouti scheme and linear transformation of the factor graph. A new decision rule is derived in terms of the mean vector and covariance matrix of modulation symbols. We employ the K-best algorithm with reduced complexity to justify the effectiveness of our receiver.
Ocean waves synthesis using a spectrum-based turbulence function

The representation of ocean waves is not a resolved problem in computer graphics yet. There is still no existing method that allows one to simply describe an agitated surface of any size that is visually sufficiently realistic, without using entirely physical models that are usually very complex. We present a simple method to represent and animate an ocean surface in deep water by considering it as a procedural texture. This texture is defined by a combination of two levels of detail. The first one is a superposition of 2D trochoids whose parameters are determined by ocean wave characteristics infrequency domain. In order to increase the visual complexity of this model and to reduce computation, we incorporate a 3D turbulence function to provide a second level of detail. This turbulence function is also determined by frequency characteristics of ocean waves. Since our synthesized ocean waves spectrum approaches a real ocean waves spectrum, we obtain realistic water waves in the spatial domain. The animation of our model is performed by shifting the phase of the trochoids and by moving into the 3D turbulence function. Since our definition is procedural and continuous, it permits us to obtain any size of water surface with any level of detail as well as a simple, direct, antialiasing method. Our model can be used to generate ocean waves using 2D textures or bump maps as well as 3D textures.
Slowing of bone loss in patients with rheumatoid arthritis by long-term high-intensity exercise: results of a randomized, controlled trial.

OBJECTIVE Patients with rheumatoid arthritis (RA) are more at risk for the development of osteoporosis and osteoporotic fractures than are their healthy peers. In this randomized, controlled, multicenter trial, the effectiveness of a 2-year high-intensity weight-bearing exercise program (the Rheumatoid-Arthritis-Patients-In-Training [RAPIT] program) on bone mineral density (BMD) was compared with usual care physical therapy, and the exercise modalities associated with changes in BMD were determined. METHODS Three hundred nine patients with RA were assigned to an intervention group, either the RAPIT program or usual care physical therapy. The primary end points were BMD of the hip and spine. The exercise modalities examined were aerobic fitness, muscle strength, and, as a surrogate for those effects not directly measured by the RAPIT program, attendance rate. RESULTS The data on the 136 RAPIT participants and 145 usual care participants who completed the study were analyzed. The mean rate of decrease in hip BMD, but not in lumbar spine BMD, was smaller in patients participating in the RAPIT program when compared with that in the usual care group, with a mean decrease of 1.6% (95% confidence interval [95% CI] 0.8-2.5) over the first year and 0.5% (95% CI 1.1-2.0) over the second year. The change in hip BMD was significantly and independently associated with changes in both muscle strength (multivariate odds ratio [OR] 1.75, 95% CI 1.07-2.86) and aerobic fitness (OR 1.79, 95% CI 1.10-2.90), but not with the attendance rate (OR 1.00, 95% CI 0.99-1.00). CONCLUSION A long-term high-intensity weight-bearing exercise program for RA patients is effective in slowing down the loss of BMD at the hip. The exercise modalities associated with this effect are muscle strength and aerobic fitness.