Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry proteomic profiling: identification of alpha 2‐HS glycoprotein B‐chain as a biomarker of diet

Biomarkers have the potential to impact a wide range of public health concerns, including early detection of diseases, drug discovery, and improved accuracy of monitoring effects of interventions. Given new technological developments, broad‐based screening approaches will likely advance biomarker discovery at an accelerated pace. Matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS) allows for the elucidation of individual protein masses from a complex mixture with high throughput. We have developed a method for identifying serum biomarkers using MALDI‐TOF and statistical analysis. However, before applying this approach to screening of complex diseases, we evaluated the approach in a controlled dietary intervention study. In this study, MALDI‐TOF spectra were generated using samples from a randomized controlled trial. During separate feeding periods, 38 participants ate a basal diet devoid of fruits and vegetables and a basal diet supplemented with cruciferous (broccoli) family vegetables. Serum samples were obtained at the end of each 7‐day feeding period and treated to remove large, abundant proteins. MALDI‐TOF spectra were analyzed using peak picking algorithms and logistic regression models. Our bioinformatics methods identified two significant peaks at m/z values of 2740 and 1847 that could classify participants based on diet (basal vs. cruciferous) with 76% accuracy. The 2740 m/z peak was identified as the B‐chain of alpha 2‐HS glycoprotein, a serum protein previously found to vary with diet and be involved in insulin resistance and immune function.
Imaging Techniques for Uveal Melanoma

Uveal melanoma is the most frequent primary malignant intraocular tumor of adults. Overall, the diagnostic accuracy is more than 99% in eyes with clear media, based on indirect ophthalmoscopy, ultrasonographic, and angiographic studies. However, in atypical cases, various imaging modalities are used to establish the diagnosis. There is a wide choice of imaging techniques for the diagnosis of patients with uveal melanoma. This chapter discusses imaging modalities for iris, ciliary body, and choroidal melanomas.
A review of the identification and titration of antibodies to herpes simplex viruses type 1 and type 2 in human sera.

SUMMARY Because of the strong cross-neutralization between herpes simplex viruses types 1 and 2 and because of the high inci dence of antibody to the type 1 virus in the community, the unequivocal identification of type 2 antibody in serum sam ples is sometimes difficult. A variety of serological tech niques have been used for the comparative titration of anti bodies to the type 1and type 2 viruses. The plaque reduction test, the microneutralization test, and the measurement of the kinetics of neutralization all seem to give similar results; the antibody titers can also be measured by the indirect fluorescent antibody technique using the presence of viral antigens in the surface membranes of infected cells and by the passive hemagglutination test using sheep erythrocytes sensitized with either type 1 or type 2 antigens. But with each of these tests difficulty is often encountered in reach ing a decision on whether or not specific type 2 antibody is present. The fluorescent antibody test and the passive he magglutination test have been modified, with some degree of success, for detection of specific type 2 antibodies. The lysis of infected cells by herpes antibody in the presence of complement has also been used in a specific test. The cytolysis is detected by the release of 51Crfrom infected cells that have been appropriately labeled; the sera are rendered specific by prior absorption with nonlabeled cells infected with type 1 virus. The use of this test has indicated that some individuals who already have type 1 antibody do not develop specific type 2 antibody when subsequently in fected with type 2 virus. Studies of the appearance, with increase in age, of anti bodies in the community and of experimental infections of rabbits indicate that sera with "dual" or "intermediate" antibody properties are indeed the outcome of infection with both serotypes, although the existence in nature of interme diate serotypes of virus cannot, as yet, be totally excluded. The identification and titration of antibodies to herpes simplex viruses types 1 and 2 when both of these antibodies are present in the same serum have presented some prob lems. The delineation of these antibodies from one another has been difficult because of the strong cross-neutralization between the two viruses. The close relationship is shown in the neutralization kinetics presented in Charts 1 and 2; several workers (10, 19) have been unable to differentiate between the 2 viruses using antisera prepared against type 2.
Resonant Torque Magnetometry A New In-situ Technique For Determining The Magnetic Properties Of Thin Film MFM Tips

A new high sensitivity Resonant Torque Magnetometry (RTM) technique has been developed enabling the determination of the magnetic properties of Magnetic Force Microscope (MFM) tips in-situ. A sensitivity of better than 10/sup -12/ emu (10/sup -15/ Am/sup 2/) has been achieved at ambient temperature and pressure. We have studied the micromagnetic properties of a variety of tip coatings including hard CoCr and CoPt films and soft permalloy. In-situ determination of the magnetic properties of MFM tips is vital if quantitative interpretation of MFM images is to be achieved especially when images are made in the presence of bias fields. The m(/spl mu//sub 0/H) loops obtained for CoPt tips have a shape similar to a standard magnetisation loop when the field is applied parallel to the tip axis. With the field applied perpendicular to the tip both CoPt and CoCr demonstrate behaviour consistent with partial demagnetisation of the axial moment, to which the RTM is sensitive.
Lesion segmentation in whole-body images of PET

In PET, identification of lesion boundaries in general is not a trivial problem as whole-body images exhibit inhomogeneity. Manual segmentation methods in current commercial software packages to identify lesion boundaries and to quantify in terms of standard uptake value (SUV) are very laborious and tedious. They discourage physicians from taking advantage of the inherently quantitative data and compel them to use qualitative means in their diagnosis and assessment of patient response to therapy. An automated segmentation method will enable physicians to extract maximum or mean SUV values from a lesion volume. It may also allow them to track changes in lesion size. In this study, a segmentation algorithm based on the Markov random field modeling has been proposed to segment lesions, as well as other structures, in whole-body PET images for mainly the purpose of diagnosis and the assessment of tumor response to therapy. The method was applied to phantom and whole-body images. The preliminary results indicate that the method can successfully segment lesions.
Determining the relevance of input features for multilayer perceptrons

This paper presents an approach to determine the relevance of individual input attributes for trained Multilayer Perceptrons (MLPs). To reflect the impact of an input attribute on the output of an MLP, the relevance is aimed at representing the output sensitivity of the MLP to the attribute variation. The sensitivity is defined as the mathematical expectation of output deviations of an MLP due to its input deviation with respect to overall input patterns. The basic idea for the introduction of such a relevance measure is that a well-trained MLP can capture salient features of the problem it deals with and thus become more sensitive to those input attributes that make more contributions to the MLP's behavior. The relevance can be employed as a relative criterion for assessing individual input attributes. The results from the experiments on two typical problems demonstrate the effectiveness of the relevance in identifying irrelevant input attribute.
Scalable kernels for graphs with continuous attributes

While graphs with continuous node attributes arise in many applications, state-of-the-art graph kernels for comparing continuous-attributed graphs suffer from a high runtime complexity. For instance, the popular shortest path kernel scales as O(n4), where n is the number of nodes. In this paper, we present a class of graph kernels with computational complexity O(n2(m + log n + δ2 + d)), where δ is the graph diameter, m is the number of edges, and d is the dimension of the node attributes. Due to the sparsity and small diameter of real-world graphs, these kernels typically scale comfortably to large graphs. In our experiments, the presented kernels outperform state-of-the-art kernels in terms of speed and accuracy on classification benchmark datasets.
Hepatitis C virus core, NS3, NS5A, NS5B proteins induce apoptosis in mature dendritic cells

Although reasons for hepatitis C virus (HCV) persistence are still unknown, specific cellular immune responses appear to influence the pathogenesis and outcome of the infection. Apoptosis of cells infected by viruses may appear suicidal to the viruses that induce programmed cell death of its host. However, apoptosis has been suggested to be a response to virus infection as a mean of facilitating virus dissemination. Annexin V‐propidium iodide staining and DNA fragmentation, were used to show that expression of the core, NS3, NS5A, or NS5B protein induces apoptosis in mature dendritic cells. In addition, immunoblotting was used to demonstrate that expression level of p21waf1/cip1 protein decreased in cells expressing one of these HCV proteins. No expression of p53 could be detected and expression of Akt was independent of HCV proteins expression. These results suggest that the effect of these HCV proteins on HCV associated pathogenesis may be linked (at least partially) to its ability to modulate apoptosis pathways in mature dendritic cells. J. Med. Virol. 75:402–411, 2005. © 2005 Wiley‐Liss, Inc.
Feature selection method for network intrusion based on GQPSO attribute reduction

Aiming to problem of classification algorithm with low detection speed and low detection rate in high dimensional network data intrusion detection. A novel approach for feature selection based on Genetic Quantum Particle Swarm Optimization(GQPSO) attribute reduction in network intrusion detection is proposed in the paper. In the approach, selection and variation of genetic algorithm with QPSO algorithm are combined to form GQPSO algorithm; normalized mutual information between attributes defined as GQPSO algorithm fitness function to guide it's reduction of attributes to realize optimal selection of network data feature subset. KDD99 data-set are used to experiment. The experimental result shows that the approach is more effective than QPSO and PSO algorithms in discarding independent and redundancy attributes. As a result, intrusion detection rate and speed of classification algorithm are greatly heightened by using the method.
Perceptible affordances and feedforward for gestural interfaces : assessing effectiveness of gesture acquisition with unfamiliar interactions

The move towards touch-based interfaces disrupts the established ways in which users manipulate and control graphical user interfaces. The predominant mode of interaction established by the desktop interface is to ‘double-click’ an icon in order to open an application, file or folder. Icons show users where to click and their shape, colour and graphic style suggests how they respond to user action. In sharp contrast, in a touch-based interface, an action may require a user to form a gesture with a certain number of fingers, a particular movement, and in a specific place. Often, none of this is suggested in the interface. This thesis adopts the approach of research through design to address the problem of how to inform the user about which gestures are available in a given touch-based interface, how to perform each gesture, and, finally, the effect of each gesture on the underlying system. Its hypothesis is that presenting automatic and animated visual prompts that depict touch and preview gesture execution will mitigate the problems users encounter when they execute commands within unfamiliar gestural interfaces. Moreover, the thesis claims the need for a new framework to assess the efficiency of gestural UI designs. A significant aspect of this new framework is a rating system that was used to assess distinct phases within the users’ evaluation and execution of a gesture. In order to support the thesis hypothesis, two empirical studies were conducted. The first introduces the visual prompts in support of training participants in unfamiliar gestures and gauges participants’ interpretation of their meaning. The second study consolidates the design features that yielded fewer error rates in the first study and assesses different interaction techniques, such as the moment to display the visual prompt. Both studies demonstrate the benefits in providing visual prompts to improve user awareness of available gestures. In addition, both studies confirm the efficiency of the rating system in identifying the most common problems users have with gestures and identifying possible design features to mitigate such problems. The thesis contributes: 1) a gesture-and-effect model and a corresponding rating system that can be used to assess gestural user interfaces, 2) the identification of common problems users have with unfamiliar gestural interfaces and design recommendations to mitigate these problems, and 3) a novel design technique that will improve user awareness of unfamiliar gestures within novel gestural interfaces.
Simultaneous/multiple cause-delay (SIMCAD): an epidemiological approach to projecting mortality.

Methods being used to project mortality are based on the hypothetical elimination of one or more diseases from the population or on extrapolation from observed mortality rates. This research presents an alternative projection method based on an epidemiological theory of aging and mortality change that is consistent with recent mortality transitions. The model is founded on the observation that recent mortality declines in the United States are attributable to improved life styles and advances in the prevention and treatment of degenerative diseases and that the risk of dying from such diseases is being redistributed (or delayed) from younger to older ages. A test using U.S. mortality and population data indicates that this alternative method is promising--particularly for projecting mortality rates from major chronic degenerative diseases among populations in middle and older ages.
A Supervised Learning Approach to Predicting Coronary Heart Disease Complications in Type 2 Diabetes Mellitus Patients

A supervised machine learning approach that incorporates genetic algorithms (GA) and weighted k-nearest neighbours (WkNN) was applied to classify type 2 diabetes mellitus (T2DM) patients according to the presence or absence of coronary heart disease (CHD) complications. The investigation was carried out by analyzing potential risk factors recorded at the Ulster Hospital in Northern Ireland. A GA initialization technique that integrates medical expert knowledge was compared with traditional data-driven GA initialization techniques. The results indicate that the incorporation of expert knowledge provides only a small improvement of CHD classification performance compared with models based on data-driven initialization techniques. This may be due to data incompleteness and noise or due to the beneficial effects of treatment, which masks the complication of CHD in the dataset. Further incorporation of expert knowledge at different levels of the GA need to be addressed to improve decision support in this domain
Ab initio parametrized MM3 force field for the metal‐organic framework MOF‐5

A new valence force field has been developed and validated for a particular class of coordination polymers known as nanoporous metal‐organic frameworks (MOFs), introduced recently by the group of Yaghi. The experimental, structural, and spectroscopic data in combination with density functional theory calculations on several model systems were used to parametrize the bonded terms of the force field, which explicitly treats the metal–oxygen interactions as partially covalent as well as distinguishes different types of oxygens in the framework. Both the experimental crystal structure of MOF‐5 and vibrational infrared spectrum are reproduced reasonably well. The proposed force field is believed to be useful in atomistic simulations of adsorption/diffusion of guest molecules inside the flexible pores of this important class of MOF materials. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
A perimetric learner's index.

PURPOSE Certain individuals need earlier perimetric experience before producing normal fields on automated static threshold perimetry. Mid-peripheral depressions and an unaffected central field are typical findings in such cases. We have devised a learner's index, to detect defect patterns that may be due to such perimetric inexperience. METHODS The central visual field was partitioned into 5 concentric zones and averages of deviations from the age-corrected normal threshold values were studied in each zone. The third test session in 74 randomly selected normal subjects provided an experienced reference material. Visual field results typical of normal individuals lacking perimetric experience were represented by the first field test obtained from each of 7 subjects ('learners') from the same group, who showed significant learning during three test sessions. A linear discriminant function, learner's index, was constructed that discriminates between typically experienced and typically inexperienced field results in normals. RESULTS Average deviation from age-corrected normal threshold increased with increasing eccentricity in the learner's initial fields. Clinical examples illustrate the intended use of the new index. CONCLUSIONS The learner's index highlights those first field tests from eyes with normal visual fields, that deviate significantly from a normal experienced result in the direction of a learner's result. Patients showing significant learner's index are candidates for repeated visual field testing.
Spectral Clustering as Mapping to a Simplex

Spectral methods have been widely used to study the structural properties of unlabeled datasets. In this work we describe a clustering approach that exploits the structural properties in the configuration space of objects as well as the spectral sub-space, quite unlike earlier methods. We propose a spectral clustering approach, where we formalize the notion of clusters as vertices of a simplex in the spectral subspace. We define clustering as memberships of data points to vertices of this simplex. We empirically demonstrate that our method is comparable to the state-of-theart methods in a variety of domains and outperforms other generic clustering algorithms.
Anti-tumor activity of four Ayurvedic herbs in Dalton lymphoma ascites bearing mice and their short-term in vitro cytotoxicity on DLA-cell-line.

The anti-tumor activity and chemopreventive potential of four Ayurvedic herbs viz. Curcuma longa L. , Ocimum sanctum L. , Tinospora cordifolia (Wild) Miers ex Hook.f & Thomas and Zizyphus mauritiana Lam. were evaluated using Dalton Lymphoma ascites (DLA) tumor model in Swiss Albino mice. The outcome was assessed using survival time, peritoneal ascitic fluid (Tumor volume) and hematological indices as parameters. Animals were divided into five groups (n = 6) viz. one DLA control and four Herb + DLA treated groups. All the four herb + DLA groups were pre-treated with respective herbs for 7 days and hematological indices were measured for entire five groups. On day-8 animals were inoculated with 1x10(6) DLA cells i.p., and Herb + DLA groups were continued with oral herbal treatment for 21-days. Hematological parameters and tumor volume were assessed to find the effects of herbs. Short term in vitro cytotoxicity was determined by Trypan Blue exclusion method and LDH leakage assay using different concentrations of herbal extracts and 5-FU as a positive control and IC(50) for each herbal extract and 5-FU were determined. Oral administration of crude herb increased the survival time and decreased the peritoneal ascitic fluid content significantly. Hb, RBCs and total WBC which were altered by DLA inoculation were restored significantly by all the herbs except O. sanctum. All the four herbs showed in vitro cytotoxic activity against DLA cell-line. Moreover inter group comparison of all the four herbs for anti-tumor activity showed efficacy in the following order--T. cordifolia > Z. mauritiana > or = C. longa > O. sanctum respectively.
Cellular responses to nanotopology of polymeric surfaces fabricated with AAO nanoimprinting

We made various patterns on the PMMA surfaces and observed the cellular responses on them. Nanoimprinting using AAO (anodized aluminum oxide) template was used for the topology control of polymeric culture surfaces. AAO has numerous regularly-spaced nanopores. The pore diameter and the center-to-center pore distance can be easily controlled by altering the anodizing and etching conditions. One of the main advantages of using AAO as a template in nanoimprinting is that nanometer-scale structure templates larger than 25 cm/sup 2/ are easily, economically and quickly fabricated, which are suitable for various cellular studies. We cultured fibroblast on the variously nanopatterned surfaces directly or after surface treatment with collagen, O/sub 2/ plasma, or both. The cellular activities of fibroblasts on 420 nm-nodule pattern treated with both were significantly retarded at 24 hours. Fibroblasts also showed significantly different activities among different patterns. In the time-lapse observation of initial adhesion in stressed condition (ambient temperature and no CO/sub 2/ supply) from 3.5 hours to 5.5 hours after seeding, we could conclude that fibroblast do not like 420 nm-nodule pattern for their initial adhesion as fibroblasts on 420 nm-nodule pattern markedly changed their shape to round form while those on 90 nm-nodule pattern maintained their shape.
An improved integration sensor of non-invasive blood glucose

This work is intended to design an integration sensor for non-invasive blood glucose detection (ISNBGD) with low power consumption, fast detection speed and high accuracy. Based on the modified conservation of energy metabolism theory, the blood glucose level (BGL) is acquired by a multi-linear regression equation of a rate of human metabolism, blood flow, oxygen saturation of hemoglobin, and pulse frequency. These physiological parameters are obtained by ISNBGD with a size of 60mm × 30mm × 85.5mm, which is integrated with temperature sensors, humidity sensors, radiation sensors, and dual wavelength photo-detectors with 660nm and 905nm. 30 healthy volunteers are involved in the preliminary clinical experiment. These blood glucose concentrations ranging from 3.5 to 6.5mmol/L are compared with automatic biochemical analyzer (ABA) as the gold standard. The correlation coefficient of BGL is up to 0.8621 between the ISNBGD and ABA, and the ISNBGD has strong correlation and good coherence. Moreover, multi-physiological parameters can be measured by the ISNBGD including body temperature, local metabolic rate, blood flow, oxygen saturation, and heart rate simultaneously.