Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust multimodality registration for brain mapping

We present a robust intrasubject registration method for the synergistic use of multiple neuroimaging modalities, with applications to magnetic resonance imaging (MRI), functional MRI, perfusion MRI, MR spectroscopy, and single‐photon emission computed tomography (SPECT). This method allows user‐friendly processing of difficult examinations (low spatial resolution, advanced pathology, motion during acquisition, and large areas of focal activation). Registration of three‐dimensional (3D) brain scans is initially estimated by first‐order moment matching, followed by iterative anisotrophic chamfer matching of brain surfaces. Automatic brain surface extraction is performed in all imaging modalities. A new generalized distance definition and new specific methodologies allow registration of scans that cover only a limited range of brain surface. A new semiautomated supervision scheme allows fast and intuitive corrections of possible false automatic registration results. The accuracy of the MRI/SPECT anatomical‐functional correspondence obtained was evaluated using simulations and two difficult clinical populations (tumors and degenerative brain disorders). The average discrimination capability of SPECT (12.4 mm in‐plane resolution, 20 mm slice thickness) was found to be better than 5 mm after registration with MRI (5 mm slice thickness). Registration accuracy was always better than imaging resolution. Complete 3D MRI and SPECT registration time ranged between 6–11 min, in which surface matching represented 2–3 min. No registration failure occurred. In conclusion, the application of several new image processing techniques allowed efficient and robust registration. Hum. Brain Mapping 5:3–17, 1997. © 1997 Wiley‐Liss, Inc.
Secure Scalar Product for Big-Data in MapReduce

Organizations and individuals nowadays are more and more willing to outsource their data to save storage and management costs, especially with the push of cloud computing which offers both storage and computation scalability. However, the data, once being released to a server, is no longer under its owner's control, and its privacy and security herein become a primary concern. To this end, users usually encrypt the private data before outsourcing it, which however makes cloud data mining be very thorny and challenging as data is both big and encrypted. Under such new circumstance, we consider secure scalar product in this paper, which is a building block of data mining used to compute the sum of the products of corresponding values of two vectors. Existing methods either prevent privacy violation in the price of sacrificing accuracy, or requires users to take huge overhead. So, we propose a protocol called Secure Scalar Product in MapReduce (S2PM), which is able to perform massive data processing for encrypted big-data securely. S2PM lets the cloud be responsible for most of the operations while user only need to carry out a decryption operation to get the final result. We formally proved that S2PM can return the correct result and is secure. We also conducted performance analysis for S2PM.
An improved decision tree algorithm and its application in maize seed breeding

The application of information technology in agriculture accelerates the digitization of agriculture information. How to analyze mass of agriculture data and reveal inherent knowledge are becoming new research points. Effective application of data mining technology can achieve this purpose. This paper presents a new improved CA algorithm based on traditional decision tree method. It introduces a pretreatment theory about double dimension reduction which can deal with large and high-scale datasets. By using CA algorithm in maize seed breeding, we can analyze the potential rules and find useful information from it to direct the growth of maize. The experiments show the improved CA algorithm can obtain more intuitive and efficient information.
Modulation Spectra Morphological Parameters: A New Method to Assess Voice Pathologies according to the GRBAS Scale

Disordered voices are frequently assessed by speech pathologists using perceptual evaluations. This might lead to problems caused by the subjective nature of the process and due to the influence of external factors which compromise the quality of the assessment. In order to increase the reliability of the evaluations, the design of automatic evaluation systems is desirable. With that in mind, this paper presents an automatic system which assesses the Grade and Roughness level of the speech according to the GRBAS perceptual scale. Two parameterization methods are used: one based on the classic Mel-Frequency Cepstral Coefficients, which has already been used successfully in previous works, and other derived from modulation spectra. For the latter, a new group of parameters has been proposed, named Modulation Spectra Morphological Parameters: MSC, DRB, LMR, MSH, MSW, CIL, PALA, and RALA. In methodology, PCA and LDA are employed to reduce the dimensionality of feature space, and GMM classifiers to evaluate the ability of the proposed features on distinguishing the different levels. Efficiencies of 81.6% and 84.7% are obtained for Grade and Roughness, respectively, using modulation spectra parameters, while MFCCs performed 80.5% and 77.7%. The obtained results suggest the usefulness of the proposed Modulation Spectra Morphological Parameters for automatic evaluation of Grade and Roughness in the speech.
Diameter of Afferent Arterioles during Autoregulation Estimated from Microsphere Data in the Dog Kidney

Afferent arteriolar diameters, relative flow distribution, and flow conductance factors are estimated by nonlinear regression analysis of the sieving effect on microspheres in different vascular structures of the dog renal cortex. The data presented are from experiments in which microspheres of 10-30 μm were injected into the abdominal aorta during normotension and after lowering the blood pressure to the lower limit of autoregulation. Microscopic examination of the spheres trapped in the glomeruli and the renal arteries showed an increasing exclusion of microspheres greater than 15 μ from the afferent arterioles during normotension. This effect was most pronounced for the deeper cortical layers and can be explained mainly as geometrical exclusion of spheres from afferent arterioles. During hypotension, progressively larger microspheres entered glomeruli and afferent arterioles, presumably due to vasodilation of the vessels. There was a significant redistribution of microspheres larger than 15μ from the outer to the inner cortex during hypotension without a corresponding redistribution of smaller spheres or the estimated blood flow. Approximately the same degree of dilation of afferent arterioles was observed during autoregulatory hypotension in three cortical layers.
Constitutive secretion of Interleukin-4 dictates CD133+ side population cells to resist drug treatment and cell death.

PURPOSE In the present study, we made an attempt to elucidate the role of oversecretion of interleukin-4 (IL-4) in cancer stem cells (CSCs) of head and neck squamous cell carcinoma (HNSCC). METHODS HNSCC samples were analyzed for the presence of CSCs by flow cytometry. In addition, we have performed drug and apoptosis resistance assays to determine the role of IL-4 in CSCs. RESULTS HNSCC samples contained 3.3% of CD133+ cancer stem like side population (SP) cells in HNSCC which displayed infinite cell proliferation and they had high self-renewal capacity. These CD133+ cells displayed enhanced expression of IL-4, which promoted multidrug and apoptosis resistance. After neutralizing IL-4, the CD133+ SP cells became more sensitive to drug treatment and apoptosis. CONCLUSIONS Our data suggest that the autocrine secretion of IL-4 is a potential target for the development of novel anticancer drugs to prevent the CSCs-mediated therapy failure and tumorigenesis.
Record linkage with uniqueness constraints and erroneous values

Many data-management applications require integrating data from a variety of sources, where different sources may refer to the same real-world entity in different ways and some may even provide erroneous data. An important task in this process is to recognize and merge the various references that refer to the same entity. In practice, some attributes satisfy a uniqueness constraint---each real-world entity (or most entities) has a unique value for the attribute (e.g., business contact phone, address, and email). Traditional techniques tackle this case by first linking records that are likely to refer to the same real-world entity, and then fusing the linked records and resolving conflicts if any. Such methods can fall short for three reasons: first, erroneous values from sources may prevent correct linking; second, the real world may contain exceptions to the uniqueness constraints and always enforcing uniqueness can miss correct values; third, locally resolving conflicts for linked records may overlook important global evidence. This paper proposes a novel technique to solve this problem. The key component of our solution is to reduce the problem into a k-partite graph clustering problem and consider in clustering both similarity of attribute values and the sources that associate a pair of values in the same record. Thus, we perform global linkage and fusion simultaneously, and can identify incorrect values and differentiate them from alternative representations of the correct value from the beginning. In addition, we extend our algorithm to be tolerant to a few violations of the uniqueness constraints. Experimental results show accuracy and scalability of our technique.
Review and interpretation of MR imaging studies with PACS: creating uniform series descriptors for radiologists and referring physicians.

OBJECTIVE We sought to identify a limited set of standardized descriptors for various MR image series on a picture archiving and communications system (PACS) and to apply these descriptors to both existing and newly acquired MR images. CONCLUSION Of the 47,028 MR image series in our PACS, approximately 2500 had been assigned unique descriptors, and nearly 82% of the descriptors had a frequency of appearance of less than 5%. We reduced the number of descriptors to 146 without loss of essential information. Use of standardized descriptors may facilitate identification of various MR image series.
LinES: An English-Swedish Parallel Treebank

This paper presents an English-Swedish Parallel Treebank, LinES, that is currently under development. LinES is intended as a resource for the study of variation in translation of common syntactic constructions from English to Swedish. For this reason, annotation in LinES is syntactically oriented, multi-level, complete and manually reviewed according to guidelines. Another aim of LinES is to support queries made in terms of types of translation shifts.
Security overview for m-payed virtual ticketing

The use of wireless and mobile devices is expanding worldwide; with a growing eagerness to find new and useful ways to apply mobile technologies. New applications, as mobile ticketing, can benefit of mobile-payment facility. This paper aims to provide a mobile ticketing system design for PDA, scalable to other mobile devices, presenting a wireless weaknesses overview and security building blocks for mobile ticket and mobile payment relying on.
Security Analysis and Enhancements of Computer Operating Systems

Abstract : This is one of a series of documents prepared as part of a project on computer security and privacy at the Institute for Computer Sciences and Technology of the National Bureau of Standards. This document is intended primarily for use by those who are responsible for managing and operating government data processing installations. It provides an understanding of the types of security problems that arise in current computer operating systems, and it suggests ways in which the security of these operating systems can be enhanced. The document may also be of use to: (1) those engaged in the development of computer security techniques; (2) the manufacturers of computer systems and software; and (3) those responsible for managing and operating computer systems in the private sector. This document concerns the security problems that arise in computer operating systems. In order to develop a balanced set of security safeguards, one should use it in conjunction with documents that treat other specific aspects of the security problem.
Comparative Analysis of Two Commercial Phenotypic Assays for Drug Susceptibility Testing of Human Immunodeficiency Virus Type 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) isolates from 50 plasma specimens were analyzed for phenotypic susceptibility to licensed reverse transcriptase inhibitors and protease inhibitors by the Antivirogram and PhenoSense HIV assays. Twenty of these specimens were from recently seroconverted drug-naïve persons, and 30 were from patients who were the sources of occupational exposures to HIV-1; 16 of the specimens in the latter group were from drug-experienced patients. The phenotypic results of the Antivirogram and PhenoSense HIV assays were categorized as sensitive or reduced susceptibility on the basis of the cutoff values established by the manufacturers of each assay. Data for 12 to 15 drugs were available by both assays for 38 specimens and represented a total of 529 pairs of results. The two data sets had a 91.5% concordance by phenotypic category. The discordant results (n = 45) were distributed randomly among 26 specimens and included 28 results (62.2%) which were within a twofold difference of the assay cutoff values. None of the discordant results were associated with primary resistance mutations that predicted high-level (>20-fold) resistance. Discordant results were distributed equally among specimens from drug-experienced and drug-naïve individuals and were slightly higher for protease inhibitors than for nonnucleoside reverse transcriptase inhibitors or nucleoside reverse transcriptase inhibitors. The findings of the present study demonstrate that the results of the Antivirogram and PhenoSense HIV assays correlate well, despite the use of different testing strategies.
Requirement for CD40 Ligand in Costimulation Induction, T Cell Activation, and Experimental Allergic Encephalomyelitis

The mechanism of CD40 ligand (CD40L)-mediated in vivo activation of CD4+ T cells was examined by investigation of the development of experimental allergic encephalomyelitis (EAE) in CD40L-deficient mice that carried a transgenic T cell receptor specific for myelin basic protein. These mice failed to develop EAE after priming with antigen, and CD4+ T cells remained quiescent and produced no interferon-γ (IFN-γ). T cells were primed to make IFN-γ and induce EAE by providing these mice with B7.1+ antigen-presenting cells (APCs). Thus, CD40L is required to induce costimulatory activity on APCs for in vivo activation of CD4+ T cells to produce IFN-γ and to evoke autoimmunity.
A distributed Wireless Sensor Network testbed with energy consumption estimation

In this paper, we design and implement a WSN testbed with a distributed architecture. It allows researchers to submit their experiments and to retrieve the results from the central server. In the testbed, we also propose a software-based hardware-supported scheme to measure the energy consumption of running sensor nodes. And we compare our energy-consumption estimation with oscilloscope measurements. The results show that the energy consumption is very close to oscilloscope measurements.
Effect of Tomato Industrial Processing on Phenolic Profile and Antiplatelet Activity

Background: Regular consumption of fruits and vegetables (e.g., tomatoes) has been shown to be beneficial in terms of reducing the incidence of cardiovascular diseases. The industrial processing of tomatoes into tomato-based products includes several thermal treatments. Very little is known on the effect of tomato industrial processing on antiaggregatory activity and phenolic profile. Methods: It was assessed the effect of tomato and by-products extracts on platelet aggregation induced by ADP, collagen, TRAP-6 and arachidonic acid. These in vitro antithrombotic properties were further supported in an in vivo model of thrombosis. A set of antiplatelet compounds has been selected for HPLC analysis in the different extracts. Results: Some natural compounds such as chlorogenic, caffeic, ferulic and p-coumaric acids were identified by HPLC in tomatoes and its products may inhibit platelet activation. Red tomatoes, tomato products (sauce, ketchup and juice) and by-products extracts inhibited platelet aggregation induced adenosine 5'-diphosphate, collagen, thrombin receptor activator peptide-6 and arachidonic acid, but to a different extent. Also, pomace extract presents antithrombotic activity. Conclusions: Processed tomatoes may have a higher content of health-benefiting compounds than fresh ones. Pomace even presents the best antiplatelet activity. Finally, tomato products may be used as a functional ingredient adding antiplatelet activities to processed foods.
Particle swarm optimisation for object classification

This paper describes a new approach to the use of particle swarm optimisation (PSO) for object classification problems. Instead of using PSO to evolve only a set of good parameter values for another machine learning method for object classification, the new approach developed in this paper can be used as a stand alone method for classification. Two new methods are developed in the new approach. The first new PSO method treats all different features equally important and finds an optimal partition matrix to separate a data set into distinct class groups. The second new PSO method considers the relative importance of each feature with the noise factor, and evolves a weight matrix to mitigate the effects of noisy partitions and feature dimensions. The two methods are examined and compared with a popular method using PSO combined with the nearest centroid and another evolutionary computing method, genetic programming, on three image data sets of increasing difficulty. The results suggest that the new weighted PSO method outperforms these existing methods on these object classification problems.
Electrical resistivity tomography: monitoring of hydro-chemical processes and parameter estimation

Electrical resistivity tomography (ERT) is a useful tool for site characterization and monitoring. This paper describes some 3D laboratory applications of ERT, used to monitor wetting processes in unsaturated soils and the transport of contaminants in water-saturated samples. ERT was used to create maps of electrical conductivity of the monitored domain at different time intervals. Electrical conductivity changes were used to infer degree of saturation or concentration variations within the pore space. Test results confirm the applicability of the technique for problems involving movement of water in unsaturated soils, salt transport and oil migration. The observations in laboratory under controlled conditions proved very useful for validation and calibration of models to be used for full-scale analyses. As a further application, ERT was used for the hydraulic characterization of unsaturated soil samples, in terms of hydraulic conductivity and retention curve. The results are compared to the retention curve as obtained with the classical approach of axis translation technique and provide an encouraging agreement.
Groundwater flow path determination during riverbank filtration affected by groundwater exploitation: a case study of Liao River, Northeast China

ABSTRACT The groundwater flow path plays an important role in maintaining hydrological and ecological quality and security, which are important in the comprehensive management and use of both groundwater and surface water. In this study, an integrated multi-tracer-constrained framework was used to determine the groundwater flow path. The results show that there are shallow and deep flow paths in riverbank filtration, controlled by the different permeabilities of riverbed sediments and aquifers at different depths. The contribution of river water to shallow groundwater is less than that to deep groundwater because of the low permeability of the riverbed sediment in the dense muddy layer in the shallow slope of the river valley. This contribution decreases with increasing distance from the Liao River. The shallow groundwater quality is better than the deep groundwater quality because of its longer residence time.
Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data

Here I present the R package 'plantecophys', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO2 in the leaf. The 'plantecophys' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO2 response curves ('A-Ci curves'), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN.
Histochemical Characterization of Low Density Lipoprotein Receptors in Internalization‐Defective Familial Hypercholesterolemia

We studied the localization of low density lipoprotein (LDL) bound to the receptors on the cultured fibroblasts from a patient (MN) with homozygous familial hypercholesterolemia and a defect in internalization of LDL and compared the localization with normal fibroblasts and with those from another internalization-defective cell, GM2408A. Monolayers of cells were cultured with lipoprotein-deficient human serum, and the cells were incubated with 125I-or ferritin-labeled LDL. The LDL binding was observed by autoradiography or by an electron microscope. Autoradiographs of bound 125I-LDL confirmed that MN's cells could not internalize LDL inside the cell at 37° C. In these cells, ferritin LDL was found mainly in noncoated regions at 4° C; it was not found in endocytic vesicles after incubation at 37° C. Ferritin cores that bound on the surface of the cells from the normal subject, from GM2408A, from MN, and from MN's parents, were counted and quantitatively analyzed at 4° C. In normal cells, 62% of the ferritin cores were bound in the coated pits; in MN's cells, only 11% of the ferritin LDL was found in the coated pits; in the GM2408A cells, 12% of the ferritin LDL was found in the coated pits; in the cells from MN's parents, 40% of the ferritin LDL was found on the coated pits. The results indicate that the internalization defect in MN's cells is the same as that in the GM2408A cells; neither can localize the LDL and LDL receptor complex in coated pits.