Miracle-dz/UniFAR-FTUs huggingface dataset:
An Algorithm for Anomaly-based Botnet Detection

We present an anomaly-based algorithm for detecting IRC-based botnet meshes. The algorithm combines an IRC mesh detection component with a TCP scan detection heuristic called the TCP work weight. The IRC component produces two tuples, one for determining the IRC mesh based on IP channel names, and a sub-tuple which collects statistics (including the TCP work weight) on individual IRC hosts in channels. We sort the channels by the number of scanners producing a sorted list of potential botnets. This algorithm has been deployed in PSU's DMZ for over a year and has proven effective in reducing the number of botnet clients.
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis. Using a semi-automated reconstruction algorithm, we reconstructed a genome-scale metabolic model, ToxoNet1. The reconstruction process and flux-balance analysis of the model offer a systematic overview of the metabolic capabilities of this parasite. Using ToxoNet1 we have identified significant gaps in the current knowledge of Toxoplasma metabolic pathways and have clarified its minimal nutritional requirements for replication. By probing the model via metabolic tasks, we have further defined sets of alternative precursors necessary for parasite growth. Within a human host cell environment, ToxoNet1 predicts a minimal set of 53 enzyme-coding genes and 76 reactions to be essential for parasite replication. Double-gene-essentiality analysis identified 20 pairs of genes for which simultaneous deletion is deleterious. To validate several predictions of ToxoNet1 we have performed experimental analyses of cytosolic acetyl-CoA biosynthesis. ATP-citrate lyase and acetyl-CoA synthase were localised and their corresponding genes disrupted, establishing that each of these enzymes is dispensable for the growth of T. gondii, however together they make a synthetic lethal pair.
Genealogical particle analysis of rare events

In this paper an original interacting particle system approach is developed for studying Markov chains in rare event regimes. The proposed particle system is theoretically studied through a genealogical tree interpretation of Feynman--Kac path measures. The algorithmic implementation of the particle system is presented. An estimator for the probability of occurrence of a rare event is proposed and its variance is computed, which allows to compare and to optimize different versions of the algorithm. Applications and numerical implementations are discussed. First, we apply the particle system technique to a toy model (a Gaussian random walk), which permits to illustrate the theoretical predictions. Second, we address a physically relevant problem consisting in the estimation of the outage probability due to polarization-mode dispersion in optical fibers.
Effect of off-pump coronary artery bypass graft surgery on postoperative acute kidney injury and mortality*

Objective:Risk of mortality after cardiac surgery is associated with severity of acute kidney injury. The aim of this study is to examine the effect of off-pump coronary artery bypass surgery on the risk of postoperative acute kidney injury and its association with mortality. Design:Observational cohort study. Setting:Tertiary care center. Patients:Some 10,061 patients underwent coronary artery bypass surgery (1998–2002), of which 1,365 patients underwent off-pump surgery. Interventions:Acute kidney injury was defined as either requirement of dialysis or ≥50% decline in postoperative glomerular filtration rate but not requiring dialysis. We compared on- and off-pump surgeries and used propensity score matching to examine the effect of off-pump surgery on acute kidney injury and mortality. Measurements and Main Results:We found that 2.6% on-pump and 1.2% off-pump patients developed acute kidney injury requiring dialysis among the 2,370 matched subjects (relative risk, 2.06; 95% confidence interval [CI], 1.36–3.36); 5.0% of on-pump patients suffered a ≥50% decline in glomerular filtration rate compared with 2.5% in off-pump group (relative risk, 2.00; 95% CI, 1.48–2.82). The mortality rate in the matched cohort was 2.3% for on-pump group vs. 0.6% in off-pump group (relative risk, 3.88; 95% CI, 2.29–9.50). Among matched patients with acute kidney injury, the risk of mortality was 13.14 (95% CI, 8.43–30.50) in patients requiring dialysis and 9.33 (95% CI, 4.83–19.00) in those with ≥50% decline in glomerular filtration rate but not requiring dialysis. Conclusions:Off-pump surgery is associated with a lower risk of developing acute kidney injury (regardless of its definition). The risk of mortality is incremental with worsening degrees of acute kidney injury. Lower risk of acute kidney injury may be one of the factors that offer a survival advantage after off-pump surgery.
A Double Antibody Sandwich ELISA Assay for the Detection of Salmonella in Food Original Samples

Development of monoclonal antibody based sandwich ELISA for rapid detection of Salmonella and optimization of enrichment procedures to increase the sensitivity. Spleen cells from Balb/c mice immunized with flagellin (H=d) antigen of S. typhi were fused with NSO myeloma clones for preparation of mAbs and New Zealand rabbits were used to produce polyclonal antibody. Different enrichment broths were also evaluated. Out of six specific clones to H=d antigen, mAb L2D3G6 was chosen to establish the sELISA curve, which had the detection limit of 104-105 CFU of S. typhi, and the incubation time could be shorten to 4 h. Of the various broths, BPW was found to yield maximum ELISA values. When tested in artificially inoculated food samples, this assay could detect 102 S. typhi CFU/mL within 10 h from various food rinses (meat, vegetable) and milk samples. In comparison to culture, the enrichment-sELISA is rapid and sensitive, and may be used as a rapid screening procedure for environmental monitoring during outbreak situation. KeywordsSalmonella; S. typhi; Monoclonal antibody; Sandwich ELISA
The Effect of Meperidine on Thermoregulation in Mice: Involvement of &agr;2-Adrenoceptors

Meperidine has potent antishivering properties. The underlying mechanisms are not fully elucidated, but recent investigations suggest that &agr;2-adrenoceptors are likely to be involved. We performed the current study to investigate the effects of meperidine on nonshivering thermogenesis in a model of thermoregulation in mice. After injection (0.1 mL/kg intraperitoneally) of saline, meperidine (20 mg/kg), the specific &agr;2-adrenoceptor antagonist atipamezole (2 mg/kg), plus saline or atipamezole plus meperidine, respectively, mice were positioned in a Plexiglas chamber. Rectal temperature and mixed expired carbon dioxide were measured after provoking thermoregulatory effects by whole body cooling. Maximum response intensity of nonshivering thermogenesis and the thermoregulatory threshold for nonshivering thermogenesis, which was defined as the temperature at which a sustained increase in expiratory carbon dioxide can be measured, were investigated. Meperidine significantly decreased the threshold of nonshivering thermogenesis (36.6°C ± 0.7°C) versus saline (37.9°C ± 0.6°C) and versus atipamezole plus saline (37.8°C ± 0.4°C; P < 0.01). This effect was abolished after administration of meperidine combined with atipamezole (37.7°C ± 0.6°C; P < 0.05). Meperidine did not decrease the maximum intensity of nonshivering thermogenesis. The results suggest a major role of &agr;2-adrenoceptors in the inhibition of thermoregulation by meperidine in mice.
Lesions Limited to the Human Thalamic Principal Somatosensory Nucleus (Ventral Caudal) Are Associated with Loss of Cold Sensations and Central Pain

Central pain is neuropathic pain resulting from a lesion of the CNS, such as a stroke [poststroke central pain (CPSP)]. Lesions involving the posterior thalamus lead to reduction or loss of sensation and to CPSP, although the responsible nuclei have not been identified. We now examine the hypotheses that thalamic lesions must extend posterior to the ventral caudal nucleus (Vc) and include ventral medial posterior nucleus (VMpo), to result in loss of cold sensibility and CPSP. Patients with small thalamic strokes associated with CPSP were evaluated by atlas-based mapping of magnetic resonance imaging scans, and by somatosensory testing. All lesions involved posterior Vc; two lesions also involved nuclei posterior to Vc, but not VMpo. All patients tested had alterations of cold pain sensation and tactile sensation, as measured by von Frey hairs. Three patients had altered cool sensation, and the patient with the least involvement of Vc had normal cool thresholds, suggesting that a critical volume of Vc must be involved before cool sensation is impaired. Perception of warm was impaired only in lesions involving nuclei posterior to Vc. Heat pain perception was never affected. In a subject with cold allodynia, a single-subject protocol PET study measured the responses to immersion of either hand in a 20°C waterbath. The scan during stimulation of the affected hand was characterized by intense activation of contralateral sensorimotor cortex. Therefore, there are modality-specific subnuclear structures in the posterior thalamus, but lesions of Vc not involving VMpo are sufficient to impair cold sensibility and to produce CPSP.
Ethnic Variables and Negative Life Events as Predictors of Depressive Symptoms and Suicidal Behaviors in Latino College Students

In the present study, we examined ethnic variables (viz., multigroup ethnic identity and other group orientation) along with negative life events as predictors of depressive symptoms and suicidal behaviors in a sample of 156 (38 male and 118 female) Latino college students. Results of conducting hierarchical regression analyses indicated that the set of ethnic variables accounted for significant variance in both depressive symptoms and suicidal behaviors. The inclusion of negative life events was found to account for significant additional variance in both outcomes, beyond what was accounted for by ethnic variables. Interestingly, beyond main effects, results indicated a significant Other Group Orientation × Negative Life Events interaction effect to account for additional variance in depressive symptoms and suicidal behaviors. Some implications of the present findings are discussed, including the potential value for Latinos to broaden their attitudes and interactions with other ethnic groups.
Obscured clusters. I. GLIMPSE 30 – A young Milky Way star cluster hosting Wolf-Rayet stars

Context. Young massive clusters are usually deeply embedded in dust and gas. They represent excellent astrophysical laboratories for the study of massive stars. Clusters with Wolf-Rayet (WR) stars are of special importance, since this enables us to study a coeval WR population at a uniform metallicity and known age. Aims. We started a long-term project to search the inner Milky Way for hidden star clusters and to study them in detail. GLIMPSE 30 (G30) is one of these clusters. It is situated near the Galactic plane (l = 298. ◦ 756, b = −0. 408) and we determine its physical parameters and investigate its high-mass stellar content especially WR stars. Methods. Our analysis is based on SOFI/NTT JSHKS imaging and low resolution (R ∼ 2000) spectroscopy of the brightest cluster members in the K atmospheric window. For the age determination we applied isochrone fits for MS and Pre-MS stars. We derived stellar parameters of the WR stars candidates using a full nonLTE modeling of the observed spectra. Results. Using a variety of techniques we found that G30 is very young cluster, with age t ≈ 4 Myr. The cluster is located in the Carina spiral arm, it is deeply embedded in dust and suffers reddening of AV ∼ 10.5 ± 1.1 mag. The distance to the object is d = 7.2 ± 0.9 kpc.
Inversion of Atmospheric Parameters from Sky Radiance Measurements with a Sun Photometer

NASA has organized a worldwide Aerosol Robotic Network (AERONET) of Sun photometers. These well characterized instruments (CIMEL Sun photometer) make aerosol optical depth measurements based on the transmission of the direct sunlight through the atmosphere in 5 and 8 spectral bands. AERONET aerosol retrievals are limited to clear sky conditions (no clouds or no cirrus clouds) and retrieve aerosol optical depth. To retrieve other parameters such as aerosol size distribution, single scattering albedo, refractive index, etc., retrievals based on algorithms from Nakajima [2] and Dubovik [1] are used. Since the algorithms are limited to clear sky conditions and not available to the public, we decided to write our own retrieval algorithm which uses the solar principal plane and almucantar scans from the CIMEL instrument. We studied a variety of radiative transfer methods that are able to simulate ground measurements by computing the hemispherical sky radiance. For various reasons we decided to use the Santa Barbara DISORT Atmospheric Radiative Transfer (SBDART) code [4,5] and combined it with IDL’s Amoeba (down-hill simplex method) [3] to retrieve five parameters: (1) water cloud optical depth, (2) ice cloud optical depth, (3) cloud water droplet radius, (4) horizontal visibility (related to aerosol optical depth), and (5) RH factor which couples relative humidity and aerosol size distribution, from principal plane and almucantar scans. The SBDART computed sky radiances are very close to the measured sky radiances 40 degrees away from the solar aureole since the Discrete Ordinates Radiative Transfer (DISORT) algorithm [6] is not accurate in the forward scattering direction. In this paper we will show results of the inversion of AERONET data using SBDART. KeywordsAerosol retrieval, model inversion, radiative transfer, Sun-photometer.
Deriving difference between the Bayesian networks based patterns of the effective connectivity using permutation test in fMRI studies

Recently introduced in analyzing data from functional MRI (fMRI) and other neuroimaging techniques, Bayesian networks (BN) is a method to characterize effective connectivity patterns among multiple brain regions. So far, interests of using BN have been primarily on learning the connectivity pattern for each single group with well investigated computational algorithms. Examination of the connectivity pattern differences between groups, on the other hand, lacks rigorous statistical inference procedure. In this study, we propose using random permutation, a type of non-parametric statistical significance test in which a reference distribution is obtained by calculating all possible values of the test statistic under re-arrangements of the group labels on the observed data points, to infer whether the difference is significant. Two different approaches to perform the permutation test are introduced, compared to each other and both compared to the routinely used parametric t-test. Permutation approach 1 permutes the group labels first followed by learning BN pattern for each of the newly formed groups. Approach 2 learns BN pattern for each individual and connection parameters are then subjected to the group label permutations. Synthetic data generated under varying signal-to-noise ratios are used to investigate the performances of the proposed methods. Our results demonstrated that permutation approach 1 in detecting the effective connectivity pattern difference between two groups is superior to permutation approach 2 and to the common-sense two sample t-test.
Gender Differences in Physical Activity

We examined gender differences in leisure-time physical activity (LTPA) in 50 women and 28 men using questionnaire data and identified how LTPA status may be misclassified based on physical activity questionnaire content. LTPA was determined using the Four Week Physical Activity History modification of the Minnesota LTPA questionnaire. LTPA was classified as total, light- (≤ 4.0 METS), moderate- (4.5-5.5 METS), and heavy-intensity (≥ 6.0 METs), and household LTPA. The questionnaire was administered 14 times (every 26 days). Scores were computed as kcal·day−1 and min·day−1 with the 14 visits averaged to yield one year LTPA scores. Skewed data were log-transformed and are presented as the geometric mean. There were no gender differences in kcal·day−1 for total- (385 vs 421), moderate- (28.2 vs 23.3), and light-intensity LTPA (72.2 vs 52.6, p > .05). Heavy-intensity LTPA was greater in men than in women (98.1 vs 50.5, p = 0.01), while household LTPA was greater in women than in men (238.2 vs 134.7, p < . 0001.
Reliability of the AO/ASIF classification for pertrochanteric femoral fractures

20 radiographs of pertrochanteric femoral fractures were classified as to fracture "group" and "subgroup" according to the AO/ASIF Fracture Classification (type 31A) by 15 observers. 3 months later, the same radiographs were reviewed by the same observers. Mean agreement of the observers with the final consensus ranged from 53% (with subgroup classification) to 81% (without subgroup). The mean kappa value for interobserver reliability was 0.33 and 0.34 for classification with subgroup in both observer sessions, respectively. Omission of the subgroup classification resulted in better mean kappa values (0.67 and 0.63, respectively). Mean intraobserver reliability was 0.48 in the fracture "subgroup" and 0.78 in the "group" classification. In conclusion, the results show that the AO/ASIF classification for pertrochanteric fractures is reliable for fracture subgroups 31A1, A2 or A3. The group classification should be used to compare scientific data and determine the best treatment. Further classification of fracture subgroups leads to poor reproducibility of results.
SOME EXPERT SYSTEM NEED COMMON SENSE

An expert system is a computer program intended to embody the knowledge and ability of an expert in a certain domain. The ideas behind them and several examples have been described in other lectures in this symposium. Their performance in their specialized domains are often very impressive. Nevertheless, hardly any of them have certain common sense knowledge and ability possessed by any non-feeble-minded human. This lack makes them “brittle”. By this is meant that they are difficult to extend beyond the scope originally contemplated by their designers, and they usually don’t recognize their own limitations. Many important applications will require common sense abilities. The object of this lecture is to describe common sense abilities and the problems that require them. Common sense facts and methods are only very partially understood today, and extending this understanding is the key problem facing artificial intelligence. This isn’t exactly a new point of view. I have been advocating “Computer Programs with Common Sense”since I wrote a paper with that title in
Affine structure from translational motion with varying and unknown focal length

In this paper a method for obtaining affine structure from an image sequence taken by a translating camera with varying and unknown focal length is presented. A general geometric constraint, expressed using the camera matrices, is derived and this constraint is used in a least squares solution of the problem. The proposed algorithm extends the previous result of affine structure recovery from an image sequence with a translating camera with constant intrinsic parameters to the case with a camera with varying and unknown focal length and otherwise known intrinsic parameters. The noise sensitivity of the method is evaluated in simulated experiments.
Demonstration of Epstein-Barr virus in carcinomas of various sites.

EBV is an etiological agent in infectious mononucleosis, is implicated in some malignant lymphomas and lymphoepithelioma-like carcinomas, and has been sporadically reported in carcinomas of the breast, lung, and other sites. We studied immunohistochemically benign and malignant tumors of the breast, lung, colon, and prostate and found EBV in some carcinomas of those sites. Also, EBV reactions were noted in hyperplasias and dysplasias, e.g., breast carcinomas in situ and prostatic intraepithelial neoplasia. Benign tumor counterparts were negative. PCR analysis of selected cases confirmed the presence of EBV. Our results suggest that EBV is not restricted to lymphoepithelioma-like carcinomas but may play an oncogenic role in frequent epithelial cancers and possibly also in hyperplasias and certain dysplasias preceding carcinomas.
Enhanced Comprehension of Dynamic Cardiovascular Anatomy By Three‐Dimensional Echocardiography With the Use of Mixed Shading Techniques

Advances in ultrasound instrumentation and computer technology provide us an opportunity to develop methods to perform three‐dimensional echocardiography in patients. Optimal methods of displaying three‐dimensional images are critical for the perception of depth and distances. We examined the utility of various shading techniques in volume‐rendered three‐dimensional images in 22 patients with a variety of cardiac defects. Distance coding, gray level gradient shading, texture shading, and mixtures of these shading techniques were used. Our observations suggest that the mixture of shading techniques portray the dynamic three‐dimensional anatomy better than a single type of shading. Appropriate mix of shadings could provide dynamic three‐dimensional echocardiograms of clinical utility.
Accurate detection of symmetries in 3D shapes

We propose an automatic method for finding symmetries of 3D shapes, that is, isometric transforms which leave a shape globally unchanged. These symmetries are deterministically found through the use of an intermediate quantity: the generalized moments. By examining the extrema and spherical harmonic coefficients of these moments, we recover the parameters of the symmetries of the shape. The computation for large composite models is made efficient by using this information in an incremental algorithm capable of recovering the symmetries of a whole shape using the symmetries of its subparts. Applications of this work range from coherent remeshing of geometry with respect to the symmetries of a shape to geometric compression, intelligent mesh editing, and automatic instantiation.
Educational applications of multi-client synchronization through improved Web graph semantics

The MMM (Multi-head, Multi-tail, Multi-client) browsing project is a continuing effort to bring stronger graph semantics to the World Wide Web, thereby increasing the Web's usefulness for collaboration and education. The first modified browser provided facilities for links with multiple heads and tails, thereby giving the content author the ability to direct concurrent and synchronized browsing streams. The Web author can direct the paths of his readers and ensure that they visit pages in the correct context and order desired. Our most recent effort was the construction of a layer that filters content between the reader and the Web. This layer allows the ready composition of graph protocols so that Web content can be interpreted according to a variety of graph models. The model of the first project was expanded to be a full colored Petri net, thereby allowing synchronization of multiple browsing streams; the application of the MMM project to education now extends to a full collaborative classroom.