gebhart/patrepeval huggingface dataset:
New statistical approaches for anomaly detection (2009)

Abstract Computer security is a growing problem. Over the last years, the number and variety of security attacks in IP‐ based network infrastructures have increasingly grown, leading to the need of developing new security architectures. In this scenario, the use of intrusion detection systems (IDSs) has emerged as a key element, since it permits to tackle security threats by masquerader, misfeasor, and clandestine users. In this paper, we address the problem considering some new statistical techniques for detecting network anomalies. In more detail, the paper discusses the use of several statistical models to characterize the normal behavior of the network traffic running over TCP, so that anomalies can be revealed as significant deviations from such behavior. Namely, our proposal is based on the use of Markov chains, co‐ occurrence matrices, and compression algorithms, for modeling the TCP connections, in terms of statistical analysis of some of the packet header fields. The performance analysis, presented in this paper, demonstrates the effectiveness of the proposed methods. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Synergistic effect of α-glucosidase inhibitors and dipeptidyl peptidase 4 inhibitor treatment (2010)

Monotherapy of α-glucosidase inhibitor (α-GI) or dipeptidyl peptidase 4 (DPP4) inhibitor does not sufficiently minimize glucose fluctuations in the diabetic state. In the present study, we evaluated the combined effects of various of α-GI inhibitors (acarbose, voglibose or miglitol) and sitagliptin, a DPP4 inhibitor, on blood glucose fluctuation, insulin and active glucagon-like peptide-1 (GLP-1) levels after nutriment loading in mice. Miglitol and sitagliptin elicited a 47% reduction (P < 0.05) of the area under the curve of blood glucose levels for up to 2 h after maltose-loading, a 60% reduction (P < 0.05) in the range of blood glucose fluctuation, and a 32% decrease in plasma insulin compared with the control group. All three of the combinations elicited a 2.5-4.9-fold synergistic increase in active GLP-1 (P < 0.05 vs control). Thus, combined treatment with the α-GI miglitol, which more strongly inhibits the early phase of postprandial hyperglycemia, and DPP4 inhibitor yields both complementary and synergistic effects, and might represent a superior anti-hyperglycemic therapy. (J Diabetes Invest, doi: 10.1111/j.2040-1124.2010.00081.x, 2011).
DiamondTouch SDK:Support for Multi-User, Multi-Touch Applications (2002)

DiamondTouch is a multi-touch input technology that supports multiple, simultaneous users; it can distinguish who is touching where. We present the DiamondTouch SDK; it provides support for the development of applications that utilize DiamondTouch s capabilities to implement computer-supported collaboration and rich input modalities (such as gestures). Our first demo illustrates the basic utilities and functionality of our system. Our second demo, a multi-user map application, highlights DiamondTouch s ability to sup-port input from multiple, simultaneous users and exploits Di-amondTouch s ability to identify the owner of each touch. Our third demo illustrates DiamondTouch s ability to run with existing applications by providing a mouse emulation mode. DiamondTouch is well-suited to shared-display applications. It is suitable for front-projected video of the computer dis-play, which facilitates direct manipulation of user interface elements and provides a shared focus of attention for collab-orating users. Possible applications include command-and-control command posts, control rooms, business or technical meetings, and a variety of casual applications in the home, at schools, and in retail settings.
Movement‐Related effects in fMRI time‐series (1996)

This paper concerns the spatial and intensity transformations that are required to adjust for the confounding effects of subject movement during functional MRI (fMRI) activation studies. An approach is presented that models, and removes, movement-related artifacts from fMRI time-series. This approach is predicated on the observation that movement-related effects are extant even after perfect realignment. Movement-related effects can be divided into those that are a function of position of the object in the frame of reference of the scanner and those that are due to movement in previous scans. This second component depends on the history of excitation experienced by spins in a small volume and consequent differences in local saturation. The spin excitation history thus will itself be a function of previous positions, suggesting an autoregression-moving average model for the effects of previous displacements on the current signal. A model is described as well as the adjustments for movement-related components that ensue. The empirical analyses suggest that (in extreme situations) over 90% of fMRI signal can be attributed to movement, and that this artifactual component can be successfully removed.
Distribution of Chromosomes into Discrete Groups in Colchicine-Induced C-Metaphases of Barley (1984)

Roots of barley were treated with 0.1-0.01%solutions of colchicine.After treatment with 0.1% or 0.05% colchicine, c-metaphases were seen in which chromosomes, each consisting of two sister-chromatids, were distributed into 2, and rarely into > 2, distinct groups.Each group of chromosomes gave rise to a restitution nucleus.The result of these distributive c-mitoses was the formation of binucleate or multinucleate cells.The pattern of distribution of the diploid complement of 14 chromosomes has been determined.It was not random: 7:7 distributions were relatively infrequent but 6:8 or 4:10 distributions occurred in high frequencies.This could result from the arrangement of chromosomes as they were released from the prophase nucleus but it appears also to involve movement of chromosomes, probably under the influence of cytoskeletal components.Bi-and multinucleate cells completed interphase and divided.In most of the binucleate cells, the two nuclei entered prophase in synchrony but a low percentage of asynchronous divisions were seen.The division of binucleate cells is related to the formation of homozygous cell lineages in colchicine treated plants.
ANALGESIC ACTIVITY OF CERTAIN FLAVONE DERIVATIVES: A STRUCTURE‐ACTIVITY STUDY (1993)

1. Flavone, its methoxy derivatives and flavanone were synthesized by standard methods and were tested for analgesic activity in mice by employing acetic acid writhing and tail flick methods. 2. All the tested compounds except flavanone exhibited significant dose-dependent analgesic activity in both the assay models. Some of the compounds were found to involve opioid mechanisms in their analgesic effect. 3. A definite structure-activity relationship was observed in the analgesic activity of flavone derivatives as well as in their mechanism of action.
The Mouse Y Chromosome Interval Necessary for Spermatogonial Proliferation is Gene Dense with Syntenic Homology to the Human AZFa Region (1998)

The Delta Sxrb deletion interval of the mouse Y chromosome contains Spy, a spermatogenesis factor gene(s) whose expression is essential for the postnatal development of the mitotic germ cells, spermatogonia. The boundaries of Delta Sxrb are defined by the duplicated genes Zfy1 and Zfy2 and four further genes have previously been mapped within the interval: Ube1y and Smcy, linked with Zfy1 on a contig of 250 kb, and Dffry and Uty, which were unanchored. The interval was estimated to be >450 kb. In order to identify any further gene(s) that may underlie Spy, systematic exon trapping was performed on an extended contig, anchored on Zfy1, which covers 750 kb of the Delta Sxrb interval. Exons from two novel genes were isolated and placed together with Dffry and Uty on the contig in the order Dffry-Dby-Uty-Tspy-Eif2gammay-Smcy- Ube1y-Zfy1. All the genes, with the double exception of Tspy, are X-Y homologous and produce putatively functional, spliced transcripts. The tight linkage and order of Dffry, Dby and Uty was shown to be conserved in deletion intervals 5C/5D of the human Y chromosome by the construction of a contig of human PAC and YAC clones; this represents the first example of syntenic homology between Y chromosomes from two distinct mammalian orders. Interval 5C/5D contains the distal boundary of the AZFa interval, which, like Delta Sxrb, is believed to be necessary for spermatogonial development in the prepubertal testis. Our results therefore show that AZFa and Spy may be encoded by homologous genes.
Determination and Interpretation of the Optimal Operating Point for ROC Curves Derived Through Generalized Linear Models (2003)

Abstract Sensitivity and specificity summarize the performance of a diagnostic test with a positive/negative outcome determined by a gold standard. When the test is quantitative, receiver operating characteristic (ROC) curves are used to display the performance of all possible cutpoints of the quantitative diagnostic marker. The ROC curve offers a graphical interpretation of the trade-off between sensitivity and specificity of the range of possible cutpoints. Various methods are used to estimate the ROC curve including empirical, parametric, semiparametric, and regression methods. Similarly, various software packages provide ROC curve estimation. Regression methods based on using generalized linear models are discussed as well as their implementation with the SAS procedures PROC LOGISTIC and PROC GENMOD. Recent attention has been given to determining the optimal decision rule, also called the optimal operating point (OOP). Similar to the ROC curve, the OOP provides a graphical interpretation for decision making. Three methods are presented for determination of the OOP and interpretations of the advantage and disadvantage of each are discussed. An example for prediction of remission from a psychological study on depression is illustrated.
Automatic calculation of total lung capacity from automatically traced lung boundaries in postero-anterior and lateral digital chest radiographs (1998)

Total lung capacity (TLC) is a very important parameter in the study of pulmonary function. In the pulmonary function laboratory, it is normally obtained using plethysmography or helium dilution techniques. Several authors have developed methods of calculating the TLC using postero-anterior (PA) and lateral chest radiographs. These methods have not been often used in clinical practice. In the present work, we have developed and automated computer-based method for the calculation of TLC, by determining the pulmonary contours from digital PA and lateral radiographs of the thorax. The automatic tracing of the pulmonary borders is carried out using: (1) a group of reference lines is determined in each radiograph; (2) a family of rectangular regions of interest (ROIs) defined, which include the pulmonary borders, and in each of them the pulmonary border is identified using edge enhancement and thresholding techniques; (3) removing outlaying points from the preliminary boundary set; and (4) the pulmonary border is corrected and completed by means of interpolation, extrapolation, and arc fitting. The TLC is calculated using a computerized form of the radiographic ellipses method of Barnhard. The pulmonary borders were automatically traced in a total of 65 normal radiographs (65 PA and 65 lateral views of the same patients). Three radiologists carried out a subjective evaluation of the automatic tracing of the pulmonary borders, with a finding of no error or only one minor error in 67.7% of the PA evaluations, and in 75.9% of the laterals. Comparing the automatically traced borders with borders traced manually by an expert radiologists, we obtained a precision of 0.990 +/- 0.001 for the PA view, and 0.985 +/- 0.002 for the lateral. The values of TLC obtained by the automatic calculation described here showed a high correlation (r = 0.98) with those obtained by applying the manual Barnhard method.
Endothelial‐like cells expanded from CD34 + blood cells improve left ventricular function after experimental myocardial infarction (2005)

Mobilization and recruitment of endothelial progenitor cells (EPC) contributes to vasculogenesis in vivo. So far, applications for cell therapy are limited by the number of available cells. Expansion of EPC or their progeny may, therefore, facilitate its therapeutic use in ischemic disease. The aim of this study was to expand CD34+ EPC-derived progeny from different sources, characterize them, and investigate their potential for use in therapeutic vasculogenesis. CD34+ cells from G-CSF-mobilized peripheral blood (PB) and cord blood (CB) were isolated using immunomagnetic beads and cultured in endothelial cell medium. Cells were expanded up to 16 (PB) and up to 46 (CB) population doublings, respectively. Immunophenotypic and mRNA expression analyses showed a high degree of similarity between the cultured cells and human umbilical vein endothelial cells (HUVEC). By day 14 after transplantation, transplanted human CD31-positive EPC-derived cells were detected. These cells expressed the proliferation marker Ki67 and formed vessel-like structures in ischemic myocardium. Most strikingly, transplantation of EPC-derived cells improved left ventricular function after experimental ischemia, as shown by echocardiography. In conclusion, cells cultured from CD34+ EPC can be expanded in vitro to clinically relevant numbers. In vivo, these cells proliferate, form vascular structures, and improve left ventricular function after experimental myocardial infarction. Therefore, in vitro expanded EPC-derived endothelial cells may be beneficial in the treatment of ischemic disease.
A molten-salt route for synthesis of Si and Ge nanoparticles: chemical reduction of oxides by electrons solvated in salt melt (2012)

Silicon is one of the major constituents of the earth's crust and, in its elemental form, the base of many semiconductor applications, including electronics and energy conversion. Downsizing Si to the nanoscale dimension extends its application to diverse fields, which, however, is often plagued by expensive and inefficient fabrication methods. We report herein a facile chemical synthetic method for Si nanoparticles from SiO2 in a liquid environment of molten metal chlorides containing magnesium. The results show that Si nanocrystals (NCs) start to grow at 550 °C in the molten salt solvent and that the growth is controllable through the adjustment of the temperature, as well as the type of salt. We also show that the method can be generalized, as illustrated by the synthesis of Ge nanoparticles at a temperature of 450 °C. The growth of NCs is interpreted in terms of the chemical reduction of oxide by electrons solvated in the molten salts.
Antigen retrieval technique utilizing citrate buffer or urea solution for immunohistochemical demonstration of androgen receptor in formalin-fixed paraffin sections. (1993)

We developed a staining protocol for demonstration of androgen receptor (AR) in formalin-fixed, paraffin-embedded tissue sections. The method is based on the antigen retrieval microwave (MW) heating technique. Results are compared with different types of enzyme digestion pre-treatments. The strongest immunostaining signal and clearest background were obtained by MW heating of dewaxed paraffin sections in 5% urea or citrate buffer solution (pH 6); pure distilled water gave less consistent results. Enzymatic digestion with pepsin (0.05% in 2 N HCl) for 30 min at room temperature, or trypsin followed by pronase, or pronase digestion alone, also produced enhanced staining of AR in some cases, but there was more nonspecific background, and specific reactivity was less intense. The antigen retrieval MW method can be used to demonstrate AR epitope in prostate tissue after fixation in formalin for as long as 7 days. AR immunolocalization was also compared in frozen and paraffin sections processed from the same specimen of prostate carcinoma tissue and was found to be qualitatively and quantitatively similar. This study also provided new information concerning the basic principles of the antigen retrieval MW method that may be helpful in further development of this technique.
The Role of Atelocollagen-Based Cell Transfection Array in High- Throughput Screening of Gene Functions and in Drug Discovery (2004)

The human genome project has been completed, but the function of many genes is unknown. It is, therefore, necessary to elucidate the function of a large number of genes within a short time. To achieve this goal, materials are needed that condense or package DNA into nano-particles that can easily be taken up by cells and would allow DNA to be retained without degradation. Atelocollagen is a reliable carrier for gene delivery because it is considered safe and appropriate for practical use. We developed a basic technique for high-throughput gene transfer and expression screening by pre-coating a multi-well plate with an Atelocollagen/DNA complex in which cells are then seeded. Complexes with a nano-particle form were efficiently transduced into cells without the use of additional transfection reagents, and they allowed for long-term gene expression. The complex spotted onto the well of a plate was stable for a long period and allowed the cells to transduce and express reporter genes. We also showed that the present method with Atelocollagen-based gene transfer is applicable to gene medicines, such as antisense ODNs, siRNA, and adenovirus vectors. These results suggest that an Atelocollagen-based cell transfection array may be appropriate for general use in the high-throughput screening of large sets of gene medicines with functions in mammalian cells.
Collagen-induced morphogenesis and expression of the alpha 2-integrin subunit is inhibited in c-erbB2-transfected human mammary epithelial cells. (1993)

The c-erbB2 (or Her2) oncogene is amplified and/or overexpressed in a significant proportion of breast cancers. To assess the role of the c-erbB2 oncogene in mammary tumorigenesis, we have transfected the corresponding human c-erbB2 cDNA into an immortalized human mammary epithelial cell line, MTSV1-7, that was derived from luminal epithelial cells cultured from milk. Three transfectants expressing different levels of the c-erbB2 gene product have been isolated which form colonies in agar and produce tumours in nude mice with high efficiency. We have observed that MTSV1-7 cells form three-dimensional structures in collagen gels and that alpha 2 beta 1-integrin plays a crucial role in the process of morphogenesis. We now find that the c-erbB2 transfectants exhibit an impaired ability to undergo morphogenesis in collagen gels as compared with the parental cell line or the control neomycin transfectant, and that the degree of impairment is related to the level of c-erbB2 expression. Moreover, overexpression of the c-erbB2 product was found to be correlated with a specific decrease in the expression of alpha 2-integrin subunit and in the alpha 2-mRNA. The breast cancer cell line SKBr3, which carries multiple copies of the c-erbB2 gene and overexpresses the 185-kDa product, was also found to express very low levels of the alpha 2-integrin protein and mRNA. Our results confirm the involvement of the alpha 2 beta 1-integrin in collagen-induced morphogenesis of mammary epithelial cells and suggest that the c-erbB2 gene product may inhibit this morphogenesis by inhibiting the expression of the alpha 2-integrin subunit.
Influence of Polydispersity on the Self-Assembly of Diblock Copolymers (2005)

The domain sizes and morphological boundaries in diblock copolymers have been predicted to be influenced by changes in the molecular weight distribution of one or both of the blocks. To systematically explore these effects, we prepared several sets of poly(ethylene-alt-propylene)-b-poly(dl-lactide) diblock copolymers with controlled molecular weights, compositions, and polydispersity indices. The polydispersity of the polylactide block was controlled by taking advantage of the equilibrium nature of the ring-opening polymerization of lactide. Small-angle X-ray scattering was used to evaluate the influence of block copolymer polydispersity on the equilibrium domain spacing and resultant ordered state morphology. We found that the domain spacing increased with increasing polydispersity and demonstrated that an increase in polydispersity at constant polylactide composition can result in a change in morphology for compositionally asymmetric diblock copolymers. More specifically, when the polylactide block is the minority component, a polydispersity increase in that block results in a change of morphology to one with larger mean interfacial curvature. Conversely, an increase in the polydispersity of the polylactide segment in a block copolymer with a majority of polylactide drives transitions to structures with smaller mean interfacial curvature. The experimental results were corroborated by self-consistent mean-field theory.
Lambda placMu insertions in genes of the leucine regulon: extension of the regulon to genes not regulated by leucine (1992)

The leucine regulon coordinates the expression of several Escherichia coli genes according to the presence of exogenous leucine, which interacts with the lrp gene product, Lrp. We isolated and characterized 22 strains with lambda placMu insertions in Lrp-regulated genes. Lrp and leucine influenced gene expression in a surprising variety of ways. We identified two genes that are regulated by Lrp and not affected by L-leucine. We therefore rename this the leucine-lrp regulon. Genes coding for glycine cleavage and leucine biosynthesis enzymes have been identified as members of the leucine-lrp regulon. We suggest that the lrp gene product activates genes needed for growth in minimal medium, and we show that the gene is repressed by its own product and is highly repressed during growth in rich medium.
Blood Flow through the Calf during Recovery from Fractures of the Lower Limb (1976)

1. Venous occlusion plethysmography has been used to measure the blood flow in the calves of nineteen patients with fractures of the lower limb and in six normal control subjects. 2. The resting blood flows were significantly higher in the injured legs than in uninjured legs, irrespective of the site of injury. Flows in the uninjured limbs were similar to those of the control subjects. 3. During reactive hyperaemia after 10 min arterial occlusion, the increase of flows in both legs of the patients was significantly lower than in the control subjects. Because of the increased resting flow, the maximal flow in the injured leg was similar to that in the control subjects, whereas the maximal flow in the uninjured leg was significantly lower than in the control group. 4. The changes in resting flow cannot be accounted for by a change in the proportions of tissues in the limb but they may be explained by an increase of the flow through muscle secondary to a relative increase in the mass of slow to fast muscle fibres.
Rapid DNA mapping by fluorescent single molecule detection (2006)

DNA mapping is an important analytical tool in genomic sequencing, medical diagnostics and pathogen identification. Here we report an optical DNA mapping strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs on the molecules. Individual genomic DNA molecules were labeled with fluorescent dyes at specific sequence motifs by the action of nicking endonuclease followed by the incorporation of dye terminators with DNA polymerase. The labeled DNA molecules were then stretched into linear form on a modified glass surface and imaged using total internal reflection fluorescence (TIRF) microscopy. By determining the positions of the fluorescent labels with respect to the DNA backbone, the distribution of the sequence motif recognized by the nicking endonuclease can be established with good accuracy, in a manner similar to reading a barcode. With this approach, we constructed a specific sequence motif map of lambda-DNA. We further demonstrated the capability of this approach to rapidly type a human adenovirus and several strains of human rhinovirus.