gebhart/patrepeval huggingface dataset:
Web mining for web personalization (2003)

Web personalization is the process of customizing a Web site to the needs of specific users, taking advantage of the knowledge acquired from the analysis of the user's navigational behavior (usage data) in correlation with other information collected in the Web context, namely, structure, content, and user profile data. Due to the explosive growth of the Web, the domain of Web personalization has gained great momentum both in the research and commercial areas. In this article we present a survey of the use of Web mining for Web personalization. More specifically, we introduce the modules that comprise a Web personalization system, emphasizing the Web usage mining module. A review of the most common methods that are used as well as technical issues that occur is given, along with a brief overview of the most popular tools and applications available from software vendors. Moreover, the most important research initiatives in the Web usage mining and personalization areas are presented.
An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research (2010)

The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent validation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.
Punch biopsy wounds treated with Monsel's solution or a collagen matrix. A comparison of healing (1986)

• Adjacent punch biopsy wounds in 20 subjects were treated with a collagen matrix or Monsel's solution. Both techniques were easy to use and were hemostatically effective. The collagen matrix produced less inflammation, had a lower incidence of wound infection, was associated with a faster reepithelialization rate, and healed with a modestly better appearance at four weeks than did Monsel's solution. (<i>Arch Dermatol</i>1986;122:546-549)
BACE2, a β-secretase homolog, cleaves at the β site and within the amyloid-β region of the amyloid-β precursor protein (2000)

Production of amyloid-beta protein (Abeta) is initiated by a beta-secretase that cleaves the Abeta precursor protein (APP) at the N terminus of Abeta (the beta site). A recently identified aspartyl protease, BACE, cleaves the beta site and at residue 11 within the Abeta region of APP. Here we show that BACE2, a BACE homolog, cleaves at the beta site and more efficiently at a different site within Abeta. The Flemish missense mutation of APP, implicated in a form of familial Alzheimer's disease, is adjacent to this latter site and markedly increases Abeta production by BACE2 but not by BACE. BACE and BACE2 respond identically to conservative beta-site mutations, and alteration of a common active site Arg inhibits beta-site cleavage but not cleavage within Abeta by both enzymes. These data suggest that BACE2 contributes to Abeta production in individuals bearing the Flemish mutation, and that selective inhibition of these highly similar proteases may be feasible and therapeutically advantageous.
Signal processing and fabrication of a biomimetic tactile sensor array with thermal, force and microvibration modalities (2009)

We have developed a finger-shaped sensor array that provides simultaneous information about the contact forces, microvibrations and thermal fluxes induced by contact with external objects. In this paper, we describe a microprocessor-based signal conditioning and digitizing system for these sensing modalities and its embodiment on a flex-circuit that facilitates efficient assembly of the entire system via injection molding. Thermal energy from the embedded electronics is used to heat the finger above ambient temperature, similar to the biological finger. This enables the material properties of contacted objects to be inferred from thermal transients measured by a thermistor in the sensor array. Combining sensor modalities provides synergistic benefits. For example, the contact forces for exploratory movements can be calibrated so that thermal and microvibration data can be interpreted more definitively.
Enhanced benefit from adjuvant chemotherapy in breast cancer patients classified high-risk according to urokinase-type plasminogen activator (uPA) and plasminogen activator inhibitor type 1 (n = 3424). (2002)

Risk assessment and prediction of response to treatment are prerequisites for individualized adjuvant therapy decisions in breast cancer. The strong prognostic impact of the two invasion factors urokinase-type plasminogen activator (uPA) and its inhibitor, plasminogen activator inhibitor type 1 (PAI-1), in breast cancer has recently been validated at level-I evidence. This article considers the predictive impact of uPA/PAI-1 on response to adjuvant chemo- and endocrine therapy in 3424 primary breast cancer patients from two different data sets. uPA and PAI-1 antigen levels were measured by ELISA in primary tumor tissue extracts. After a median follow-up of 83 months, uPA/PAI-1 has a significant impact on disease-free survival in Cox multivariate analysis (P < 0.001; hazard ratio, 2.0; 95% confidence interval, 1.8-2.3). Patients with high uPA/PAI-1 levels benefit more strongly from adjuvant chemotherapy than those with low levels. This effect is seen as a significant interaction between chemotherapy and uPA/PAI-1 for the entire collective (P < 0.003; hazard ratio, 0.68; 95% confidence interval, 0.53-0.88) and separately within nodal subgroups. This enhanced benefit in the high uPA/PAI-1 patients occurs over and above the significant impact of both therapies in all patients. We find no corresponding significant interaction between endocrine therapy and uPA/PAI-1; i.e., no significant difference in benefit between patients with high and low uPA/PAI-1. In conclusion, uPA and PAI-1 levels in primary tumor tissue provide clinically relevant information on relapse risk and treatment response that will help to tailor adjuvant therapy concepts in breast cancer, accounting for individual biological tumor characteristics.
Soil To Genomics: The Streptomyces Chromosome (2006)

The 8-9-Mb Streptomyces chromosome is linear, with a "core" containing essential genes and "arms" carrying conditionally adaptive genes that can sustain large deletions in the laboratory. Bidirectional chromosome replication from a central oriC is completed by "end-patching," primed from terminal proteins covalently bound to the free 5'-ends. Plasmid-mediated conjugation involves movement of double-stranded DNA by proteins resembling other bacterial motor proteins, probably via hyphal tip fusion, mediated by these transfer proteins. Circular plasmids probably transfer chromosomes by transient integration, but linear plasmids may lead the donor chromosome end-first into the recipient by noncovalent association of ends. Transfer of complete chromosomes may be the rule. The recipient mycelium is colonized by intramycelial spreading of plasmid copies, under the control of plasmid-borne "spread" genes. Chromosome partition into prespore compartments of the aerial mycelium is controlled in part by actin- and tubulin-like proteins, resembling MreB and FtsZ of other bacteria.
Functional implications of the influence of ABCA1 on lipid microenvironment at the plasma membrane: a biophysical study (2009)

The ABCA1 transporter orchestrates cellular lipid homeostasis by promoting the release of cholesterol to plasmatic acceptors. The molecular mechanism is, however, unknown. We report here on the biophysical analysis in living HeLa cells of the ABCA1 lipid microenvironment at the plasma membrane. The modifications of membrane attributes induced by ABCA1 were assessed at both the outer and inner leaflet by monitoring either the lifetime of membrane inserted fluorescent lipid analogues by fluorescence lifetime imaging microscopy (FLIM) or, respectively, the membrane translocation of cationic sensors. Analysis of the partitioning of dedicated probes in plasma membrane blebs vesiculated from these cells allowed visualization of ABCA1 partitioning into the liquid disordered-like phase and corroborated the idea that ABCA1 destabilizes the lipid arrangement at the membrane. Specificity was demonstrated by comparison with cells expressing an inactive transporter. The physiological relevance of these modifications was finally demonstrated by the reduced membrane mobility and function of transferrin receptors under the influence of an active ABCA1. Collectively, these data assess that the control of both transversal and lateral lipid distribution at the membrane is the primary function of ABCA1 and positions the effluxes of cholesterol from cell membranes downstream to the redistribution of the sterol into readily extractable membrane pools.
T2 shuffling: Sharp, multicontrast, volumetric fast spin‐echo imaging (2016)

Purpose A new acquisition and reconstruction method called T 2 Shuffling is presented for volumetric fast spin‐echo (three‐dimensional [3D] FSE) imaging. T 2 Shuffling reduces blurring and recovers many images at multiple T 2 contrasts from a single acquisition at clinically feasible scan times (6–7 min). Theory and Methods The parallel imaging forward model is modified to account for temporal signal relaxation during the echo train. Scan efficiency is improved by acquiring data during the transient signal decay and by increasing echo train lengths without loss in signal‐to‐noise ratio (SNR). By (1) randomly shuffling the phase encode view ordering, (2) constraining the temporal signal evolution to a low‐dimensional subspace, and (3) promoting spatio‐temporal correlations through locally low rank regularization, a time series of virtual echo time images is recovered from a single scan. A convex formulation is presented that is robust to partial voluming and radiofrequency field inhomogeneity. Results Retrospective undersampling and in vivo scans confirm the increase in sharpness afforded by T 2 Shuffling. Multiple image contrasts are recovered and used to highlight pathology in pediatric patients. A proof‐of‐principle method is integrated into a clinical musculoskeletal imaging workflow. Conclusion The proposed T 2 Shuffling method improves the diagnostic utility of 3D FSE by reducing blurring and producing multiple image contrasts from a single scan. Magn Reson Med 77:180–195, 2017. © 2016 Wiley Periodicals, Inc.
Thermoprecipitation of Glutathione S‐Transferase by Glutathione–Poly(N‐isopropylacrylamide) Prepared by RAFT Polymerization (2010)

Herein, we report an effective and rapid method to purify glutathione S-transferase (GST) using glutathione (GSH)-modified poly(N-isopropylacrylamide) (pNIPAAm) and mild, thermal conditions. A chain transfer agent modified with pyridyl disulfide was employed in the reversible addition-fragmentation chain transfer (RAFT) polymerization of NIPAAm. The resulting polymer had a narrow molecular weight distribution (polydispersity index = 1.21). Conjugation of GSH to the pyridyl disulfide-pNIPAAm reached 95% within 30 min as determined by UV-Vis monitoring of the release of pyridine-2-thione. GST was successfully thermoprecipitated upon heating the GSH-pNIPAAm above the lower critical solution temperature (LCST). The pull down assay was repeated with bovine serum albumin (BSA) and T4 lysozyme (T4L), which demonstrated the specificity of the polymer for GST. Due to its simplicity and high efficiency, this method holds great potential for large-scale purification of GST-tagged proteins.
Intramolecular ene reactions catalyzed by NbCl5, TaCl5 and InCl3 (2004)

Niobium pentachloride, tantalum pentachloride and indium trichloride efficiently catalysed the cyclization of (R)-citronellal to a mixture of isopulegol and neoisopulegol in good yields. A comparative study was carried out which demonstrated that NbCl5 is the most active Lewis acid whereas InCl3 is the most selective one. The selectivity of the reactions varied according to the Lewis acid used and to the solvent. The ene reaction of a 1,7-diene was also investigated. In this case, all Lewis acids tested showed excellent selectivity.
Serum spreading factor (vitronectin) is present at the cell surface and in tissues. (1983)

Monoclonal antibodies were prepared against a cell attachment-promoting protein, serum spreading factor, which had been partially purified from human serum by chromatography on glass bead columns. The antibodies selected were those that reacted with polypeptides that had cell attachment-promoting activity after sodium dodecyl sulfate/polyacrylamide gel electrophoresis. Immunochromatography of human plasma on columns containing the monoclonal antibodies followed by affinity chromatography on heparin-Sepharose yielded material that in sodium dodecyl sulfate/polyacrylamide gel electrophoretic analysis gave polypeptides of molecular mass 65 and 75 kilodaltons. Both polypeptides bound each of three monoclonal antibodies and had cell attachment-promoting activity after transfer to nitrocellulose filters. Immunofluorescent staining of tissues with the monoclonal antibodies revealed a fibrillar pattern that was mostly associated with loose connective tissue and overlapped with fibronectin fibrils. Fetal membrane tissue, which showed strong staining with the antibodies in immunofluorescence, also gave 65- and 75-kilodalton polypeptides with cell attachment-promoting activity after chromatography on columns containing the monoclonal antibodies. One source of the tissue protein may be fibroblastic cells, because cultured human fibroblasts also stained with the monoclonal antibodies. The staining was fibrillar and appeared to be associated with the cell surface extracellular matrix. We propose the name "vitronectin" for the various forms of this protein, on the basis of its binding to glass and its adhesive properties.
Covariance analysis of strapdown INS considering gyrocompass characteristics (1995)

Presented in this paper is a complete error covariance analysis for strapdown inertial navigation system (SDINS). We have found that in SDINS the cross-coupling terms in gyrocompass alignment errors can significantly influence the SDINS error propagation. Initial heading error has a close correlation with the east component of gyro bias error, while initial level tilt errors are closely related to accelerometer bias errors. In addition, pseudostate variables are introduced in covariance analysis for SDINS utilizing the characteristics of gyrocompass alignment errors. This approach simplifies the covariance analysis because it makes the initial error covariance matrix to a diagonal form. Thus a real implementation becomes easier. The approach is conformed by comparing the results for a simplified case with the covariance analysis obtained from the conventional SDINS error model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improved cancer immunotherapy by a CD25-mimobody conferring selectivity to human interleukin-2 (2016)

Interleukin-2 (IL-2) immunotherapy is an attractive approach in treating advanced cancer. However, by binding to its IL-2 receptor α (CD25) subunit, IL-2 exerts unwanted effects, including stimulation of immunosuppressive regulatory T cells (T<sub>regs</sub>) and contribution to vascular leak syndrome. We used a rational approach to develop a monoclonal antibody to human IL-2, termed NARA1, which acts as a high-affinity CD25 mimic, thereby minimizing association of IL-2 with CD25. The structure of the IL-2-NARA1 complex revealed that NARA1 occupies the CD25 epitope of IL-2 and precisely overlaps with CD25. Association of NARA1 with IL-2 occurs with 10-fold higher affinity compared to CD25 and forms IL-2/NARA1 complexes, which, in vivo, preferentially stimulate CD8<sup>+</sup> T cells while disfavoring CD25<sup>+</sup> T<sub>regs</sub> and improving the benefit-to-adverse effect ratio of IL-2. In two transplantable and one spontaneous metastatic melanoma model, IL-2/NARA1 complex immunotherapy resulted in efficient expansion of tumor-specific and polyclonal CD8<sup>+</sup> T cells. These CD8<sup>+</sup> T cells showed robust interferon-γ production and expressed low levels of exhaustion markers programmed cell death protein-1, lymphocyte activation gene-3, and T cell immunoglobulin and mucin domain-3. These effects resulted in potent anticancer immune responses and prolonged survival in the tumor models. Collectively, our data demonstrate that NARA1 acts as a CD25-mimobody that confers selectivity and increased potency to IL-2 and warrant further assessment of NARA1 as a therapeutic.
Immunization of Experimental Animals with Reconstituted Glycoprotein Mixtures of Herpes Simplex Virus 1 and 2: Protection Against Challenge with Virulent Virus (1987)

Artificial mixtures of the glycoproteins B, C, D, and E of herpes simplex virus 1 and 2 (HSV-1 and HSV-2), purified individually from infected Vero cell lysates by immunoaffinity to monoclonal antibodies, were bound to an aluminum hydroxide gel and were used to immunize mice, guinea pigs, and owl monkeys (Aotus trivirgatus) once or twice (mice and guinea pigs) to as many as four times (owl monkeys). In all animals tested, low levels of neutralizing antibodies were detected only after two or more immunizations. Lymphocyte transformation tests in owl monkeys suggested low or borderline levels of cellular immunity. The survival of immunized mice after intracerebral challenge was inversely related to the challenge dose. Immunized guinea pigs challenged by intravaginal inoculation showed reduced morbidity at the site of inoculation and were protected from CNS disease. Both immunized and nonimmunized monkeys were highly susceptible and could not be differentiated with respect to morbidity or mortality when challenged with 1,000 pfu of HSV-2 by the intravaginal route.
Presentation of exogenous protein antigens by dendritic cells to T cell clones. Intact protein is presented best by immature, epidermal Langerhans cells. (1989)

The capacity of dendritic cells to present protein antigens has been studied with two MHC class II-restricted, myoglobin-specific, T cell clones. Spleen dendritic cells and cultured epidermal Langerhans cells (LC) presented native myoglobin weakly and often not at all. These same populations were powerful stimulators of allogeneic T cells in the primary MLR. Freshly isolated LC were in contrast very active in presenting proteins to T cell clones but were weak stimulators of the MLR. Both fresh and cultured LC could present specific peptide fragments of myoglobin to the clones. These results suggest that dendritic cells in nonlymphoid tissues like skin can act as sentinels for presenting antigens in situ, their accessory function developing in two phases. First antigens are captured and appropriately presented. Further handling of antigen then is downregulated while the cells acquire strong sensitizing activity for the growth and function of resting T lymphocytes. The potent MLR stimulating activity of cultured epidermal LC and lymphoid dendritic cells probably reflects prior handling of antigens leading to the formation of allogeneic MHC-peptide complexes.
The battle against phishing (2005)

Phishing is a model problem for illustrating usability concerns of privacy and security because both system designers and attackers battle using user interfaces to guide (or misguide) users.We propose a new scheme, Dynamic Security Skins, that allows a remote web server to prove its identity in a way that is easy for a human user to verify and hard for an attacker to spoof. We describe the design of an extension to the Mozilla Firefox browser that implements this scheme.We present two novel interaction techniques to prevent spoofing. First, our browser extension provides a trusted window in the browser dedicated to username and password entry. We use a photographic image to create a trusted path between the user and this window to prevent spoofing of the window and of the text entry fields.Second, our scheme allows the remote server to generate a unique abstract image for each user and each transaction. This image creates a "skin" that automatically customizes the browser window or the user interface elements in the content of a remote web page. Our extension allows the user's browser to independently compute the image that it expects to receive from the server. To authenticate content from the server, the user can visually verify that the images match.We contrast our work with existing anti-phishing proposals. In contrast to other proposals, our scheme places a very low burden on the user in terms of effort, memory and time. To authenticate himself, the user has to recognize only one image and remember one low entropy password, no matter how many servers he wishes to interact with. To authenticate content from an authenticated server, the user only needs to perform one visual matching operation to compare two images. Furthermore, it places a high burden of effort on an attacker to spoof customized security indicators.
A Soluble Activin Receptor Type IIB Does Not Improve Blood Glucose in Streptozotocin-Treated Mice (2015)

Type 1 diabetes mellitus (T1DM), or insulin dependent DM, is accompanied by decreased muscle mass. The growth factor myostatin (MSTN) is a negative regulator of muscle growth, and a loss of MSTN signaling has been shown to increase muscle mass and prevent the development of obesity, insulin resistance and lipodystrophic diabetes in mice. The effects of MSTN inhibition in a T1DM model on muscle mass and blood glucose are unknown. We asked whether MSTN inhibition would increase muscle mass and decrease hyperglycemia in mice treated with streptozotocin (STZ) to destroy pancreatic beta cells. After diabetes developed, mice were treated with a soluble MSTN/activin receptor fused to Fc (ACVR2B:Fc). ACVR2B:Fc increased body weight and muscle mass compared to vehicle treated mice. Unexpectedly, ACVR2B:Fc reproducibly exacerbated hyperglycemia within approximately one week of administration. ACVR2B:Fc treatment also elevated serum levels of the glucocorticoid corticosterone. These results suggest that although MSTN/activin inhibitors increased muscle mass, they may be counterproductive in improving health in patients with T1DM.