gebhart/patrepeval huggingface dataset:
Fast Risley prisms camera steering system: calibration and image distortions correction through the use of a three-dimensional refraction model (2007)

To improve airborne search and rescue operations and the general aerial surveillance efficiency, new concepts of multiple field-of-view and variable-resolution imagers have been developed. These imagers provide surveillance operators with simultaneous wide area coverage and high-resolution imaging. Over the last years, several optical steering systems have been developed and field tested in operational conditions. These developments helped us to develop a novel camera steering system using achromatic Risley prisms. This simple and sturdy steering system allowed us to move rapidly and precisely the field of view of an infrared camera. To improve its performance, a three-dimensional (3D) refraction model was applied to enable fast pointing direction calibration and correction of distorted images. Image deformations were analyzed, and a fast linear image correction based on homographic transformation and the 3D refraction model are presented. Experimental results of mosaicking applications with real imaging systems in the 3- to 5-µm, 8- to 12-µm infrared, and 850- to 860-nm visible bands demonstrate the improvements achieved with the homographic image distortions correction and the fast pointing calibration procedure.
Follicular lymphoma-like B cells in healthy individuals: a novel intermediate step in early lymphomagenesis (2006)

Follicular lymphoma is one of the most common adult lymphoma, and remains virtually incurable despite its relatively indolent nature. t(14;18)(q32;q21) translocation, the genetic hallmark and early initiating event of follicular lymphoma (FL) pathogenesis, is also present at low frequency in the peripheral blood of healthy individuals. It has long been assumed that in healthy individuals t(14;18) is carried by circulating quiescent naive B cells, where its oncogenic potential would be restrained. Here, we question this current view and demonstrate that in healthy individuals, t(14;18) is actually carried by an expanding population of atypical B cells issued from germinal centers, displaying genotypic and phenotypic features of FL, and prone to constitute potent premalignant FL niches. These findings strongly impact both on the current understanding of disease progression and on the proper handling of t(14;18) frequency in blood as a potential early biomarker for lymphoma.
Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway (2010)

Acetoacetyl-CoA is the precursor of 3-hydroxy-3-methylglutaryl (HMG)-CoA in the mevalonate pathway, which is essential for terpenoid backbone biosynthesis. Acetoacetyl-CoA is also the precursor of poly-beta-hydroxybutyrate, a polymer belonging to the polyester class produced by microorganisms. The de novo synthesis of acetoacetyl-CoA is usually catalyzed by acetoacetyl-CoA thiolase via a thioester-dependent Claisen condensation reaction between two molecules of acetyl-CoA. Here, we report that nphT7, found in the mevalonate pathway gene cluster from a soil-isolated Streptomyces sp. strain, encodes an unusual acetoacetyl-CoA synthesizing enzyme. The recombinant enzyme overexpressed in Escherichia coli catalyzes a single condensation of acetyl-CoA and malonyl-CoA to give acetoacetyl-CoA and CoA. Replacement of malonyl-CoA with malonyl-(acyl carrier protein) resulted in loss of the condensation activity. No acetoacetyl-CoA synthesizing activity was detected through the condensation of two molecules of acetyl-CoA. Based on these properties of NphT7, we propose to name this unusual enzyme of the thiolase superfamily acetoacetyl-CoA synthase. Coexpression of nphT7 with the HMG-CoA synthase gene and the HMG-CoA reductase gene in a heterologous host allowed 3.5-fold higher production of mevalonate than when only the HMG-CoA synthase and HMG-CoA reductase genes were expressed. This result suggests that nphT7 can be used to significantly increase the concentration of acetoacetyl-CoA in cells, eventually leading to the production of useful terpenoids and poly-beta-hydroxybutyrate.
Yersinia V–Antigen Exploits Toll-like Receptor 2 and CD14 for Interleukin 10–mediated Immunosuppression (2002)

A characteristic of the three human-pathogenic Yersinia spp. (the plague agent Yersinia pestis and the enteropathogenic Yersinia pseudotuberculosis and Yersinia enterocolitica) is the expression of the virulence (V)-antigen (LcrV). LcrV is a released protein which is involved in contact-induced secretion of yersinia antihost proteins and in evasion of the host's innate immune response. Here we report that recombinant LcrV signals in a CD14- and toll-like receptor 2 (TLR2)-dependent fashion leading to immunosuppression by interleukin 10 induction. The impact of this immunosuppressive effect for yersinia pathogenesis is underlined by the observation that TLR2-deficient mice are less susceptible to oral Y. enterocolitica infection than isogenic wild-type animals. In summary, these data demonstrate a new ligand specificity of TLR2, as LcrV is the first known secreted and nonlipidated virulence-associated protein of a Gram-negative bacterium using TLR2 for cell activation. We conclude that yersiniae might exploit host innate pattern recognition molecules and defense mechanisms to evade the host immune response.
Identification of acyltransferases required for cutin biosynthesis and production of cutin with suberin-like monomers (2007)

Cutin and suberin are the two major lipid-based polymers of plants. Cutin is the structural polymer of the epidermal cuticle, the waterproof layer covering primary aerial organs and which is often the structure first encountered by phytopathogens. Suberin contributes to the control of diffusion of water and solutes across internal root tissues and in periderms. The enzymes responsible for assembly of the cutin polymer are largely unknown. We have identified two Arabidopsis acyltransferases essential for cutin biosynthesis, glycerol-3-phosphate acyltransferase (GPAT) 4 and GPAT8. Double knockouts gpat4/gpat8 were strongly reduced in cutin and were less resistant to desiccation and to infection by the fungus Alternaria brassicicola. They also showed striking defects in stomata structure including a lack of cuticular ledges between guard cells, highlighting the importance of cutin in stomatal biology. Overexpression of GPAT4 or GPAT8 in Arabidopsis increased the content of C16 and C18 cutin monomers in leaves and stems by 80%. In order to modify cutin composition, the acyltransferase GPAT5 and the cytochrome P450-dependent fatty acyl oxidase CYP86A1, two enzymes associated with suberin biosynthesis, were overexpressed. When both enzymes were overexpressed together the epidermal polyesters accumulated new C20 and C22 omega-hydroxyacids and alpha,omega-diacids typical of suberin, and the fine structure and water-barrier function of the cuticle were altered. These results identify GPATs as partners of fatty acyl oxidases in lipid polyester synthesis and indicate that their cooverexpression provides a strategy to probe the role of cutin composition and quantity in the function of plant cuticles.
A Virtual Machine Introspection Based Architecture for Intrusion Detection. (2003)

Today&amp;apos;s architectures for intrusion detection force the IDS designer to make a difficult choice. If the IDS resides on the host, it has an excellent view of what is happening in that host&amp;apos;s software, but is highly susceptible to attack. On the other hand, if the IDS resides in the network, it is more resistant to attack, but has a poor view of what is happening inside the host, making it more susceptible to evasion. In this paper we present an architecture that retains the visibility of a host-based IDS, but pulls the IDS outside of the host for greater attack resistance. We achieve this through the use of a virtual machine monitor. Using this approach allows us to isolate the IDS from the monitored host but still retain excellent visibility into the host&amp;apos;s state. The VMM also offers us the unique ability to completely mediate interactions between the host software and the underlying hardware. We present a detailed study of our architecture, including Livewire, a prototype implementation. We demonstrate Livewire by implementing a suite of simple intrusion detection policies and using them to detect real attacks.
Development of a name translation system using CRAY T94 (2002)

Natural language processing (NLP) is an important research direction, since it addresses the needs of the approaching information age. In this paper, we report our study on the problem of translating people's English names into their corresponding Chinese Pinyin names. A name translation system (NTS) has been developed based on statistical approaches. There are two components in the NTS: dictionary creation and name translation. The dictionary is generated using a statistics-based dictionary generator (SBDG), and the name translation is done by using a modified address normalization system (ANS). As in many other NLP applications, the SBDG and ANS suffer the drawback of requiring extremely large computational resources, both in terms of computation time and memory. To make the NTS fast and feasible, therefore, the use of a high-performance computer becomes necessary. The CRAY T94 is a powerful large-scale and general-purpose parallel-vector supercomputer. In this paper, we first describe the system design of the NTS, and then explain how the NTS is optimized to execute on the CRAY T94. The results we obtained are also discussed. Our experience shows that algorithms and data structures are very important in obtaining optimal performance. The performance monitoring/analysis tools provided by The CRAY T94 programming environment are also proved to be very useful in making optimization decisions. In addition, our study also demonstrates that using the CRAY T94, performance improvements can be achieved not only in the traditional areas of scientific computation but also in NLP applications.
Solid-phase synthesis and characterization of human salivary statherin: a tyrosine-rich phosphoprotein inhibitor of calcium phosphate precipitation. (1997)

Human statherin, at low molecular weight (M 5380 Da. 43 amino acid residues) acidic tyrosine-rich phosphoprotein secreted mainly by salivary glands, has been synthesized successfully for the first time following standard solid-phase Fmoc chemistry. Synthesis of this phosphoprotein was accomplished using preformed phosphoserin building blocks. The phosphorylated protein thus synthesized was analyzed and compared with the native molecule and was found to have identical characteristics in its entirety, is evidenced by various analytical methods including mass spectral analysis. Analysis of both the synthetic and native statherin by circular dichroism spectroscopy showed an increase in helicity upon the addition of an organic cosolvent, trifluoroethanol (50%, vol/vol), indicating the presence of potentially amphipathic helical regions. Circular dichroism studies and hydrophobic moment calculations on this synthetic phosphoprotein revealed that the molecule adopts an amphipathic helical conformation at the N-terminus connected to a long poly-L-proline type II segment, which, in turn, is linked to an extended beta-strand. In correlation with previous studies. It appears that the strong binding affinity of statherin for hydroxyapatite can be attributed primarily to the N-terminal sequence, which prefers to adopted helical conformation and provides both electrostatic and hydrogen bonding interactions, thereby inhibiting its mineralization. Production of this highly homogenous synthetic statherin by chemical means may circumvent the prevailing obstacles encountered in conducting its tertiary structural investigations under various physiological conditions.
Grouping Contours by Iterated Pairing Network (1990)

We describe in this paper a network that performs grouping of image contours. The input to the net are fragments of image contours, and the output is the partitioning of the fragments into groups, together with a saliency measure for each group. The grouping is based on a measure of overall length and curvature. The network decomposes the overall optimization problem into independent optimal pairing problems performed at each node. The resulting computation maps into a uniform locally connected network of simple computing elements. 1 The Problem: Contour Grouping A problem that often arises in visual information processing is the linking of contour fragments into optimal groups. For example, certain subsets of contours spontaneously form perceptual groups, as illustrated in Fig. 1, and are often detected immediately without scanning the image in a systematic manner. Grouping process of this type are likely to play an important role in object recognition by segmenting the image and sel...
Randomized Phase III Placebo-Controlled Trial of Carboplatin and Paclitaxel With or Without the Vascular Disrupting Agent Vadimezan (ASA404) in Advanced Non–Small-Cell Lung Cancer (2011)

The addition of ASA404 to carboplatin and paclitaxel, although generally well tolerated, failed to improve frontline efficacy in advanced NSCLC.
A Multiparametric Serum Kallikrein Panel for Diagnosis of Non–Small Cell Lung Carcinoma (2008)

We propose a multiparametric panel of kallikrein markers for lung cancer diagnosis with relatively good accuracy. This model requires validation with a larger series and may be further improved by addition of other biomarkers.
Phosphorylation of Thr 495 Regulates Ca 2+ /Calmodulin-Dependent Endothelial Nitric Oxide Synthase Activity (2001)

The activity of the endothelial nitric oxide synthase (eNOS) can be regulated independently of an increase in Ca(2+) by the phosphorylation of Ser(1177) but results only in a low nitric oxide (NO) output. In the present study, we assessed whether the agonist-induced (Ca(2+)-dependent, high-output) activation of eNOS is associated with changes in the phosphorylation of Thr(495) in the calmodulin (CaM)-binding domain. eNOS Thr(495) was constitutively phosphorylated in porcine aortic endothelial cells and was rapidly dephosphorylated after bradykinin stimulation. In the same cells, bradykinin enhanced the phosphorylation of Ser(1177), which was maximal after 5 minutes, and abolished by the CaM-dependent kinase II (CaMKII) inhibitor KN-93. Bradykinin also enhanced the association of CaMKII with eNOS. Phosphorylation of Thr(495) was attenuated by the protein kinase C (PKC) inhibitor Ro 31-8220 and after PKC downregulation using phorbol 12-myristate 13-acetate. The agonist-induced dephosphorylation of Thr(495) was completely Ca(2+)-dependent and inhibited by the PP1 inhibitor calyculin A. Little CaM was bound to eNOS immunoprecipitated from unstimulated cells, but the agonist-induced dephosphorylation of Thr(495) enhanced the association of CaM. Mutation of Thr(495) to alanine increased CaM binding to eNOS in the absence of cell stimulation, whereas the corresponding Asp(495) mutant bound almost no CaM. Accordingly, NO production by the Ala(495) mutant was more sensitive to Ca(2+)/CaM than the aspartate mutant. These results suggest that the dual phosphorylation of Ser(1177) and Thr(495) determines the activity of eNOS in agonist-stimulated endothelial cells. Moreover, the dephosphorylation of Thr(495) by PP1 precedes the phosphorylation of Ser(1177) by CaMKII. The full text of this article is available at http://www.circresaha.org.
Distinct Expression of CXCL8 and Its Receptors CXCR1 and CXCR2 and Their Association With Vessel Density and Aggressiveness in Malignant Melanoma (2006)

We examined the expression of CXCL8 (interleukin-8), its receptors, CXCR1 and CXCR2, and vessel density in human melanoma by immunohistochemical analysis of tumors from different Clark levels, depths, and thicknesses. Expression of CXCL8 and CXCR2 was lower in Clark level I and II specimens than in level III through V specimens and metastases. CXCR1 expression was observed ubiquitously in the majority of human melanoma tumor specimens irrespective of disease state, with the highest intensity in Clark level III specimens. We observed a significant difference in CXCL8 and CXCR2 expression between thin (<or=0.75 mm) and thick (>0.75 mm) melanomas and between thin and metastatic lesions. Positive correlations were observed between Clark level and CXCL8 or CXCR2 and between thickness and CXCR2 expression. We found no correlation between vessel density and Clark level or thickness. Our data suggest that expression of CXCL8 and CXCR2 contributes to aggressive growth and metastasis in human malignant melanoma. Consistent with the transition from radial to vertical growth phase melanoma, expression of CXCL8 and its receptor, CXCR2, may be key in the switch to an aggressive, more metastatic phenotype.
Cloning and heterologous expression of a cDNA encoding 1‐deoxy‐D‐xylulose‐5‐phosphate reductoisomerase of Arabidopsis thaliana1 (1999)

Various plant isoprenoids are synthesized via the non-mevalonate pathway of isopentenyl diphosphate formation. In this pathway, 1-deoxy-D-xylulose 5-phosphate (DOXP), the first intermediate, is transformed to 2-C-methyl-D-erythritol 4-phosphate (MEP) by an enzyme which was recently cloned from Escherichia coli. In order to find a plant homologue of this 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) we cloned a cDNA fragment from Arabidopsis thaliana which has high homology to the E. coli DXR. By expression of this fragment in E. coli we could demonstrate that it encodes a protein which transforms DOXP to MEP. The antibiotic fosmidomycin specifically inhibits this DXR enzyme activity.
Detection of the factor V Leiden mutation by direct allele-specific hybridization of PCR amplicons to photoimmobilized locked nucleic acids. (1999)

The simplicity of the assay and its procedural relatedness to the widely used ELISA format should make it useful for routine factor V testing in the clinical laboratory.
Addition of Clonidine to Epidural Morphine Enhances Postoperative Analgesia After Cesarean Delivery (1995)

A low dose of clonidine such as 75 micrograms doubled the duration of analgesia produced by 2 mg of morphine and a dose of 150 micrograms further increased the duration of postoperative complete analgesia without increasing the incidence of side effects. The morphine requirements during the postoperative period (36 hours) was greatly reduced by the addition of clonidine to the analgesic epidural mixture.
Combined treatment with dendritic cell vaccine and low-dose cyclophosphamide in patients with malignant melanoma. (2010)

e13032 Background: Cancer vaccines based on dendritic cells (DC) have been tested in several clinical trials; in general, efficacy has been low, which might be due to inefficient immune activation. Regulatory T cells (Tregs) are known to posses immunosuppressive function; in the present study we investigate the ability of cyclophosphamide (Cy) to reduce the number of Tregs and increase efficacy of DC vaccination. Methods: Patients with progressive advanced melanoma received treatment with autologous DCs pulsed with p53, survivin and telomerase derived peptides (HLA-A2+) or tumor lysate (HLA- A2−). Cy 50 mg x 2 daily for a week, every second week, celecoxib (Ce) 200 mg daily, and IL-2 2MIU day 1-5 following each vaccine, were given concomitantly. Vaccine no. 1-4 was given weekly and vaccine 5-10 biweekly. If the patient achieved stable disease (SD) vaccines was continued monthly, until progression. The aims of this nonrandomized open labeled phase II trial were to evaluate tolerability, safety and the induced clinical and immunological responses. Results: 14 of 24 patients (58%) achieved SD after 6 vaccinations and 10 progressed. One patient maintained SD for 16 vaccines (10 months). No objective responses were seen. Two patients were excluded prior to their first vaccine and 1 was excluded in SD after 4 vaccines due to anemia and refusal of blood transfusion. Those 3 patients are not included in the results. The treatment was associated with a marked increase in the proportion of Tregs from baseline to the 4th vaccine followed by a decrease from the 4th to the 6th vaccine although not to the baseline values. Conclusions: The combination of DC vaccination and Cy was well tolerated. The induction of Tregs was not decreased by adding Cy, on the contrary a higher Treg level was maintained. However, the fraction of patients who achieved SD was more than doubled as compared to a comparable cohort of patients treated with DC vaccination without Cy. No significant financial relationships to disclose.
Polydisperse ethoxylated fatty alcohol surfactants as accelerators of cuticular penetration. 1. Effects of ethoxy chain length and the size of the penetrants (1997)

The effects of polydisperse ethoxylated fatty alcohol (EFA) surfactants on the penetration of six organic compounds varying in size (molar volumes, 107–282 cm3 mol-1) and lipophilicity (log Kow 0·8–6·5) were investigated using astomatous isolated cuticular membranes (CM) of Citrus and pear leaves. Mobilities of model compounds in CM were measured by unilateral desorption from the outer surface (UDOS). Rate constants (k*) obtained in these experiments are directly proportional to diffusion coefficients and, in the absence of EFA, k* values decreased by a factor of 52 when molar volumes increased only 2·64-fold. Under UDOS conditions using micellar surfactant solutions as desorption media, surfactants are sorbed in the CM and the volume fractions sorbed were found to decrease from approximately 0·062 to 0·018 when the average number of ethoxy groups (nE) increased from 5 to 17. In the presence of the EFA surfactants in the CM, solute mobilities increased markedly though this effect diminished with increasing nE. Surfactants with nE=17 affected solute mobilities only marginally. Surfactant effects on solute mobility increased with the size of the solutes leading to almost identical mobilities of the model compounds. With the current range of our model compounds, lipophilicity increased with increasing molar volumes, though evidence is presented showing that the mobilities of solutes depend on their molar volumes while lipophilicity has no effect. Effects of micellar aqueous solutions of polydisperse surfactants on solute mobilities followed the pattern observed with monodisperse ones. © 1997 SCI
A global maximum power point tracking DC-DC converter (2005)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.
MGMT Promoter Methylation Status Can Predict the Incidence and Outcome of Pseudoprogression After Concomitant Radiochemotherapy in Newly Diagnosed Glioblastoma Patients (2008)

PsPD has a clinical impact on chemotherapy-treated GBM, as it may express the glioma killing effects of treatment and is significantly correlated with MGMT status. Improvement in the early recognition of psPD patterns and knowledge of mechanisms underlying this phenomenon are crucial to eliminating biases in evaluating the results of clinical trials and guaranteeing effective treatment.