gebhart/patrepeval huggingface dataset:
A New PEG−β-Alanine Active Derivative for Releasable Protein Conjugation (2008)

A new PEGylating agent, PEG-betaAla-NHCO-OSu, has been studied for protein amino conjugation using human growth hormone (hGH) and granulocyte colony stimulating factor (G-CSF) as model therapeutic proteins. This new activated PEG possesses a convenient property for protein modification when compared to other activated carboxylate PEGs, namely, lower reactivity. When this polymer reacts with a protein, its features lead to fewer PEG-protein conjugate isomers because it preferentially binds the most nucleophilic and exposed amines. Furthermore, the conjugates obtained with PEG-betaAla-NHCO-OSu showed an interesting slow release of polymer chains upon incubation under physiological conditions. Further investigations determined that the PEG chains released are those coupled to histidine residues, and this finally yields less PEGylated species as well as free protein. This release allows a partial recovery of protein activity that is often remarkably and permanently reduced after stable PEGylation, and it occurs in water or blood without the involvement of enzymes. On the other hand, the rate of PEG release, tuned by the chemical structure of this new PEGylating agent, is not too high, and therefore, the achievement of a desired prolongation of protein half-life in vivo is still feasible. The pharmacokinetics of hGH-PEG6k-betaAla conjugate was compared to that of native hGH in rats and monkeys, and the blood residence times were increased by 10- and 7-fold, respectively. The conjugate potency was evaluated in hypophysectomized rats demonstrating a superior pharmacodynamic profile with respect to native hGH.
The role of EKLF in human beta-globin gene competition. (1996)

We have investigated the role of erythroid Kruppel-like factor (EKLF) in expression of the human beta-globin genes in compound EKLF knockout/human beta-locus transgenic mice. EKLF affects only the adult mouse beta-globin genes in homozygous knockout mice; heterozygous mice are unaffected. Here we show that EKLF knockout mice express the human epsilon and gamma-globin genes normally in embryonic red cells. However, fetal liver erythropoiesis, which is marked by a period of gamma- and beta-gene competition in which the genes are alternately transcribed, exhibits an altered ratio of gamma- to beta-gene transcription. EKLF heterozygous fetal livers display a decrease in the number of transcriptionally active beta genes with a reciprocal increase in the number of transcriptionally active gamma genes. beta-Gene transcription is absent in homozygous knockout fetuses with coincident changes in chromatin structure at the beta promoter. There is a further increase in the number of transcriptionally active gamma genes and accompanying gamma gene promoter chromatin alterations. These results indicate that EKLF plays a major role in gamma- and beta-gene competition and suggest that EKLF is important in stabilizing the interaction between the Locus Control Region and the beta-globin gene. In addition, these findings provide further evidence that developmental modulation of globin gene expression within individual cells is accomplished by altering the frequency and/or duration of transcriptional periods of a gene rather than changing the rate of transcription.
Nanowire–Bacteria Hybrids for Unassisted Solar Carbon Dioxide Fixation to Value-Added Chemicals (2015)

Direct solar-powered production of value-added chemicals from CO2 and H2O, a process that mimics natural photosynthesis, is of fundamental and practical interest. In natural photosynthesis, CO2 is first reduced to common biochemical building blocks using solar energy, which are subsequently used for the synthesis of the complex mixture of molecular products that form biomass. Here we report an artificial photosynthetic scheme that functions via a similar two-step process by developing a biocompatible light-capturing nanowire array that enables a direct interface with microbial systems. As a proof of principle, we demonstrate that a hybrid semiconductor nanowire-bacteria system can reduce CO2 at neutral pH to a wide array of chemical targets, such as fuels, polymers, and complex pharmaceutical precursors, using only solar energy input. The high-surface-area silicon nanowire array harvests light energy to provide reducing equivalents to the anaerobic bacterium, Sporomusa ovata, for the photoelectrochemical production of acetic acid under aerobic conditions (21% O2) with low overpotential (η < 200 mV), high Faradaic efficiency (up to 90%), and long-term stability (up to 200 h). The resulting acetate (∼6 g/L) can be activated to acetyl coenzyme A (acetyl-CoA) by genetically engineered Escherichia coli and used as a building block for a variety of value-added chemicals, such as n-butanol, polyhydroxybutyrate (PHB) polymer, and three different isoprenoid natural products. As such, interfacing biocompatible solid-state nanodevices with living systems provides a starting point for developing a programmable system of chemical synthesis entirely powered by sunlight.
Transcriptional profiling of host responses in mouse lungs following aerosol infection with type A Francisella tularensis (2006)

Tularaemia caused by inhalation of type A Francisella tularensis bacteria is one of the most aggressive infectious diseases known, but the reasons for the very rapid spread of the organism from the lungs to internal organs and the ensuing mortality are unknown. The present study used the mouse model to examine in detail the host immune response in the lung. After an aerosol challenge with 20 c.f.u. of the type A strain FSC033, all mice developed clinical signs of severe disease, showed weight loss by day 4 of infection and died the next day. Histopathological findings in the lung revealed acute inflammation and intense vasculitis and perivasculitis on day 4. Gene transcriptional changes in the mouse lung samples were examined on days 1, 2 and 4 of infection using a cDNA microarray with 20,600 mouse clones representing 18,500 genes. In total, 424 genes were found to be differentially expressed, some of which were both up- and downregulated at different time points, 192 of which were upregulated and 234 of which were downregulated for at least one time point. A high percentage of selected genes identified by the microarray analysis were confirmed to be differentially regulated by quantitative real-time PCR. Categorization of the differentially expressed genes showed that those preferentially involved in host immune responses were activated extensively on day 4 but hardly or not at all on days 1 and 2. Further analysis revealed that several of the genes upregulated on day 4 are known to depend on gamma interferon or tumour necrosis factor alpha for their regulation. In keeping with this finding, tumour necrosis factor alpha and gamma interferon levels were found to be increased significantly in bronchoalveolar lavage on day 4.
Global warming impact on the cement and aggregates industries (1994)

CO[sub 2] related energy taxes are focusing essentially on fuel consumption, not on actual CO[sub 2] emission measured at the chimneys. Ordinary Portland cement, used in the aggregates and industries, results from the calcination of limestone and silica. The production of 1 ton of cement directly generates 0.55 tons of chemical-CO[sub 2] and requires the combustion of carbon-fuel to yield an additional 0.40 tons of CO[sub 2]. The 1987 1 billion metric tons world production of cement accounted for 1 billion metric tons of CO[sub 2], i.e., 5% of the 1987 world CO[sub 2] emission. A world-wide freeze of CO[sub 2] emission at the 1990 level as recommended by international institutions, is incompatible with the extremely high cement development needs of less industrialized countries. Present cement production growth ranges from 5% to 16% and suggests that in 25 years from now, world cement CO[sub 2] emissions could equal 3,500 million tons. Eco-taxes when applied would have a spectacular impact on traditional Portland cement based aggregates industries. Taxation based only on fuel consumption would lead to a cement price increase of 20%, whereas taxation based on actual CO[sub 2] emission would multiply cement price by 1.5 to 2. A 25--30% minormore » reduction of CO[sub 2] emissions may be achieved through the blending of Portland cement with replacement materials such as coal-fly ash and iron blast furnace slag.« less
Sharp interface limits of phase-field models (2001)

The use of continuum phase-field models to describe the motion of well-defined interfaces is discussed for a class of phenomena that includes order-disorder transitions, spinodal decomposition and Ostwald ripening, dendritic growth, and the solidification of eutectic alloys. The projection operator method is used to extract the "sharp-interface limit" from phase-field models which have interfaces that are diffuse on a length scale xi. In particular, phase-field equations are mapped onto sharp-interface equations in the limits xi(kappa)<<1 and xi(v)/D<<1, where kappa and v are, respectively, the interface curvature and velocity and D is the diffusion constant in the bulk. The calculations provide one general set of sharp-interface equations that incorporate the Gibbs-Thomson condition, the Allen-Cahn equation, and the Kardar-Parisi-Zhang equation.
Network Endpoint Assessment (NEA): Overview and Requirements (2008)

This document defines the problem statement, scope, and protocol
requirements between the components of the NEA (Network Endpoint
Assessment) reference model. NEA provides owners of networks (e.g., an
enterprise offering remote access) a mechanism to evaluate the posture
of a system. This may take place during the request for network access
and/or subsequently at any time while connected to the network. The
learned posture information can then be applied to a variety of
compliance-oriented decisions. The posture information is frequently
useful for detecting systems that are lacking or have out-of-date
security protection mechanisms such as: anti-virus and host-based
firewall software. In order to provide context for the requirements, a
reference model and terminology are introduced. This memo provides
information for the Internet community.
Characterisation of cell adhesion in airway epithelial cell types using electric cell–substrate impedance sensing (2009)

Research on epithelial cell lines and primary epithelium is required to dissect the mechanisms underlying the structural abnormalities in airway epithelium observed for respiratory diseases, including asthma and chronic obstructive pulmonary disease. The novel electric cell-substrate impedance sensing technique was used to monitor cell adhesion/spreading, barrier function and wound healing. Primary bronchial epithelium was compared with airway epithelial cell lines 16HBE14o-, BEAS-2B, NCI-H292 and A549. BEAS-2B, A549 and primary cells form a confluent monolayer more rapidly than do 16HBE14o- cells. In contrast, 16HBE14o- cells form stronger intercellular contacts, with a 10-fold higher resistance than BEAS-2B, A549 and NCI-H292 cells and a five-fold increase over primary cells. Accordingly, expression of the adhesion molecules zona occludens-1 and E-cadherin was highest in 16HBE14o- cells. These molecules were localised in intercellular junctions in both 16HBE14o- and primary cells. Finally, restoration of barrier function upon injury was impaired in BEAS-2B compared to 16HBE14o- cells. In conclusion, epithelial cell types display remarkable phenotypic differences and should, accordingly, be used to address specific research questions. 16HBE14o- cells appear most suitable for studies on barrier formation, whereas resemblance in attachment of primary and BEAS-2B and A549 cells makes the latter more important for translational research on cell-matrix contact.
Organ specificity of lymphocyte migration: mediation by highly selective lymphocyte interaction with organ‐specific determinants on high endothelial venules (1980)

Evidence is presented that the organ specificity of lymphocyte migration is determined by selective interaction of lymphocytes with specialized endothelial cells. Mouse Peyer's patch and lymph node lymphocytes bind preferentially to high endothelial venules (HEV) in frozen sections of Peyer's patches and peripheral nodes, respectively, and this in vitro binding preference accurately predicts their differential segregation in vivo 30 min after i.v. injection. Both in vivo and in vitro, about 1.4 times as many as many Peyer's patch as lymph node lymphocytes bind HEV in Peyer's patches, and, conversely, twice as many lymph node cells interact with HEV in nonmesenteric lymph nodes. Even greater specificity is shown by certain homogeneous lymphocyte populations, i.e. thymic lymphomas. Some lymphomas bind with remarkable selectivity to HEV in Peyer's patches, and others interact almost exclusively with those in lymph nodes indicating that the mechanisms mediating selective recognition of HEV are capable of nearly absolute discrimination. Mesenteric node HEV are unique in that they allow both Peyer's patch- and lymph node-specific cells to bind. It is proposed that lymphocyte surface receptors specific for organ-restricted endothelial cell determinants mediate the antigen-independent organ specificity of lymphocyte migration. According to this model, there are at least 2 sets of complementary lymphocyte and endothelial cell receptors, one mediating lymphocyte-HEV adherence in Peyer's patches, the other in lymph nodes.
Locally Uniform Comparison Image Descriptor (2012)

Keypoint matching between pairs of images using popular descriptors like SIFT or a faster variant called SURF is at the heart of many computer vision algorithms including recognition, mosaicing, and structure from motion. However, SIFT and SURF do not perform well for real-time or mobile applications. As an alternative very fast binary descriptors like BRIEF and related methods use pairwise compar-isons of pixel intensities in an image patch. We present an analysis of BRIEF and related approaches revealing that they are hashing schemes on the ordinal correla-tion metric Kendall’s tau. Here, we introduce Locally Uniform Comparison Image Descriptor (LUCID), a simple description method based on linear time permuta-tion distances between the ordering of RGB values of two image patches. LUCID is computable in linear time with respect to the number of pixels and does not require floating point computation. 1
Heterogeneity of rat tropoelastin mRNA revealed by cDNA cloning (1990)

A lambda gt11 library constructed from poly(A+) RNA isolated from aortic tissue of neonatal rats was screened for rat tropoelastin cDNAs. The first screen, utilizing a human tropoelastin cDNA clone, provided rat tropoelastin cDNAs spanning 2.3 kb of carboxy-terminal coding sequence and extended into the 3'-untranslated region. A subsequent screen using a 5' rat tropoelastin cDNA clone yielded clones extending into the amino-terminal signal sequence coding region. Sequence analysis of these clones has provided the complete derived amino acid sequence of rat tropoelastin and allowed alignment and comparison with published bovine cDNA sequence. While the overall structure of rat tropoelastin is similar to bovine sequence, numerous substitutions, deletions, and insertions demonstrated considerable heterogeneity between species. In particular, the pentapeptide repeat VPGVG, characteristic of all tropoelastins analyzed to date, is replaced in rat tropoelastin by a repeating pentapeptide, IPGVG. The hexapeptide repeat VGVAPG, the bovine elastin receptor binding peptide, is not encoded by rat tropoelastin cDNAs. Variations in coding sequence between rat tropoelastin cDNA clones were also found which may represent mRNA heterogeneity produced by alternative splicing of the rat tropoelastin pre-mRNA.
A signal abnormality index for arterial blood pressure waveforms (2006)

Fidelity of the arterial blood pressure (ABP) waveform is often critical to computations that involve processing of the waveform. The ABP waveform may be used for cardiac output (CO) estimation, suppression of ECG-based false alarms, and tracking long term trends such as mean pressure. An abnormal ABP waveform may cause these applications to give undesirable results. In this paper, we present a signal abnormality index (SAI) algorithm that detects abnormal beats in ABP waveforms. The algorithm flags ABP beats by intelligently setting constraints on physiologic, noise/artifact, and beat-to-beat variation values. Compared to an expert annotator, the algorithm’s sensitivity=1, specificity=0.91, positive predictive value=0.73, and negative predictive value=1. We also perform a sensitivity analysis to show SAI’s robustness. Finally, we use SAI to identify clean ABP segments from our study population and show that CO estimation error is 30 % less in the clean subset than in the entire population. 1.
Time‐of‐flight MR angiography with Gd‐DTPA hexamethylene diamine co‐polymer blood pool contrast agent: Comparison of enhanced MRA and conventional angiography for arterial stenosis induced in rabbits (2000)

Vascular stenoses were induced in the external iliac arteries of New Zealand white rabbits by a combination of hypercholesterolemic diet and repeat balloon injury. Two-dimensional (2D) and three-dimensional (3D) time-of-flight (TOF) magnetic resonance angiography (MRA) was performed with a specifically designed phased array coil in a 1.5 T system. Enhancement with gadolinium-diethylene triamine pentaacetic acid (Gd-DTPA) hexamethylene diamine co-polymer (Nycomed: NC 22181), a blood pool MR contrast agent, was measured after contrast administration and compared with pre-contrast images at the same levels. Vessel diameter measurements were obtained at multiple levels and compared with comparable levels on conventional angiograms of the same animals. Stable enhancement, averaging 227% above baseline, was observed with the 3D TOF MRA over the 40 minutes of this study. Enhancement was not observed with the 2D TOF technique. Measurement of the smallest vessels in this study with 3D TOF MRA was slightly improved following contrast enhancement, although both pre- and post-contrast diameter measurements tended to underestimate the assumed true vessel diameter. Thus, Gd-DTPA hexamethylene diamine co-polymer (Nycomed: NC 22181), a blood pool MR contrast agent, produces significant, stable enhancement with the 3D TOF technique and may improve MRA measurement of small vessels. J. Magn. Reson. Imaging 2000;11:638–646. © 2000 Wiley-Liss, Inc.
Using Kullback-Leibler Divergence to Analyze the Performance of Collaborative Positioning (2016)

Geolocation accuracy is a very crucial and a life-or-death factor for rescue teams. Natural disasters or man-made disasters are just a few convincing reasons why fast and accurate position location is necessary. One way to unleash the potential of positioning systems is through the use of collaborative positioning. It consists of simultaneously solving for the position of two nodes that need to locate themselves. Although the literature has addressed the benefits of collaborative positioning in terms of accuracy, a theoretical foundation on the performance of collaborative positioning has been disproportionally lacking. This dissertation uses information theory to perform a theoretical analysis of the value of collaborative positioning.The main research problem addressed states: 'Is collaboration always beneficial? If not, can we determine theoretically when it is and when it is not?' We show that the immediate advantage of collaborative estimation is in the acquisition of another set of information between the collaborating nodes. This acquisition of new information reduces the uncertainty on the localization of both nodes. Under certain conditions, this reduction in uncertainty occurs for both nodes by the same amount. Hence collaboration is beneficial in terms of uncertainty. However, reduced uncertainty does not necessarily imply improved accuracy. So, we define a novel theoretical model to analyze the improvement in accuracy due to collaboration. Using this model, we introduce a variational analysis of collaborative positioning to deter- mine factors that affect the improvement in accuracy due to collaboration. We derive range conditions when collaborative positioning starts to degrade the performance of standalone positioning. We derive and test criteria to determine on-the-fly (ahead of time) whether it is worth collaborating or not in order to improve accuracy. The potential applications of this research include, but are not limited to: intelligent positioning systems, collaborating manned and unmanned vehicles, and improvement of GPS applications.
Three-level H-bridge flying capacitor converter voltage balance dynamics analysis (2009)

Flying capacitor converter is an attractive choice due to its natural voltage balance property. Voltage balance dynamics analytical research methods reported to date are essentially based on a frequency domain analysis. They require high mathematical skills and the solutions are not truly analytical and difficult to use in an everyday practice. In this paper, a straightforward time domain approach based on stitching of consecutive switching intervals analytical solutions is applied to an H-bridge three-level flying capacitor converter. Small parameter analysis yields simple accurate expressions for voltage balance time constants revealing their dependences on load parameters, carrier frequency, and normalized voltage command. Voltage balance dynamics for AC PWM is obtained by averaging DC PWM exponential term decay factors on AC fundamental period.
Fast Object Detection Using Multistage Particle Window Deformable Part Model (2014)

For object detection, evaluating all sliding windows at various scales draws a computational efficiency issue. In this paper, we propose a fast object detection framework using the multistage particle window strategy to accelerate the cascade deformable part model (DPM). Coupling this strategy with the proposed early jump scheme, adaptive particle window generation, and efficient preprocessing, we demonstrate that the proposed method runs 34.5 times faster than the conventional DPM to detect objects in images, and is able to efficiently detect vehicles and pedestrians in on-road videos.
Sequestration of TT Virus of Restricted Genotypes in Peripheral Blood Mononuclear Cells (2000)

Peripheral blood mononuclear cells (PBMC) harbored TT virus (TTV) of genotypes (3 and 4) different from those (1 and 2) of free virions in plasma of the same individuals. PBMC may act as a reservoir, and TTV of particular genotypes might have tropism for hematopoietic cells.
Cortical Vascular Blood Flow Pattern By Laser Speckle Imaging (2005)

The cor tical vascular blood flow pattern is associated with the functional response in cerebral cortex. The pattern of the vascular blood flow can be used to study the spatiotemporal activities of the somatosensory center and the diagnosis of the focal stroke or ischemia. In this present study, tempor al laser speckle analysis is used to obtain the cortical blood flow information. By centerline modeling method based on ridge tracking, we extracted the cortical vessels. By fusing with the laser speckle contrast results, we obtained the image of the cortical vascular blood flow pattern in which both the vessels and the blood velocity can be visualized.
WSI architecture of a neurocomputer module (2002)

Discusses application and technology related constraints on the implementation of neurocomputing systems on a wafer. The resulting neurocomputer architecture builds on the experience obtained with a 42 cm/sup 2/ soft-configured chip which carries a 2-dimensional array of multipliers in CMOS. The architecture is specially adapted to pattern recognition of video images by means of generalized multilayer-perceptrons.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>