gebhart/patrepeval huggingface dataset:
<title>Review of watermarking and the importance of perceptual modeling</title> (1997)

A watermark embeds an imperceptible signal into data such as audio, video and images, for a variety of purposes, including captioning and copyright control. In this paper, we first outline the desirable characteristics of digital watermarks. Previous work in digital watermarking is then reviewed. Early work identified redundant properties of an image (or its encoding) that can be modified to encode watermarking information. The early emphasis was on hiding data, since the envisioned applications were not concerned with signal distortions or intentional tampering that might remove a watermark. However, as watermarks are increasingly used for purposes of copyright control, robustness to common signal transformations and resistance to tampering have become important considerations. Researchers have recently recognized the importance of perceptual modeling and the need to embed a signal in perceptually significant regions of an image, especially if the watermark is to survive lossy compression. However, this requirement conflicts with the need for the watermark to be imperceptible. Several recent approaches that address these issues are discussed.
A fast method for designing time-optimal gradient waveforms for arbitrary k-space trajectories (2008)

A fast and simple algorithm for designing time-optimal waveforms is presented. The algorithm accepts a given arbitrary multidimensional k-space trajectory as the input and outputs the time-optimal gradient waveform that traverses k-space along that path in minimum time. The algorithm is noniterative, and its run time is independent of the complexity of the curve, i.e., the number of switches between slew-rate limited acceleration, slew-rate limited deceleration, and gradient amplitude limited regions. The key in the method is that the gradient amplitude is designed as a function of arc length along the k-space trajectory, rather than as a function of time. Several trajectory design examples are presented.
Overload traffic management for sensor networks (2007)

There is a critical need for new thinking regarding overload traffic management in sensor networks. It has now become clear that experimental sensor networks (e.g., mote networks) and their applications commonly experience periods of persistent congestion and high packet loss, and in some cases even congestion collapse. This significantly impacts application fidelity measured at the physical sinks, even under light to moderate traffic loads, and is a direct product of the funneling effect ; that is, the many-to-one multihop traffic pattern that characterizes sensor network communications. Existing congestion control schemes are effective at mitigating congestion through rate control and packet drop mechanisms, but do so at the cost of significantly reducing application fidelity measured at the sinks. To address this problem we propose to exploit the availability of a small number of all wireless, multiradio virtual sinks that can be randomly distributed or selectively placed across the sensor field. Virtual sinks are capable of siphoning off data events from regions of the sensor field that are beginning to show signs of high traffic load. In this paper, we present the design, implementation, and evaluation of Siphon , a set of fully distributed algorithms that support virtual sink discovery and selection, congestion detection, and traffic redirection in sensor networks. Siphon is based on a Stargate implementation of virtual sinks that uses a separate longer range radio network (based on IEEE 802.11) to siphon events to one or more physical sinks, and a short-range mote radio to interact with the sensor field at siphon points. Results from analysis, simulation and an experimental 48 Mica2 mote testbed show that virtual sinks can scale mote networks by effectively managing growing traffic demands while minimizing any negative impact on application fidelity. Additionally, we show the scheme is competitive with respect to energy consumption compared to a network composed of only motes.
Structural and biochemical studies of HCMV gH/gL/gO and Pentamer reveal mutually exclusive cell entry complexes (2015)

Human cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and the leading viral cause of birth defects after congenital infection. The glycoprotein complexes gH/gL/gO and gH/gL/UL128/UL130/UL131A (Pentamer) are key targets of the human humoral response against HCMV and are required for HCMV entry into fibroblasts and endothelial/epithelial cells, respectively. We expressed and characterized soluble forms of gH/gL, gH/gL/gO, and Pentamer. Mass spectrometry and mutagenesis analysis revealed that gL-Cys144 forms disulfide bonds with gO-Cys351 in gH/gL/gO and with UL128-Cys162 in the Pentamer. Notably, Pentamer harboring the UL128-Cys162Ser/gL-Cys144Ser mutations had impaired syncytia formation and reduced interference of HCMV entry into epithelial cells. Electron microscopy analysis showed that HCMV gH/gL resembles HSV gH/gL and that gO and UL128/UL130/UL131A bind to the same site at the gH/gL N terminus. These data are consistent with gH/gL/gO and Pentamer forming mutually exclusive cell entry complexes and reveal the overall location of gH/gL-, gH/gL/gO-, and Pentamer-specific neutralizing antibody binding sites. Our results provide, to our knowledge, the first structural view of gH/gL/gO and Pentamer supporting the development of vaccines and antibody therapeutics against HCMV.
Molecular interactions of complement receptors on B lymphocytes: a CR1/CR2 complex distinct from the CR2/CD19 complex. (1991)

The complement system augments the humoral immune response to low concentrations of antigen. This effect may be partly mediated by complement receptors on the surface of B lymphocytes that bind immunogenic complexes bearing fragments of C3 and C4. We have shown by immunoprecipitation analysis that the two complement receptors expressed by B lymphocytes, complement receptor 1 (CR1) and CR2, form a detergent-sensitive complex on the surface of tonsillar B lymphocytes and on K562 erythroleukemia cells that were co-transfected with cDNAs encoding CR1 and CR2. The CR1/CR2 complex is distinct from the CR2/CD19 complex and may assist B cell activation by efficiently capturing C3b-containing immunogens and maintaining such immunogens on the B cell after CR1 and factor I-mediated cleavage to iC3b and C3dg. The complement activating immunogen may then trigger signal transduction by the CR1/CR2 complex, the CR2/CD19 complex, or membrane immunoglobulin.
[The relationship between viral hepatitis and primary liver cancer in four areas of China]. (1997)

To investigate the relationship between hepatitis B, C and G and primary liver cancer (PLC), both population-based and hospital-based case-control studies were conducted in four areas of China. The prevlence rates of HBsAg in 359 pairs of PLC cases and controls were 66.3% and 23.4% (OR = 6.60, PAR = 55.5%), respectively; the prevalence of anti-HCV in 340 pairs of PLC cases and controls were 17.9% and 6.5% (OR = 3.31, PAR = 12.4%), respectively. When both markers were positive, the OR was higher than their multiple effect of HBsAg and anti-HCV. In the Haimen Case-control study, serum HGV-RNA was detected in 11 of the 50 PLC cases, compared to 5 of the 50 controls matched with age and sex (P > 0.05). These data suggested that HBV might have played a more important role than HCV and HGV in the development of PLC in China.
Nanosecond pulsed electric field generators for the study of subcellular effects (2005)

Modeling and experimental studies have shown that pulsed electric fields of nanosecond duration and megavolt per meter amplitude affect subcellular structures but do not lead to the formation of large pores in the outer membrane. This "intracellular electromanipulation" requires the use of pulse generators which provide extremely high power but low energy pulses. In this study, we describe the concept of the required pulsed power sources, their design, operation, and the necessary diagnostics. Two types of pulse generators based on the Blumlein line principle have been developed and are described here. One system is designed to treat a large number of cells in cuvettes holding volumes from 0.1 to 0.8 ml. Pulses of up to 40 kV amplitude, with a duration of 10 ns and a rise time close to 1 ns can be applied to the cuvette. For an electrode gap of 1 mm this voltage corresponds to an average electric field of 40 MV/m. The second system allows for real time observation of individual cells under a microscope. It generates pulses of 10-300 ns duration with a rise time of 3.5 ns and voltage amplitudes up to 1 kV. Connected to a microreactor with an electrode gap of 100 microm, electric fields up to 10 MV/m are applied.
Transgenic mice expressing mutant (N279K) human tau show mutation dependent cognitive deficits without neurofibrillary tangle formation (2005)

Mutations in the tau gene, which is located on chromosome 17, were found causative for autosomal dominantly inherited frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). To determine if cognitive deficits could be caused by tau mutations, two transgenic mouse lines were generated expressing a four-repeat isoform of human tau or its mutant, containing one of the FTDP-17 mutations (WILD mice and N279K mice). In open field test, N279K mice showed hyperactivity in locomotion and rearing. In prepulse inhibition test, N279K mice but not Wild mice showed significant deficits. Both transgenic mice, especially N279K mice, showed impairment in acquisition of spatial learning in Morris water maze. Although both N279K mice and Wild mice acquired passive avoidance as well as non-transgenic mice, N279K mice but not Wild mice showed severe deficits in acquisition of active avoidance. Histological analysis of the present mutant mice did not show any signs of neurofibrillary tangle formations in the brain, and cognitive dysfunction seemed to precede such neuropathological changes or occur independently from them. The behavioral phenotype of N279K mice mimics features of human FTDP-17 and provides a basic model for elucidating mechanisms underlying cognitive deficits in not only FTDP-17, but also diverse tauopathies.
CdSe Quantum Rod Formation Aided By In Situ TOPO Oxidation (2010)

In-situ TOPO decomposition was accomplished by applying a vacuum at elevated temperatures to a precursor solution in the presence of oxygen, leading TOPO to oxidize to di-n-octylphosphinic acid (DOPA) and octylphosphonic acid (OPA). The mixed ligand system of tetradecylphosphonic acid (TDPA), DOPA and OPA produced CdSe QRs on the order of 4 nm in diameter and 20 nm in length. Solvent and ligand identification was performed by mass spectrometry and (31)P nuclear magnetic resonance spectroscopy. Transmission electron microscopy (TEM) was utilized to determine the morphology, size and crystal growth of the CdSe QRs. This method of CdSe QR synthesis is unique in that the phosphonic acids responsible for anisotropic growth are formed in situ, prior to the nucleation and growth of the nanorods. Without the oxidation of TOPO, CdSe quantum dots (QDs) were synthesized instead, as reported previously. This discovery reinforces the efficacy of DOPA and OPA molecules as critical ligands in the formation of 1-dimensional (1D) nanostructures.
A proenzyme form of human urokinase. (1982)

A culture of the human epidermoid carcinoma HEp 3 produces a plasminogen activator of Mr = 53,000 which we have purified to apparent homogeneity from serum-free conditioned medium by the combination of immunoaffinity chromatography and preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The highly purified protein has the following properties: 1) It is indistinguishable from urinary urokinase in electrophoretic mobility, in immunodiffusion, and in autoradiographically visualized tryptic peptide maps obtained from the 125I-labeled proteins. 2) The HEp 3 protein differs from urinary urokinase in the following respects: (a) although the apparent molecular weights of the two are identical (Mr = 53,000), the urinary enzyme consists of two polypeptide chains, whereas the HEp 3 protein is a single chain form. (b) Urinary urokinase can be labeled easily by incubation with radioactive diisopropylfluorophosphate but the HEp 3 protein cannot. (c) When assayed by the hydrolysis of a synthetic chromogenic peptide substrate, the HEp 3 enzyme has less than 1% of the catalytic activity of urinary urokinase. 3) On controlled exposure to plasmin, the HEp 3 protein is converted to an active enzyme that is identical with urinary urokinase in molecular weight, polypeptide chain composition, diisopropylfluorophosphate labeling, and specific catalytic activity. We conclude that the HEp 3 protein is a proenzyme that can be converted to active two-chain urokinase by plasmin, probably by a single proteolytic nick in the polypeptide chain.
Further Studies on Ethenyl and Ethynyl‐4‐phenylamino‐3‐quinolinecarbonitriles: Identification of a Subnanomolar Src Kinase Inhibitor. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Apopain/CPP32 cleaves proteins that are essential for cellular repair: a fundamental principle of apoptotic death. (1996)

Proteolysis mediated by the interleukin 1 beta-converting enzyme (ICE) homologues is an important mechanism of the apoptotic process. The ICE homologue apopain/CPP-32/Yama (subsequently referred to as apopain) cleaves poly(ADP-ribose)polymerase (PARP) early during apoptosis. Additional apoptosis-specific protein cleavages have been observed in which the direct involvement of ICE-like proteases has been postulated. These substrates include the 70-kD protein component of the U1-ribonucleoprotein (U1-70kD), and the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs). The present studies demonstrate that U1-70kD and DNA-PKcs are excellent substrates for apopain, with cleavage occurring at sites that are highly similar to the cleavage site within PARP. The fragments generated from isolated protein substrates by apopain are identical to those observed in intact apoptotic cells, in apoptotic cell extracts, and in normal cell extracts to which apopain has been added. Like PARP, cleavage of these substrates in apoptotic cell extracts is abolished by nanomolar concentrations of Ac-DEVD-CHO and micromolar amounts of Ac-YVAD-CHO, confirming the involvement of apopain or an apopain-like activity. We propose that a central function of apopain or similar homologues in apoptosis is the cleavage of nuclear repair proteins, thereby abolishing their critical homeostatic functions.
Distraction Osteogenesis for Nonunion After High Tibial Osteotomy (2002)

The purpose of this study was to determine whether distraction osteogenesis can be used to treat hypertrophic nonunion associated with angular deformity and shortening after Coventry style high tibial osteotomy. Five consecutive patients were retrospectively reviewed. In all patients the alignment had collapsed into excessive varus or valgus and leg length discrepancy was present. The leg length discrepancy, malalignment, and nonunion were treated simultaneously with distraction. Union was achieved by the time of fixator removal, which averaged 4.4 months. The Hospital for Special Surgery knee score significantly improved from 42 to 89. The mechanical axis deviation significantly improved by 5 cm. The coronal plane deformity significantly improved by 13 degrees, and leg length discrepancy improved significantly from 2.3 to 0.5 cm. Metaphyseal bone stock increased by 43%, and the Insall-Salvati ratio increased from 1.1 to 1.2 and remained within normal limits. All patients were satisfied with the procedure, and none have had or need a total knee replacement at an average followup of 4 years. Distraction osteogenesis of nonunion after high tibial osteotomy is a minimally invasive and successful procedure. It leads to bony union with correction of deformity and leg length discrepancy and prevents the need for total knee replacement at intermediate-term followup. The increase in metaphyseal bone stock may make total knee replacement technically easier.
Multiplexed Target Detection Using DNA-Binding Dye Chemistry in Droplet Digital PCR (2013)

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.
Expression of GD2 and GD3 Gangliosides in Human Embryonic Neural Stem Cells (2011)

NSCs (neural stem cells) are undifferentiated neural cells endowed with a high potential for proliferation and a capacity for self-renewal with retention of multipotency to differentiate into neurons and glial cells. It has been recently reported that GD3, a b-series ganglioside, is a marker molecule for identifying and isolating mouse NSCs. However, the expression of gangliosides in human NSCs is largely unknown. In the present study, we analysed the expression of gangliosides, GD2 and GD3, in human NSCs that were isolated from human brains at gestational week 17 in the form of neurospheres, which are floating clonal aggregates formed by NSCs in vitro. Employing immunocytochemistry, we found that human NSCs were strongly reactive to anti-GD2 antibody and relatively weakly reactive to anti-GD3 antibody. Treatment of these cells with an organic solvent such as 100% methanol, which selectively removes glycolipids from plasma membrane, abolished the immunoreactivity with those antibodies, indicating that the reactivity was due to GD2 and GD3, but not to GD2-/GD3-like glycoproteins or proteoglycans. The immunoreactivity of human NSCs to antibody against SSEA-1 (stage-specific embryonic antigen-1), a well-known carbohydrate antigen of NSCs, was not decreased by the treatment with 100% methanol, indicating that SSEA-1 is mainly carried by glycoproteins and/or proteoglycans in human NSCs. Our study suggests that GD2 and GD3 can be marker gangliosides for identifying human NSCs.
Multidimensional morphable models (2002)

We describe a flexible model for representing images of objects of a certain class, known a priori, such as faces, and introduce a new algorithm for matching it to a novel image and thereby performing image analysis. We call this model a multidimensional morphable model or just a, morphable model. The morphable model is learned from example images (called prototypes) of objects of a class. In this paper we introduce an effective stochastic gradient descent algorithm that automaticaIly matches a model to a novel image by finding the parameters that minimize the error between the image generated by the model and the novel image. Two examples demonstrate the robustness and the broad range of applicability of the matching algorithm and the underlying morphable model. Our approach can provide novel solutions to several vision tasks, including the computation of image correspondence, object verification, image synthesis and image compression.
An amber suppressor tRNA gene derived by site-specific mutagenesis: cloning and function in mammalian cells. (1982)

We describe the synthesis, cloning, expression, and in vivo function of a suppressor tRNA gene in mammalian cells. By using "primer-directed mutagenesis" on a Xenopus laevis tyrosine tRNA gene cloned into the recombinant single-strand phage M13mp5, we have generated an amber suppressor tRNA gene that has a nucleotide change--GTA leads to CTA--in the anticodon sequence. The suppressor (Su) tRNA gene was introduced into monkey kidney cells (CV-1) by using simian virus 40 (SV40) DNA as vector (SV40-tRNATyrSu+). CV-1 cells infected with virus containing the mutant, but not the wild-type, tRNA gene produce a functional amber suppressor tRNA as indicated by suppression of amber mutations in co-infecting adenovirus serotype 2-SV40 hybrids. Further evidence that suppression of these amber mutations is tRNA mediated was derived by isolation of total tRNA from CV-1 cells infected with the SV40-tRNATyr (Su+) recombinant and its use in demonstration of read through of an amber codon during in vitro translation of tobacco mosaic virus RNA in reticulocyte extracts. Interestingly, the amplification of an amber suppressor gene in CV-1 cells does not interfere with SV40 production, suggesting that suppression of amber codons may not be very deleterious to mammalian cell metabolism.
Cancer Gene Therapy with Tissue Inhibitors of Metalloproteinases (TIMPs) (2002)

Matrix metalloproteinases (MMPs) are of crucial importance for the invasive behavior of primary tumors and their metastases. MMP activity is regulated by the four naturally occurring tissue inhibitors of metalloproteinases (TIMPs). It has been shown that overexpression of TIMPs in tumors of various origins leads to reduced tumor growth and formation of metastases. More recently, antitumor efficacy by in vivo gene transfer of TIMPs has been reported in several clinically relevant animal models. This review analyses the therapeutic potential of the TIMPs from a cancer gene therapeutic point of view with particular emphasis on cell culture and in vivo data.
Suppression of monocyte function and differential regulation of IL-1 and IL-1ra by IL-4 contribute to resolution of experimental arthritis. (1993)

IL-4 has diverse effects on hematopoietic cells, including the ability to suppress certain mononuclear cell functions. To evaluate the effect of IL-4 on the evolution of acute and chronic arthritis, murine recombinant IL-4 was administered systemically to animals receiving an arthropathic dose of group A streptococcal cell wall fragments. Daily treatment with IL-4 had a minimal effect on the acute phase, but significantly suppressed the chronic, destructive phase. By 4 wk after initiation of disease, the articular index of IL-4-treated animals was reduced > 60% (articular index = 4 +/- 0.9) compared with the untreated rats (11.5 +/- 0.48, p < 0.001). A substantial decrease in the influx of inflammatory cells and virtual elimination of pannus and erosions occurred after IL-4 therapy. Associated with the reduced accumulation of mononuclear leukocytes was a decrease in their proinflammatory functions including cytokine production and reactive oxygen intermediate metabolism. These observations are consistent with the selective effects of IL-4 on phagocytic cell function demonstrated in vitro. Furthermore, IL-4 induced gene expression for IL-1ra, a protein that antagonizes the action of IL-1 by binding to the IL-1 receptor without agonist activity. Through an expanding spectrum of effects on monocyte-macrophage phenotypic and functional parameters, IL-4 is emerging as an important inhibitor of cell-mediated immune responses and pathogenic processes.