gebhart/patrepeval huggingface dataset:
Recombinant antibody 2G12 produced in maize endosperm efficiently neutralizes HIV‐1 and contains predominantly single‐GlcNAc <i>N</i>‐glycans (2007)

Antibody 2G12 is one of a small number of human immunoglobulin G (IgG) monoclonal antibodies exhibiting potent and broad human immunodeficiency virus-1 (HIV-1)-neutralizing activity in vitro, and the ability to prevent HIV-1 infection in animal models. It could be used to treat or prevent HIV-1 infection in humans, although to be effective it would need to be produced on a very large scale. We have therefore expressed this antibody in maize, which could facilitate inexpensive, large-scale production. The antibody was expressed in the endosperm, together with the fluorescent marker protein Discosoma red fluorescent protein (DsRed), which helps to identify antibody-expressing lines and trace transgenic offspring when bred into elite maize germplasm. To achieve accumulation in storage organelles derived from the endomembrane system, a KDEL signal was added to both antibody chains. Immunofluorescence and electron microscopy confirmed the accumulation of the antibody in zein bodies that bud from the endoplasmic reticulum. In agreement with this localization, N-glycans attached to the heavy chain were mostly devoid of Golgi-specific modifications, such as fucose and xylose. Surprisingly, most of the glycans were trimmed extensively, indicating that a significant endoglycanase activity was present in maize endosperm. The specific antigen-binding function of the purified antibody was verified by surface plasmon resonance analysis, and in vitro cell assays demonstrated that the HIV-neutralizing properties of the maize-produced antibody were equivalent to or better than those of its Chinese hamster ovary cell-derived counterpart.
Type 1 diabetes: recent developments (2004)

Type 1 diabetes is one of the most common chronic childhood illnesses, affecting 18 to 20 per 100 000 children a year in the United Kingdom. 1 The American Diabetes Association committee recommends the term type 1A diabetes for immune mediated diabetes with its destruction of the islet cells of the pancreas. 2 Nonimmune mediated diabetes with severe insulin deficiency is termed type 1B. In this review, we will use the term type 1 diabetes to refer to immune mediated type 1A diabetes. At present, the development of type 1 diabetes is a life sentence to a difficult therapeutic regimen that is only partially effective in preventing acute and chronic complications. We will concentrate here on recent advances in our understanding of the epidemiology, pathogenesis, prediction, and prevention of type 1 diabetes and new treatments for the disease.
Towards the complete elimination of gate/switch level simulations (2004)

This paper presents the reasoning behind eliminating full-chip gate/switch-level simulations for microprocessors/digital system designs and utilizing RTL models for the purpose, provided formal boolean equivalence between RTL and gate/switch-level models have been established using symbolic simulation for all blocks that comprise the chip. No logic bug should go undetected if only RTL models are used for full chip simulations provided existing design methodologies are enhanced to incorporate a constraints checking flow coupled with a rigorous circuit metastability/contention prevention flow.
Parity simulation of static power conversion systems (1977)

An analog/digital simulation technique employing a high degree of parity between the topology of the model and the topology of the modeled system is described. The existence of such topological Isomorphism allows a true "breadboard" approach to simulation. The application, components, and versatility of the system are discussed. Results of a current commutated chopper simulation are presented and compared with the actual circuit behavior.
Methylation-Dependent Transition Rates Are Dependent on Local Sequence Lengths and Genomic Regions (2006)

Recently, Fryxell and Moon (2005) examined methylation-dependent transition rates (5mC deamination rates), which were calculated by the difference between the CpG transition and GpC transition rates, using 4,437 transition mutations in CpG or GpC dinucleotides. They concluded that 5mC deamination rates were highly dependent on local GC content but not on local sequence lengths over which GC content was calculated or the genomic regions where the mutations occurred. Here, we reexamined these statements by using 292,216 CpG-->TpG/CpA and GpC-->GpT/ApC mutations, an increase of 66 times as much data. Contrary to Fryxell and Moon's conclusions, our analysis indicated that 5mC deamination rates in the human genome were dependent on both the local sequence length and the genomic region. Some explanations for their conclusions were provided.
Delineation of three subsets of class I human T antigens (HTA) on Molt-4 cells: serologic and regulatory relationship to HLA class I antigens. (1985)

Three subsets of class I human T antigens (HTA) were serologically identified on the surface of the Molt-4 T lymphoma cell line. The HTA 1 subset is defined by NAI/34, D47, or 10H3.9 cross-reactive m.Ab. and by BL6 m.Ab. The HTA 2 and HTA 3 subsets are defined by M241 and 4A7.6 m.Ab., respectively. We obtained no evidence of any additional HTA subset. The different HTA antigens share only few epitopes with human leukocyte antigens (HLA-A, -B, and -C). Interestingly, these epitopes all belong to the same cluster defined on HLA class I molecules, but differ from one HTA subset to another. These results would therefore suggest that HTA and HLA class I antigens display a limited structural homology, but have a conserved epitopic area whose detailed structure differs for each HTA subset. Furthermore, the cell surface expression of each HTA class I molecule type is differently enhanced by natural interferon (IFN)-alpha or -gamma. This result additionally supports the serologic delineation of HTA subsets, and suggests that the corresponding genes in Molt-4 cells, are subjected to distinct regulations.
Efficient determination of feedback DAC errors for digital correction in &#x0394;&#x03A3; A/D converters (2010)

Feedback DAC errors in a ΔΣ analog to digital converter are determined by measuring the idle channel output and removing the DAC elements one by one. This method requires simple computation, does not add excess loop delay, and requires no reconfiguration of the ΔΣ modulator. The errors so determined can be used to correct the output codes in the digital domain or the DAC elements in the analog domain. This technique is a useful alternative to the popular dynamic element matching at high speeds as excess delay cannot be tolerated and at low oversampling ratios where DEM can result in tones. Simulation results indicate that the correction values can be obtained to an accuracy that is sufficient to reduce noise and distortion to nearly ideal levels.
Coronary artery imaging using contrast‐enhanced 3D segmented EPI (2001)

The purpose of the work was to evaluate the effectiveness of extracellular contrast media in improving MR coronary angiography using breath-hold segmented echo-planar imaging (SEPI). Two protocols were designed to optimize the inversion recovery-prepared contrast-enhanced SEPI method. In 15 healthy volunteers, significant improvements in signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), vessel sharpness, and length of visualization were observed post-contrast. The method with two targeted scans to cover the left and right arteries, respectively, following separate 20-mL contrast injections, was found to yield thinner slices and longer right coronary artery (RCA) visualization than a single scan following a 40-mL contrast injection without compromising SNR and CNR. In conclusion, extracellular contrast media substantially improves the delineation of coronary arteries with SEPI. J. Magn. Reson. Imaging 2001;13:676-681.
A DNA damage response in <i>Escherichia coli</i> involving the alternative sigma factor, RpoS (2009)

We isolated an Escherichia coli mutant in the iraD gene, sensitive to various forms of DNA damage. Our data are consistent with the function of IraD to promote accumulation of the alternative transcription sigma factor, RpoS, by binding to the adaptor RssB protein that targets RpoS for degradation. Our results demonstrate the physiological importance of this mode of regulation for DNA damage tolerance. Although RpoS is best known for its regulation of genes induced in stationary phase, our work underscores the importance of the RpoS regulon in a DNA damage response in actively growing cells. We show that iraD transcription is induced by DNA damage by a mechanism independent of the SOS response. The IraD and SOS regulatory pathways appear to act synergistically to ensure survival of cells faced with oxidative or DNA damaging stress during cellular growth.
Suboptimum detection of trellis-coded CPM for transmission on bandwidth- and power-limited channels (1991)

The authors consider a communication scheme based on continuous phase modulated (CPM) signals used in conjunction with trellis-coded modulation (TCM) for transmission over a channel affected by Gaussian noise and fading. This scheme provides a power saving due to the coding gain of TCM and a reduced bandwidth occupancy due to the features of CPM signals. Moreover, CPM provides constant-envelope signals. To keep the complexity of the receiver manageable and to be able to use interleaving/deinterleaving techniques to spread the fade bursts, suboptimal detection schemes must be used. Two such schemes, based on coherent and noncoherent detection of CPM, are considered. Their performance is evaluated by computing the computational cutoff rate of the discrete channel generated by CPM.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Targeting Fatty Acid Synthase in Breast and Endometrial Cancer: An Alternative to Selective Estrogen Receptor Modulators? (2006)

There is an urgent need to identify and develop a new generation of therapeutic agents and systemic therapies targeting the estradiol (E2)/estrogen receptor (ER) signaling in breast cancer. In this regard, new information on the mechanisms of E2/ER function and/or cross talk with other prosurvival cascades should provide the basis for the development of other ideal anti-E2 therapies with the intent to enhance clinical efficacy, reduce side effects or both. Our very recent assessment of the mechanisms by which cancer-associated increased lipogenesis and its inhibition alters the E2/ER signaling discovered that fatty acid synthase (FASN), the enzyme catalyzing the terminal steps in the de novo biosynthesis of long-chain fatty acids, differentially modulates the state of sensitivity of breast and endometrial cancer cells to E2-stimulated ER transcriptional activation and E2-dependent cell growth and survival: 1) pharmacological inhibition of FASN activity induced a dramatic augmentation of E2-stimulated ER-driven gene transcription, whereas interference (RNAi)-mediated silencing of FAS gene expression drastically lowered E2 requirements for optimal activation of ER transcriptional activation in breast cancer cells; conversely, pharmacological and RNAi-induced inhibition of FASN worked as an antagonist of E2- and tamoxifen-dependent ER transcriptional activity in endometrial adenocarcinoma cells; 2) pharmacological and RNAi-induced inhibition of FASN synergistically enhanced E2-mediated down-regulation of ER protein and mRNA expression in breast cancer cells, whereas specific FASN blockade resulted in a marked down-regulation of E2-stimulated ER expression in endometrial cancer cells; and 3) FASN inhibition decreased cell proliferation and cell viability by promoting apoptosis in hormone-dependent breast and endometrial cancer cells. In this review we propose that, through a complex mechanism involving the regulation of MAPK/ER cross talk as well as critical E2-related proteins including the Her-2/neu (erbB-2) oncogene and the cyclin-dependent kinase inhibitors p21(WAF1/CIP1) and p27(Kip1), a previously unrevealed connection exists between FASN and the genomic and nongenomic ER activities in breast and endometrial cancer cells. From a clinical perspective, we suggest that if chemically stable FASN inhibitors or cell-selective systems able to deliver RNAi targeting FASN gene demonstrate systemic anticancer effects of FASN inhibition in vivo, additional preclinical studies to characterize their anti-breast cancer actions should be of great interest as the specific blockade of FASN activity may also provide a protective means against endometrial carcinoma associated with tamoxifen-based breast cancer therapy.
Surface periodic poling in lithium niobate and lithium tantalate (2005)

Periodic poling of lithium niobate crystals (PPLN) by means of electric field has revealed the best technique for finely tailoring PPLN structures and parameters, which play a central role in many current researches in the field of nonlinear integrated optics. Besides the most studied technique of bulk poling, recently a novel technique where domain inversion occurs just in a surface layer using photoresist or silica masks has been devised and studied. This surface periodic poling (SPP) approach is best suited when light is confined in a thin surface guiding layer or stripe, as in the case of optical waveguide devices. Also, we found that SPP respect to bulk poling offers two orders of magnitude reduction on the scale of periodicity, so that even nanostructures can be obtained provided a high resolution holographic mask writing technique is adopted. We were able to demonstrate 200 nm domain size, and also good compatibility with alpha-phase proton exchange channel waveguide fabrication. Our first experiments on lithium tantalate have also shown that the SPP technology appears to be applicable to this crystal (SPPLT), whose properties can allow to overcome limitations such as optical damage or UV absorption still present in PPLN devices. Finally, the issue of SPP compatibility with proton exchange waveguide fabrication will be addressed.
Angiotensin II Receptor Antagonists: The Prototype Losartan (1996)

Losartan, the first angiotensin II receptor antagonist to receive approval for use in the US, appears to be an effective new antihypertensive agent with an adverse effect profile similar to that of placebo. Losartan may be an alternative for patients who cannot tolerate ACE inhibitors. However, the effect of losartan on mortality remains to be evaluated. The role of the angiotensin II receptor antagonists in areas such as ventricular hypertrophy, renal function, and heart failure has yet to be determined.
Surface photometry of elliptical galaxies (1978)

The paper presents photographic surface photometry for 16 giant elliptical galaxies and one S0. Results are presented as radial profiles along the direction halfway between the major and minor axes and as ellipticities as a function of radius. Similarities and differences among the radial profiles of the galaxies, selected from the Minkowski observing list, are described. Ellipticities decrease outward in some galaxies and increase outward in others. The techniques and the reliability of the photometry are discussed.
Expanding the DOPA Universe with Genetically Encoded, Mussel‐Inspired Bioadhesives for Material Sciences and Medicine (2019)

Catechols are a biologically relevant group of aromatic diols that have attracted much attention as mediators of adhesion of "bio-glue" proteins in mussels of the genus Mytilus. These organisms use catechols in the form of the noncanonical amino acid l-3,4-dihydroxyphenylalanine (DOPA) as a building block for adhesion proteins. The DOPA is generated post-translationally from tyrosine. Herein, we review the properties, natural occurrence, and reactivity of catechols in the design of bioinspired materials. We also provide a basic description of the mussel's attachment apparatus, the interplay between its different molecules that play a crucial role in adhesion, and the role of post-translational modifications (PTMs) of these proteins. Our focus is on the microbial production of mussel foot proteins with the aid of orthogonal translation systems (OTSs) and the use of genetic code engineering to solve some fundamental problems in the bioproduction of these bioadhesives and to expand their chemical space. The major limitation of bacterial expression systems is their intrinsic inability to introduce PTMs. OTSs have the potential to overcome these challenges by replacing canonical amino acids with noncanonical ones. In this way, PTM steps are circumvented while the genetically programmed precision of protein sequences is preserved. In addition, OTSs should enable spatiotemporal control over the complex adhesion process, because the catechol function can be masked by suitable chemical protection. Such caged residues can then be noninvasively unmasked by, for example, UV irradiation or thermal treatment. All of these features make OTSs based on genetic code engineering in reprogrammed microbial strains new and promising tools in bioinspired materials science.
Kalinin is abnormally expressed in epithelial basement membranes of Herlitz's junctional epidermolysis bullosa patients (1992)

Kalinin is an extracellular adhesion molecule specific to epithelial basement membranes (BM) identified as a component of anchoring filaments of hemidesmosomes. This heterotrimeric protein is synthesized by cultured normal human keratinocytes and is involved in cell attachment. In indirect immunofluorescence studies, the epidermal BM of patients with junctional epidermolysis bullosa (JEB) of Herlitz's type were found not to be reactive with the anti-kalinin monoclonal antibodies ka146 and K140 and displayed a decreased immunoreactivity to two anti-kalinin antibodies cross-reacting with K-laminin, an anchoring filament component recently described. The intrinsic defect of JEB keratinocytes in the synthesis of kalinin was further documented by indirect immunofluorescence on in vitro cultures of these cells. In non-Herlitz JEB patients, staining of BM was constantly detected. Impairment of expression of kalinin correlated with the lack of reactivity to the monoclonal antibody GB3, which detects the BM component nicein/BM600. These results clearly demonstrate a defect of kalinin expression in epithelial basement membranes of Herlitz JEB patients and suggest that kalinin may play a role in the pathogenesis of the disease. Further studies are in progress to define possible relationships between kalinin and nicein.
View Maintenance in a Warehousing Environment (1999)

A warehouse is a repository of integrated information drawn from remote data sources. Since a warehouse effectively implements materialized views, we must maintain the views as the data sources are updated. This view maintenance problem differs from the traditional one in that the view definition and the base data are now decoupled. We show that this decoupling can result in anomalies if traditional algorithms are applied. We introduce a new algorithm, ECA (for Eager Compensating Algorithm), that eliminates the anomalies. ECA is based on previous incremental view maintenance algorithms, but extra compensating queries are used to eliminate anomalies. We also introduce two streamlined versions of ECA for special cases of views and updates, and we present an initial performance study that compares ECA to a view recomputation algorithm in terms of messages transmitted, data transferred, and I/O costs.
测试 PCI Express2．0 (2009)

引言 PCI Express技术现已成为许多高性能应用（包括服务器，存储器、外设、图形应用和成像应用）进行互连的最佳选择。PCIExpress‘（PCIe’）标准是由PCI—SIG。（PCI Special In-terest Group，PCI特殊兴趣小组）开发的一个标准。
One-for-All: Grouped Variation Network-Based Fractional Interpolation in Video Coding (2018)

Fractional interpolation is used to provide sub-pixel level references for motion compensation in the interprediction of video coding, which attempts to remove temporal redundancy in video sequences. Traditional handcrafted fractional interpolation filters face the challenge of modeling discontinuous regions in videos, while existing deep learning-based methods are either designed for a single quantization parameter (QP), only generating half-pixel samples, or need to train a model for each sub-pixel position. In this paper, we present a one-for-all fractional interpolation method based on a grouped variation convolutional neural network (GVCNN). Our method can deal with video frames coded using different QPs and is capable of generating all sub-pixel positions at one sub-pixel level. Also, by predicting variations between integer-position pixels and sub-pixels, our network offers more expressive power. Moreover, we perform specific measurements in training data generation to simulate practical situations in video coding, including blurring the down-sampled sub-pixel samples to avoid aliasing effects and coding integer pixels to simulate reconstruction errors. In addition, we analyze the impact of the size of blur kernels theoretically. Experimental results verify the efficiency of GVCNN. Compared with HEVC, our method achieves 2.2% in bit saving on average and up to 5.2% under low-delay P configuration.
Fabrication of graphene quantum dots via size-selective precipitation and their application in upconversion-based DSSCs (2013)

A novel approach to synthesize highly luminescent graphene quantum dots (GQDs) with well-defined sizes was explored based on simple oxidation of herringbone-type carbon nanofibers (HCNFs) and size-selective precipitation.
Minimum mean squared error impulse noise estimation and cancellation (1995)

Impulses are infrequent bursts of high amplitude noise. A wide-band communications or data acquisition receiver has a fast sampling rate, so it can capture many samples of each impulse waveform. The arrival of an impulse can be identified by its distinct waveform and amplitude. The paper models impulse waveforms as a vector subspace of low dimension. Formulas are derived for the minimum mean squared error (MMSE) estimation of the arrival time and amplitudes of impulses, given that a set of vectors that spans the subspace is known. Formulas are also derived for the adaptive MMSE estimation of a set of vectors that spans the subspace. The values of the mean squared error (MSE) of the amplitude estimates are determined. It is shown how the theory can be used to cancel impulse noise. Correlated impulse noise arriving at a reference input can be used to estimate and cancel the primary input impulse noise. The MMSE coefficients for impulse noise cancellation are derived and presented. Simulations are presented that use the equations and methods derived in the paper for modeling and canceling impulse noise measured on copper telephone loops for asymmetric digital subscriber lines (ADSL).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ozone (O3): An Out-of-Order Flash Memory Controller Architecture (2010)

Ozone (O3) is a flash memory controller that increases the performance of a flash storage system by executing multiple flash operations out of order. In the O3 flash controller, data dependencies are the only ordering constraints on the execution of multiple flash operations. This allows O3 to exploit the multichip parallelism inherent in flash memory much more effectively than interleaving. The O3 controller also provides a prioritized handling of flash operations, equipping flash management software, such as the FTL (flash translation layer), with control knobs for managing flash operations of different time criticalities. Running a range of workloads on an FPGA implementation showed that the O3 flash controller achieves 3 to 100 percent more throughput than interleaving, with 46 to 88 percent lower response times.
Sums Involving the Inverses of Binomial Coefficients (2006)

In this paper, we compute certain sums involving the inverses of binomial coefficients. We derive the recurrence formulas for certain infinite sums related to the inverses of binomial coefficients. 1