gebhart/patrepeval huggingface dataset:
Enhanced efficiency through nuclear localization signal fusion on phage phiC31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells (2002)

The integrase of the phage PhiC31 recombines an attP site in the phage genome with a chromosomal attB site of its Streptomyces host. We have utilized the integrase-mediated reaction to achieve episomal and genomic deletion of a reporter gene in mammalian cells, and provide the first comparison of its efficiency with other recombinases in a new assay system. This assay demonstrated that the efficiency of PhiC31-integrase is significantly enhanced by the C-terminal, but not the N-terminal, addition of a nuclear localization signal and becomes comparable with that of the widely used Cre/loxP system. Furthermore, we found that the improved FLP recombinase, FLPe, exhibits only 10% recombination activity on chromosomal targets as compared with Cre, whereas the Anabaena derived XisA recombinase is essentially inactive in mammalian cells. These results provide the first demonstration that a nuclear localisation signal and its position within a recombinase can be important for its efficiency in mammalian cells and establish the improved PhiC31-integrase as a new tool for genome engineering.
Distributed algorithms for control of demand response and distributed energy resources (2011)

This paper proposes distributed algorithms for control and coordination of loads and distributed energy resources (DERs) in distribution networks. These algorithms are relevant for load curtailment control in demand response programs, and also for coordination of DERs for provision of ancillary services. Both the distributed load-curtailment and DER coordination problems can be cast as distributed resource allocation problems with constraints on resource capacity. We focus on linear iterative algorithms in which each resource j maintains a set of values that is updated to be a weighted linear combination of the resource's own previous set of values and the previous sets of values of its neighboring resources. This set of values can be used by each node to determine its own contribution to load curtailment or to resource request.
ICE: a statistical approach to identifying endmembers in hyperspectral images (2004)

Several of the more important endmember-finding algorithms for hyperspectral data are discussed and some of their shortcomings highlighted. A new algorithm - iterated constrained endmembers (ICE) - which attempts to address these shortcomings is introduced. An example of its use is given. There is also a discussion of the advantages and disadvantages of normalizing spectra before the application of ICE or other endmember-finding algorithms.
Hybrid Silicon Nanocone–Polymer Solar Cells (2012)

Recently, hybrid Si/organic solar cells have been studied for low-cost Si photovoltaic devices because the Schottky junction between the Si and organic material can be formed by solution processes at a low temperature. In this study, we demonstrate a hybrid solar cell composed of Si nanocones and conductive polymer. The optimal nanocone structure with an aspect ratio (height/diameter of a nanocone) less than two allowed for conformal polymer surface coverage via spin-coating while also providing both excellent antireflection and light trapping properties. The uniform heterojunction over the nanocones with enhanced light absorption resulted in a power conversion efficiency above 11%. Based on our simulation study, the optimal nanocone structures for a 10 μm thick Si solar cell can achieve a short-circuit current density, up to 39.1 mA/cm(2), which is very close to the theoretical limit. With very thin material and inexpensive processing, hybrid Si nanocone/polymer solar cells are promising as an economically viable alternative energy solution.
Low-density-lipoprotein binding by mast-cell granules. Demonstration of binding of apolipoprotein B to heparin proteoglycan of exocytosed granules (1987)

To study the interaction between low-density lipoprotein (LDL) and granules from rat serosal mast cells in vitro, mast cells were stimulated with the degranulating agent 48/80 to induce exocytosis of the secretory granules. Subsequent incubation of the exocytosed granules with 125I-LDL resulted in binding of the labelled LDL to the granules. When increasing amounts of agent 48/80 were added to mast-cell suspensions, a dose-dependent release of granules was observed and a parallel increase in the amount of 125I-LDL bound to granules resulted. 125I-LDL bound to a single class of high-affinity binding sites on the granules. At saturation, 105 ng of LDL were bound per microgram of granule protein. The lipoprotein binding to mast-cell granules was apolipoprotein(apo)-B + E-specific. Thus 125I-LDL binding to the granules was effectively compared for by LDL (apo-B) or by dimyristoyl phosphatidylcholine vesicles containing apo-E, but not by high-density lipoprotein (HDL3) containing apo-AI as their major protein component. Neutralization by acetylation of the positively charged amino groups of apo-B of LDL or presence of a high ionic strength in the incubation medium prevented LDL from binding to the granules, indicating the presence of ionic interactions between the positively charged amino acids of LDL and negatively charged groups of the granules. It could be demonstrated that LDL bound to the negatively charged heparin proteoglycan of the granules. Thus treatment of granules with heparinase resulted in loss of their ability to bind LDL, and substances known to bind to heparin, such as Toluidine Blue, avidin, lipoprotein lipase, fibronectin and protamine, all effectively competed with LDL for binding to the granules. The results show that LDL is efficiently bound to the heparin proteoglycan component of mast-cell granules once the mast cells are stimulated to release their granules into the extracellular space.
Parametric imaging of cancer with optical coherence tomography (2010)

We present a parametric optical coherence tomography (OCT) technique to improve contrast between malignant and healthy non-neoplastic tissue. The technique incorporates a fully automated method to extract tissue attenuation characteristics. Results are represented visually as a parametric en face image, where the parameter used for contrast is indicative of the relative optical attenuation coefficient of the tissue. We present the first parametric OCT images of human lymph nodes containing malignant cells, and demonstrate improved tissue contrast over en face OCT images.
R-CVP Versus R-CHOP Versus R-FM for the Initial Treatment of Patients With Advanced-Stage Follicular Lymphoma: Results of the FOLL05 Trial Conducted by the Fondazione Italiana Linfomi (2013)

In this study, R-CHOP and R-FM were superior to R-CVP in terms of 3-year TTF and PFS. In addition, R-CHOP had a better risk-benefit ratio compared with R-FM.
Tat-mediated delivery of heterologous proteins into cells. (1994)

The Tat protein of human immunodeficiency virus 1 (HIV-1) can enter cells efficiently when added exogenously in tissue culture. To assess if Tat can carry other molecules into cells, we chemically cross-linked Tat peptides (residues 1-72 or 37-72) to beta-galactosidase, horseradish peroxidase, RNase A, and domain III of Pseudomonas exotoxin A (PE) and monitored uptake colorimetrically or by cytotoxicity. The Tat chimeras were effective on all cell types tested, with staining showing uptake into all cells in each experiment. In mice, treatment with Tat-beta-galactosidase chimeras resulted in delivery to several tissues, with high levels in heart, liver, and spleen, low-to-moderate levels in lung and skeletal muscle, and little or no activity in kidney and brain. The primary target within these tissues was the cells surrounding the blood vessels, suggesting endothelial cells, Kupffer cells, and/or splenic macrophages. Tat-mediated uptake may allow the therapeutic delivery of macromolecules previously thought to be impermeable to living cells.
Predicting term and preterm delivery with transabdominal uterine electromyography (2003)

Transabdominal uterine electromyography predicts delivery within 24 hours at term and within 4 days preterm. This methodology offers many advantages and benefits that are not available with present uterine monitoring systems.
Valence Tautomerism of Vinyl-Substituted Three-Membered Heterocycles. II. Conversion of N-Ethyl-2,3-divinylaziridine to N-Ethyl-4,5-dihydroazepine (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTValence Tautomerism of Vinyl-Substituted Three-Membered Heterocycles. II. Conversion of N-Ethyl-2,3-divinylaziridine to N-Ethyl-4,5-dihydroazepineE. L. Stogryn and S. J. BroisCite this: J. Org. Chem. 1965, 30, 1, 88–91Publication Date (Print):January 1, 1965Publication History Published online1 May 2002Published inissue 1 January 1965https://pubs.acs.org/doi/10.1021/jo01012a022https://doi.org/10.1021/jo01012a022research-articleACS PublicationsRequest reuse permissionsArticle Views211Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A high-voltage output driver in a standard 2.5 V 0.25 μm CMOS technology (2004)

A robust 7.5 V output driver is realized in standard 2.5 V 0.25 /spl mu/m CMOS. The chip delivers an output swing of 6.46 V to a 50 /spl Omega/ load with a 10 MHz input square wave. A dual-tone PWM signal at 70 kHz and 250 kHz results in an IM3 of -65 dBm. The on-resistance is 5.9 /spl Omega/.
The chemokine information source: identification and characterization of novel chemokines using the WorldWideWeb and Expressed Sequence Tag Databases (1997)

The chemokine superfamily is a large group of more than 30 small proteins. Many of these were originally identified because of their role in the selective recruitment and activation of leukocytes during inflammation. More recently, some of the chemokine receptors and ligands have been implicated in the mechanism of viral infection for primate lentiviruses such as HIV-1. From the original identification of interleukin-8 (IL-8; the most studied member of the superfamily), the number of new family members has mushroomed over the last few years. Two events have dramatically altered the speed at which sequence information concerning novel chemokines has become available to the scientific community. First, many groups have been obtaining large amounts of sequence information from cDNA libraries by sequencing the clones at random, generating expressed sequence tags (ESTs). Although these ESTs are relatively short, typically less than 500 bases, this amount of sequence is usually sufficient to obtain the entire open reading frame for chemokines. Second, there has been a rapid growth in the use of the WorldWideWeb by bioinformatics groups. The Web was originally set up by the European Centre for Particle Physics (CERN) in Geneva as a method of transferring data between collaborating groups throughout the world. It has enabled biologists throughout the world to have almost instantaneous access both to the databases containing the EST sequences and to the automated tools that are required for searching such databases. With such methods we have been able to rapidly identify more than 10 new human chemokines from public domain databases. In addition to the known categories of chemokines, which are named C, CC, and CXC based on the spacings of N-terminal cysteine residues, we have been able to identify the first member of a novel chemokine subfamily, with a novel CXXXC cysteine spacing. Furthermore, we can subdivide the CC chemokines into monocyte chemotactic protein and macrophage inflammatory protein families based on their sequence identity levels, but also their clustering on the human genome, as identified on other Web sites. The rapid availability of all this data has reduced the amount of time spent on conventional gene identification, enabling us to move quickly on to trying to understand the biology and physiological relevance of these molecules. The novel chemokine sequences obtained and alignments with existing members of the superfamily are now contained within a Chemokine Information Source on an open access server, allowing further searching of chemokine sequences and increasing the availability of such data to the scientific community.
Animal Models in von Willebrand Disease (2011)

Similar to humans with von Willebrand disease (VWD), animals affected with this disorder display a bleeding phenotype. The different subtypes of the disease (1, 2, and 3) are represented in animals, making these models invaluable tools for exploring the characteristics of VWD and for testing new treatments. This chapter will provide an update of these various models, both spontaneous and genetically engineered. Their contribution in uncovering unsuspected functions of the von Willebrand factor (VWF) in diverse pathologies besides VWD and in elucidating some aspects of VWF biology not easily addressed through in vitro approaches will also be presented.
Mitochondrial Turnover and Aging of Long-Lived Postmitotic Cells: The Mitochondrial–Lysosomal Axis Theory of Aging (2009)

It is now generally accepted that aging and eventual death of multicellular organisms is to a large extent related to macromolecular damage by mitochondrially produced reactive oxygen species, mostly affecting long-lived postmitotic cells, such as neurons and cardiac myocytes. These cells are rarely or not at all replaced during life and can be as old as the whole organism. The inherent inability of autophagy and other cellular-degradation mechanisms to remove damaged structures completely results in the progressive accumulation of garbage, including cytosolic protein aggregates, defective mitochondria, and lipofuscin, an intralysosomal indigestible material. In this review, we stress the importance of crosstalk between mitochondria and lysosomes in aging. The slow accumulation of lipofuscin within lysosomes seems to depress autophagy, resulting in reduced turnover of effective mitochondria. The latter not only are functionally deficient but also produce increased amounts of reactive oxygen species, prompting lipofuscinogenesis. Moreover, defective and enlarged mitochondria are poorly autophagocytosed and constitute a growing population of badly functioning organelles that do not fuse and exchange their contents with normal mitochondria. The progress of these changes seems to result in enhanced oxidative stress, decreased ATP production, and collapse of the cellular catabolic machinery, which eventually is incompatible with survival.
Failure analyses of 3D Sip (system-in-package) and WLP (wafer-level package) by finite element methods (2009)

In this study, three examples of failure analyses of electronic packaging by using the finite element method are presented. These are: (1) the failures (delaminations) near the interface between the filled copper and the silicon and between the copper and the silicon dioxide dielectric of the TSV of a 3D system-in-package (SiP) due to the local thermal expansion mismatch between the silicon and the filled copper; (2) the failures of the microbumps between the fine-pitch IC chip and the TSV interposer (chip) due to the global thermal expansion mismatch between the silicon IC Chip and the copper filled TSV interposer (chip); and (3) the failures of leadfree solder joints of a wafer-level chip scale package (WLCSP) due to the thermal expansion mismatch between the silicon WLCSP and the FR-4 epoxy printed circuit board (PCB). The results show that finite element method is not only able to identify the failure locations and determine the stress and strain to cause failures but also perform design for reliability.
Medical image analysis: progress over two decades and the challenges ahead (2000)

The analysis of medical images has been woven into the fabric of the pattern analysis and machine intelligence (PAMI) community since the earliest days of these Transactions. Initially, the efforts in this area were seen as applying pattern analysis and computer vision techniques to another interesting dataset. However, over the last two to three decades, the unique nature of the problems presented within this area of study have led to the development of a new discipline in its own right. Examples of these include: the types of image information that are acquired, the fully three-dimensional image data, the nonrigid nature of object motion and deformation, and the statistical variation of both the underlying normal and abnormal ground truth. In this paper, we look at progress in the field over the last 20 years and suggest some of the challenges that remain for the years to come.
Protein Splicing in Vitrowith a Semisynthetic Two-component Minimal Intein (1998)

Protein splicing elements, or inteins, catalyze their own excision from flanking polypeptide sequences, or exteins, thereby leading to the formation of new proteins in which the exteins are linked directly by a peptide bond. A trans-splicing system, using separately purified and expressed N- and C-terminal intein fragments of about 100 amino acids each, fused to appropriate exteins, was recently derived from the Mycobacterium tuberculosis RecA intein (Mills, K. V., Lew, B. M., Jiang, S.-Q., and Paulus, H. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 3543-3548). We have replaced the C-terminal intein fragment of this system with synthetic peptides comprising 35-50 of the C-terminal residues of the RecA intein. The N-terminal intein fragment and the synthetic peptide were reconstituted by renaturation from guanidinium chloride. In the absence of added reductants, a disulfide-linked dimer of the N-terminal fragment and the peptide accumulated and could be induced to splice by reduction of its disulfide bond. The intermediate and spliced products were identified by polyacrylamide gel electrophoresis, mass spectrometry, and derivatization with thiol-reactive biotin followed by Western blotting with a streptavidin-enzyme conjugate. This is the first example of protein splicing involving a synthetic intein fragment and opens the way for studying the active site structure and function of the intein by the use of different synthetic peptides, including ones with non-natural amino acids.
Human combinatorial libraries yield rare antibodies that broadly neutralize hepatitis C virus (2007)

One way to dissect the antibody response to an invading microorganism is to clone the antibody repertoire from immune donors and subsequently characterize the specific antibodies. Recently, methodological advances have allowed investigations of neutralizing antibodies against hepatitis C virus (HCV) in vitro. We have investigated three human mAbs, previously isolated from an individual infected with HCV of genotype 2b, that are known to cross-react in a binding assay to the envelope E2 protein of genotypes 1a and 1b. We now report that two of them have a neutralizing activity with a breadth not previously observed. Indeed, mAbs 1:7 and A8 recognized E2 from all of the six major genotypes, and they neutralized retroviral pseudoparticles [HCV pseudoparticles (HCVpp)] carrying genetically equally diverse HCV envelope glycoproteins. Importantly, these antibodies were also able to neutralize the cell culture infectious HCV clone JFH-1 in vitro, with IC(50) values of 60 ng/ml and 560 ng/ml, respectively. The conformational epitopes of these two broadly reactive antibodies were overlapping yet distinct and involved amino acid residues in the 523-535 region of E2, known to be important for the E2-CD81 interaction. The third antibody clone, representing a dominant population in the initial screen for these antibodies, was less broadly reactive and was unable to neutralize the genotype 2a infectious clone JFH-1. Our results confirm at the clonal level that broadly neutralizing human anti-HCV antibodies can be elicited and that the region amino acids 523-535 of the HCV envelope glycoprotein E2 carries neutralizing epitopes conserved across all genotypes.
Expression cloning of complementary DNA encoding three distinct isoforms of guinea pig Fc receptor for IgG1 and IgG2. (1993)

Three cDNA clones encoding the guinea pig Fc receptor for IgG1 and IgG2 (Fc gamma 1/gamma 2 R) have been isolated by an expression cloning strategy using mAb directed against the receptor. When transfected into COS-7 cells, these cDNA induced cell surface expression of the receptor that bound IgG1 and IgG2 antibodies complexed with the Ag. The ligand-binding affinities of these receptors were indistinguishable. Nucleotide sequencing has indicated that one of these clones, Fc gamma 1/gamma 2R-B1, is identical to the previously isolated cDNA clone homologous to the b2 isoform of human Fc gamma RIIB and that of murine Fc gamma RII, encoding a transmembrane glycoprotein containing two Ig-like extracellular domains. Two other clones, Fc gamma 1/gamma 2R-B2 and -B3, are identical to Fc gamma 1/gamma 2R-B1 except for an inframe insertion in the cytoplasmic region. The 48-nucleotide insertion found in Fc gamma 1/gamma 2R-B2 is identical to the first 48 nucleotides of the B3 insert that comprises 132 bp. Based on the size and homology of the inserted sequence, Fc gamma 1/gamma 2R-B2 and -B3 are identified as the homologues of the b1 isoform of human Fc gamma RIIB and that of murine Fc gamma RII, respectively. Reverse transcription and polymerase chain reaction of RNA revealed that macrophages and polymorphonuclear leukocytes expressed preferentially Fc gamma 1/gamma 2R-B1. On the other hand, B lymphocytes expressed all three forms, among which Fc gamma 1/gamma 2R-B2 and -B3 were selectively expressed in LPS-activated B lymphocytes that showed a dramatic increase in the levels of cell surface expression of Fc gamma 1/gamma 2R. These results suggest that the inserted sequences of Fc gamma 1/gamma 2R-B2 and -B3 are important to generate responses specific for B lymphocytes, which may include regulation of cell activation.