gebhart/patrepeval huggingface dataset:
Identification of a Small Peptide That Inhibits PCSK9 Protein Binding to the Low Density Lipoprotein Receptor (2013)

PCSK9 (proprotein convertase subtilisin/kexin type 9) is a negative regulator of the hepatic LDL receptor, and clinical studies with PCSK9-inhibiting antibodies have demonstrated strong LDL-c-lowering effects. Here we screened phage-displayed peptide libraries and identified the 13-amino acid linear peptide Pep2-8 as the smallest PCSK9 inhibitor with a clearly defined mechanism of inhibition that has been described. Pep2-8 bound to PCSK9 with a KD of 0.7 μm but did not bind to other proprotein convertases. It fully restored LDL receptor surface levels and LDL particle uptake in PCSK9-treated HepG2 cells. The crystal structure of Pep2-8 bound to C-terminally truncated PCSK9 at 1.85 Å resolution showed that the peptide adopted a strand-turn-helix conformation, which is remarkably similar to its solution structure determined by NMR. Consistent with the functional binding site identified by an Ala scan of PCSK9, the structural Pep2-8 contact region of about 400 Å(2) largely overlapped with that contacted by the EGF(A) domain of the LDL receptor, suggesting a competitive inhibition mechanism. Consistent with this, Pep2-8 inhibited LDL receptor and EGF(A) domain binding to PCSK9 with IC50 values of 0.8 and 0.4 μm, respectively. Remarkably, Pep2-8 mimicked secondary structural elements of the EGF(A) domain that interact with PCSK9, notably the β-strand and a discontinuous short α-helix, and it engaged in the same β-sheet hydrogen bonds as EGF(A) does. Although Pep2-8 itself may not be amenable to therapeutic applications, this study demonstrates the feasibility of developing peptidic inhibitors to functionally relevant sites on PCSK9.
Immunobiology of mesenchymal stem cells (2013)

Mesenchymal stem cells (MSCs) can be isolated from almost all tissues and effectively expanded in vitro. Although their true in situ properties and biological functions remain to be elucidated, these in vitro expanded cells have been shown to possess potential to differentiate into specific cell lineages. It is speculated that MSCs in situ have important roles in tissue cellular homeostasis by replacing dead or dysfunctional cells. Recent studies have demonstrated that in vitro expanded MSCs of various origins have great capacity to modulate immune responses and change the progression of different inflammatory diseases. As tissue injuries are often accompanied by inflammation, inflammatory factors may provide cues to mobilize MSCs to tissue sites with damage. Before carrying out tissue repair functions, MSCs first prepare the microenvironment by modulating inflammatory processes and releasing various growth factors in response to the inflammation status. In this review, we focus on the crosstalk between MSCs and immune responses and their potential clinical applications, especially in inflammatory diseases.
MET and MYC cooperate in mammary tumorigenesis (2005)

In human breast cancer, overexpression of the protooncogene MET is strongly associated with poor prognosis and high risk of metastasis. It stands out as a reliable prognostic indicator of survival and defines a set of tumors exclusive of those that express HER2 or hormone receptors. Studies have shown that overexpression of mutant forms of MET cause cancer in mice. However, MET mutations have not been found in human breast cancer, and the consequences of overexpression of normal MET are unknown. To investigate the role of MET and other putative oncogenes in breast cancer, we developed an experimental system that involves retroviral delivery of genes into primary mammary epithelial cells, followed by transplantation of the transduced cells into mammary fat pads. Using this approach, we found that overexpression of wild-type MET leads to the development of nonprogressive neoplasms. The lesions progressed to mammary adenocarcinoma when a second protooncogene, MYC, was overexpressed, indicating that MET and MYC cooperate in mammary tumorigenesis. Both the nonprogressive neoplasms and adenocarcinomas display characteristics consistent with transformation and expansion of mammary progenitor cells. The approach described here should provide a useful model with which to efficiently test effects of various genes on tumor development in the breast.
Elongation of the N-glycans of fowl plague virus hemagglutinin expressed in Spodoptera frugiperda (Sf9) cells by coexpression of human β1,2-N-acetylglucosaminyltransferase I (1996)

Spodoptera frugiperda (Sf9)-cells differ markedly in their protein glycosylation capacities from vertebrate cells in that they are not able to generate complex type oligosaccharide side chains. In order to improve the oligosaccharide processing properties of these cells we have used baculovirus vectors for expression of human (beta 1,2-N-acetylglucosaminyltransferase I (hGNT-I), the enzyme catalysing the crucial step in the pathway leading to complex type N-glycans in vertebrate cells. One vector (Bac/GNT) was designed to express unmodified GNT-I protein, the second vector (Bac/tagGNT) to express GNT-I protein with a tag epitope fused to its N-terminus. In Sf9-cells infected with Bac/tagGNT-virus a protein of about 50 kDa representing hGNT-I was detected with an antiserum directed against the tag epitope. HGNT-I activity was increased at least threefold in lysates of infected cells when N-acetylglucosamine (GlcNAc)-free ovalbumine was used as substrate. To monitor hGNT-I activity in intact Sf9-cells, the glycosylation of coexpressed fowl plague virus hemagglutinin (HA) was investigated employing a galactosylation assay and chromatographic analysis of isolated HA N-glycans. Coexpression of hGNT-I resulted in an at least fourfold increase of HA carrying terminal GlcNAc-residues. The only structure detectable in this fraction was GlcNAcMan3GlcNAc2. These results show that hGNT-I is functionally active in Sf9-cells and that the N-glycans of proteins expressed in the baculovirus/insect cell system are elongated by coexpression of glycosyltransferases of vertebrate origin. Complete complex type oligosaccharide side chains were not observed when hGNT-I was overexpressed, thus supporting the concept that Sf9-cells do not contain glycosyltransferases acting after hGNT-I.
Genetic algorithms for object recognition in a complex scene (2002)

A realworld computer vision module must deal with a wide variety of environmental parameters. Object recognition, one of the major tasks of this vision module, typically requires a preprocessing step to locate objects in the scenes that ought to be recognized. Genetic algorithms are a search technique for dealing with a very large search space, such as the one encountered in image segmentation or object recognition. The article describes a technique for using genetic algorithms to combine the image segmentation and object recognition steps for a complex scene. The results show that this approach is a viable method for successfully combining the image segmentation and object recognition steps for a computer vision module.
Circadian Sleep Regulation in the Absence of Light Perception: Chronic Non-24-Hour Circadian Rhythm Sleep Disorder in a Blind Man With a Regular 24-Hour Sleep—Wake Schedule (1993)

Sleep disturbances and the failure to entrain circadian rhythms to the 24-hour day have been reported in the majority of totally blind subjects. The present case study of a totally blind man with a well-documented recurring sleep disturbance was designed to investigate the mutual relationship between sleep and the circadian timing system. The 63-year-old subject, a high school teacher with a regular work schedule, had suffered from cyclically recurring insomnia for the past 28 years. Analysis of a sleep log that he had kept for the past 15 years suggested that his circadian rhythms were not entrained to the 24-hour day. During a 3-month inpatient study, the period of the endogenous circadian pacemaker was assessed by analysis of ambulatory core body temperature, urinary excretion and a series of estimates of the phase of core body temperature cycles and plasma cortisol levels during constant routines. All circadian markers revealed periods in the range of 24.22-24.27 hours, with no evidence for a modulation of the observed periods by the sleep-wake cycle. During this 3-month inpatient study, a complete cycle of the subject's sleep disturbance and remission was polysomnographically documented while the subject lived on a regular 24-hour schedule. Because the subject's circadian rhythms were free-running and his sleep times were fixed, sleep occurred at virtually all circadian phases. Analysis of sleep latency, REM sleep latency, sleep duration, wake in sleep episode and REM sleep during sleep episode revealed a strong modulation by circadian phase. These findings in this blind man suggest that: 1) the period of his cyclically recurring sleep disturbance is directly related to the nonentrained period of an endogenous circadian pacemaker that drives circadian variation in core body temperature, urinary excretion, plasma cortisol and sleep propensity; 2) both his sleep structure and the severity of his daily sleep disruption are directly related to circadian phase and 3) his circadian pacemaker, which has an endogenous period that deviates only 0.2-0.3 hours from 24 hours, cannot be entrained by periodic daily exposure to nonphotic time cues, including a very regular 24-hour sleep-wake schedule.
Structural colouration of mammalian skin: convergent evolution of coherently scattering dermal collagen arrays (2004)

For more than a century, the blue structural colours of mammalian skin have been hypothesized to be produced by incoherent, Rayleigh or Tyndall scattering. We investigated the colour, anatomy, nanostructure and biophysics of structurally coloured skin from two species of primates - mandrill (Mandrillus sphinx) and vervet monkey (Cercopithecus aethiops) - and two species of marsupials - mouse opossum (Marmosa mexicana) and wooly opossum (Caluromys derbianus). We used two-dimensional (2-D) Fourier analysis of transmission electron micrographs (TEMs) of the collagen arrays in the primate tissues to test whether these structural colours are produced by incoherent or coherent scattering (i.e. constructive interference). The structural colours in Mandrillus rump and facial skin and Cercopithecus scrotum are produced by coherent scattering by quasi-ordered arrays of parallel dermal collagen fibres. The 2-D Fourier power spectra of the collagen arrays from Mandrillus and Cercopithecus reveal ring-shaped distributions of Fourier power at intermediate spatial frequencies, demonstrating a substantial nanostructure of the appropriate spatial frequency to produce the observed blue hues by coherent scattering alone. The Fourier power spectra and the observed reflectance spectra falsify assumptions and predictions of the incoherent, Rayleigh scattering hypothesis. Samples of blue Marmosa and Caluromys scrotum conform generally to the anatomy seen in Mandrillus and Cercopithecus but were not sufficiently well preserved to conduct numerical analyses. Colour-producing collagen arrays in mammals have evolved multiple times independently within the two clades of mammals known to have trichromatic colour vision. Mammalian colour-producing collagen arrays are anatomically and mechanistically identical to structures that have evolved convergently in the dermis of many lineages of birds, the tapetum of some mammals and the cornea of some fishes. These collagen arrays constitute quasi-ordered 2-D photonic crystals.
BLUETOOTH—The universal radio interface for ad hoc, wireless connectivity (1998)

that is small enough to fit inside any electronic device or machine, that provides local connectivity, and that creates a (worldwide) micro-scale web. What applications might you use it in? In 1994, Ericsson Mobile Communications AB in Lund, Sweden, initiated a study to investigate the feasibility of a low-power, low-cost radio interface between mobile phones and their accessories. The intention was to eliminate cables between phones and PC cards, wireless headsets, and so forth. The study was part of a larger project that investigated multi-communicators connected to the cellular network via cellular telephones. The last link in the connection between a communicator and the cellular network was a short-range radio link to the phone—thus, the link was called the multicommunicator link or MC link. As the MC link project progressed, it became clear that there was no limit to the kinds of application that could use a short-range radio link. Cheap, short-range radios would make wireless communication between portable devices economically feasible. Current portable devices use infrared links (IrDA) to communicate with each other. Although infrared transceivers are inexpensive, they • have limited range (typically one to two meters); • are sensitive to direction and require direct line-of-sight; • can in principle only be used between two devices. By contrast, radios have much greater range, can propagate around objects and through various materials, and connect to many devices simultaneously. What is more, radio interfaces do not require user interaction. In the beginning of 1997, when designers had already begun work on an MC link
Synthesis and evaluation of [18F]1-amino-3-fluorocyclobutane-1-carboxylic acid to image brain tumors. (1999)

The amino acid FACBC can be radiofluorinated for clinical use. [18F]FACBC is a potential PET tracer for tumor imaging.
Glucose Catabolism in Cancer Cells. (1995)

One of the most characteristic phenotypes of rapidly growing cancer cells is their propensity to catabolize glucose at high rates. Type II hexokinase, which is expressed at high levels in such cells and bound to the outer mitochondrial membrane, has been implicated as a major player in this aberrant metabolism. Here we report the isolation and sequence of a 4.3-kilobase pair proximal promoter region of the Type II hexokinase gene from a rapidly growing, highly glycolytic hepatoma cell line (AS-30D). Analysis of the sequence enabled the identification of putative promoter elements, including a TATA box, a CAAT element, several Sp-1 sites, and response elements for glucose, insulin, cAMP, Ap-1, and a number of other factors. Transfection experiments with AS-30D cells showed that promoter activity was enhanced 3.4-, 3.3-, 2.4-, 2.1-, and 1.3-fold, respectively, by glucose, phorbol 12-myristate 13-acetate (a phorbol ester), insulin, cAMP, and glucagon. In transfected hepatocytes, these same agents produced little or no effect. The results emphasize normal versus tumor cell differences in the regulation of Type II hexokinase and indicate that transcription of the Type II tumor gene may occur independent of metabolic state, thus, providing the cancer cell with a selective advantage over its cell of origin.
Eukaryotic transient expression system dependent on transcription factors and regulatory DNA sequences of vaccinia virus. (1985)

A transient expression system in which chimeric genes are expressed in cells infected with vaccinia virus was developed. Recombinant plasmids containing the promoter regions of vaccinia virus genes ligated to the coding segment of the prokaryotic chloramphenicol acetyltransferase (CAT) gene were constructed. When the plasmids were introduced into vaccinia virus-infected cells by transfection, the chimeric gene was expressed and significant levels of CAT accumulated. CAT activity was not detected when the same recombinant plasmid was introduced into uninfected cells, nor was activity detected when the vaccinia virus promoter was absent from the plasmid or was replaced by simian virus 40 or Rous sarcoma virus promoters. This specificity indicated that expression is dependent on a cis-acting vaccinia virus promoter region within the recombinant plasmid and diffusible trans-acting transcription factors produced during virus infection. The lack of effect of a simian virus 40 enhancer element inserted upstream of the vaccinia virus promoter region also distinguished this system from systems dependent on RNA polymerase II. Although replication of the recombinant plasmid could not be detected in either uninfected or vaccinia virus-infected cells, an inhibitor of DNA synthesis significantly reduced CAT expression. This result, as well as the kinetics of CAT synthesis, suggests that replication of viral DNA templates can enhance transcription of chimeric genes in recombinant plasmids.
Psychotropic Effects of Dextromethorphan Are Altered by the CYP2D6 Polymorphism (1998)

Dextromethorphan is a nonopioid antitussive metabolized by cytochrome P450 2D6 (CYP2D6) to an active metabolite, dextrorphan. CYP2D6 is polymorphically expressed in humans, with 5 to 10% of Caucasians being homozygous deficient for the active form of the enzyme. In a pilot study, the authors investigated the pharmacologic effects of dextromethorphan in individuals phenotyped and genotyped as extensive metabolizers (EMs, N = 4) and poor metabolizers (PMs, N = 2) of CYP2D6 substrates. Dextromethorphan doses ranged from 0 to 6 mg/kg based on individual subject tolerance. All EMs tolerated 3 to 6 mg/kg dextromethorphan, whereas PMs barely tolerated 3 mg/kg dextromethorphan and therefore received lower doses. As shown in previous studies, plasma kinetics show profound differences in dextromethorphan metabolism between EMs and PMs. Dextromethorphan produced qualitatively and quantitatively different objective and subjective effects in the two groups. Objectively, PMs had greater psychomotor impairment, as measured by a joystick tracking task, compared with EMs on 3 mg/kg dextromethorphan (mean performance +/- SE, 95+/-0.5% for EMs vs. 86+/-6% for PMs; p < 0.05). At this dose, EMs also reported greater abuse potential compared with PMs (p < 0.05), and PMs reported greater sedation and dysphoria compared with EMs (p < 0.01). These data provide preliminary evidence that dextrorphan contributes to dextromethorphan abuse liability, and therefore PMs may be less likely to abuse dextromethorphan.
Historically significant events in the discovery of RANK/RANKL/OPG (2013)

After it was suggested 30 years ago that the osteoblast lineage controlled the formation of osteoclasts, methods were developed that established this to be the case, but the molecular controls were elusive. Over more than a decade much evidence was obtained for signaling mechanisms that regulated the production of a membrane - bound regulator of osteoclastogenesis, in the course of which intercellular communication in bone was revealed in its complexity. The discovery of regulation by tumor necrosis factor ligand and receptor families was made in the last few years of the twentieth century, leading since then to a new physiology of bone, and to exciting drug development.
iGroup: Weakly supervised image and video grouping (2011)

We present a generic, efficient and iterative algorithm for interactively clustering classes of images and videos. The approach moves away from the use of large hand labelled training datasets, instead allowing the user to find natural groups of similar content based upon a handful of “seed” examples. Two efficient data mining tools originally developed for text analysis; min-Hash and APriori are used and extended to achieve both speed and scalability on large image and video datasets. Inspired by the Bag-of-Words (BoW) architecture, the idea of an image signature is introduced as a simple descriptor on which nearest neighbour classification can be performed. The image signature is then dynamically expanded to identify common features amongst samples of the same class. The iterative approach uses APriori to identify common and distinctive elements of a small set of labelled true and false positive signatures. These elements are then accentuated in the signature to increase similarity between examples and “pull” positive classes together. By repeating this process, the accuracy of similarity increases dramatically despite only a few training examples, only 10% of the labelled groundtruth is needed, compared to other approaches. It is tested on two image datasets including the caltech101 [9] dataset and on three state-of-the-art action recognition datasets. On the YouTube [18] video dataset the accuracy increases from 72% to 97% using only 44 labelled examples from a dataset of over 1200 videos. The approach is both scalable and efficient, with an iteration on the full YouTube dataset taking around 1 minute on a standard desktop machine.
Morphing Low-Affinity Ligands into High-Avidity Nanoparticles by Thermally Triggered Self-Assembly of a Genetically Encoded Polymer (2010)

Multivalency is the increase in avidity resulting from the simultaneous interaction of multiple ligands with multiple receptors. This phenomenon, seen in antibody-antigen and virus-cell membrane interactions, is useful in designing bioinspired materials for targeted delivery of drugs or imaging agents. While increased avidity offered by multivalent targeting is attractive, it can also promote nonspecific receptor interaction in nontarget tissues, reducing the effectiveness of multivalent targeting. Here, we present a thermal targeting strategy--dynamic affinity modulation (DAM)--using elastin-like polypeptide diblock copolymers (ELP(BC)s) that self-assemble from a low-affinity to high-avidity state by a tunable thermal "switch", thereby restricting activity to the desired site of action. We used an in vitro cell binding assay to investigate the effect of the thermally triggered self-assembly of these ELP(BC)s on their receptor-mediated binding and cellular uptake. The data presented herein show that (1) ligand presentation does not disrupt ELP(BC) self-assembly; (2) both multivalent ligand presentation and upregulated receptor expression are needed for receptor-mediated interaction; (3) increased size of the hydrophobic segment of the block copolymer promotes multivalent interaction with membrane receptors, potentially due to changes in the nanoscale architecture of the micelle; and (4) nanoscale presentation of the ligand is important, as presentation of the ligand by micrometer-sized aggregates of an ELP showed a low level of binding/uptake by receptor-positive cells compared to its presentation on the corona of a micelle. These data validate the concept of thermally triggered DAM and provide rational design parameters for future applications of this technology for targeted drug delivery.
RESURF AlGaN/GaN HEMT for high voltage power switching (2001)

A novel HEMT configuration based on the RESURF technique is proposed for very high voltage power switching applications. It employs a p-n junction below the 2-DEG channel and two field plates, one extending from the gate and the other from the drain, to distribute the electric field over the gate to drain separation. 2-D simulations indicate a breakdown voltage >1 KV at on-resistance of /spl sim/1 m/spl Omega//spl middot/cm/sup 2/ (neglecting contact resistances) for the device.
Blends of carbon blacks and multiwall carbon nanotubes as reinforcing fillers for hydrocarbon rubbers (2008)

Abstract The reinforcement of a styrene‐butadiene rubber (SBR) by single fillers—carbon black (CB) or multiwall carbon nanotubes (MWNTs)—or by mixtures of CB and MWNTs, is investigated. The morphologies, mechanical and electrical properties of the composites, are analyzed. A significant improvement in the tensile properties is observed for samples containing a dual phase. Using atomic force (AFM) and transmission electron (TEM) microscopies, we demonstrate that the double loading improves the dispersion of the nanotubes in SBR. Electrical measurements show lower resistivity and a lower percolation threshhold for composites containing blends of fillers, which provides further evidence of better dispersion. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci 46: 1939–1951, 2008