gebhart/patrepeval huggingface dataset:
Maturation Pathways of Cross-Reactive HIV-1 Neutralizing Antibodies (2009)

Several human monoclonal antibodies (hmAbs) and antibody fragments, including the best characterized in terms of structure-function b12 and Fab X5, exhibit relatively potent and broad HIV-1 neutralizing activity. However, the elicitation of b12 or b12-like antibodies in vivo by vaccine immunogens based on the HIV-1 envelope glycoprotein (Env) has not been successful. B12 is highly divergent from the closest corresponding germline antibody while X5 is less divergent. We have hypothesized that the relatively high degree of specific somatic hypermutations may preclude binding of the HIV-1 envelope glycoprotein (Env) to closest germline antibodies, and that identifying antibodies that are intermediates in the pathways to maturation could help design novel vaccine immunogens to guide the immune system for their enhanced elicitation. In support of this hypothesis we have previously found that a germline-like b12 (monovalent and bivalent scFv as an Fc fusion protein or IgG) lacks measurable binding to an Env as measured by ELISA with a sensitivity in the μM range [1]; here we present evidence confirming and expanding these findings for a panel of Envs. In contrast, a germline-like scFv X5 bound Env with high (nM) affinity. To begin to explore the maturation pathways of these antibodies we identified several possible b12 intermediate antibodies and tested their neutralizing activity. These intermediate antibodies neutralized only some HIV-1 isolates and with relatively weak potency. In contrast, germline-like scFv X5 neutralized a subset of the tested HIV-1 isolates with comparable efficiencies to that of the mature X5. These results could help explain the relatively high immunogenicity of the coreceptor binding site on gp120 and the abundance of CD4-induced (CD4i) antibodies in HIV-1-infected patients (X5 is a CD4i antibody) as well as the maturation pathway of X5. They also can help identify antigens that can bind specifically to b12 germline and intermediate antibodies that together with Envs could be used as a conceptually novel type of candidate vaccines. Such candidate vaccines based on two or more immunogens could help guiding the immune system through complex maturation pathways for elicitation of antibodies that are similar or identical to antibodies with known properties.
Evidence that 1,25-dihydroxyvitamin D3 inhibits the hepatic production of 25-hydroxyvitamin D in man. (1984)

Previous in vitro studies in rachitic rat liver suggested that 1,25-dihydroxyvitamin D inhibits the hepatic production of 25-hydroxyvitamin D (25-OHD). An investigation therefore was carried out in eight normal subjects to determine whether concomitant administration of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] would alter the response of serum 25-OHD to challenge with vitamin D. In control studies, vitamin D, 100,000 U/d for 4 d, significantly increased mean serum 25-OHD, from 26.3 +/- 2.9 to 66.7 +/- 12.6 ng/ml (P less than 0.01). In contrast, 1,25(OH)2D3, 2 micrograms/d for 4 d, completely prevented an increase in serum 25-OHD in response to the same dose of vitamin D in the same individuals (25.1 +/- 2.2 vs. 27.4 +/- 5.3 ng/ml, NS). In a post-control study in seven of the normal subjects, vitamin D again significantly increased mean serum 25-OHD, from 18.2 +/- 3.1 to 42.8 +/- 4.7 ng/ml (P less than 0.001). In each of the three studies, mean serum calcium, phosphorus, and creatinine did not change and remained within the normal range. Whereas mean urinary calcium did not change in response to vitamin D alone during the 4 d of the two control studies, it increased significantly in the study in which vitamin D and 1,25(OH)2D3 were given together. A dose-response inhibition of the response of serum 25-OHD to vitamin D by 1,25(OH)2D3 was demonstrated in two of the normal subjects. The results provide evidence that 1,25(OH)2D3 inhibits the hepatic synthesis of its precursor 25-OHD in man.
Reversible Monoubiquitination Regulates the Parkinson Disease-associated Ubiquitin Hydrolase UCH-L1 (2007)

Deubiquitinating enzymes (DUBs) are negative regulators of protein ubiquitination and play an important role in ubiquitin-dependent processes. Recent studies have found that diverse cellular mechanisms are employed to control the activity of DUBs. Ubiquitin C-terminal hydrolase-L1 (UCH-L1) is a highly expressed neuronal DUB linked to Parkinson disease; however, little is known about its specific functions or modes of regulation. Here, we demonstrate that UCH-L1 is post-translationally modified by monoubiquitin in cells, at lysine residues near the active site. This modification restricts enzyme activity by preventing binding to ubiquitinated targets, and permanent monoubiquitination, as mimicked by a ubiquitin-UCH-L1 fusion, inhibits UCH-L1 in its capacity to increase free ubiquitin levels in cells. Interestingly, UCH-L1 catalyzes its own deubiquitination in an intramolecular manner, thereby regulating the lifetime of this modification. Our results illustrate monoubiquitination as a reversible regulatory mechanism for DUB activity involving auto-deubiquitination.
N-Terminal Pro-B–Type Natriuretic Peptide and Long-Term Mortality in Acute Coronary Syndromes (2002)

N-BNP is a powerful indicator of long-term mortality in patients with ACS and provides prognostic information above and beyond conventional risk markers.
Metadata creation system for mobile images (2004)

The amount of personal digital media is increasing, and managing it has become a pressing problem. Effective management of media content is not possible without content-related metadata. In this paper we describe a content metadata creation process for images taken with a mobile phone. The design goals were to automate the creation of image content metadata by leveraging automatically available contextual metadata on the mobile phone, to use similarity processing algorithms for reusing shared metadata and images on a remote server, and to interact with the mobile phone user during image capture to confirm and augment the system supplied metadata. We built a prototype system to evaluate the designed metadata creation process. The main findings were that the creation process could be implemented with current technology and it facilitated the creation of semantic metadata at the time of image capture.
Supercritical carbon dioxide and poly(ethylene glycol): an environmentally benign biphasic solvent system for aerobic oxidation of styrene (2007)

Aerobic oxidation of styrene catalyzed by PdCl2/CuCl can be smoothly performed in the supercritical carbon dioxide and poly(ethylene glycol) biphasic system. A high conversion of styrene and yield of acetophenone were obtained in the presence of a relatively low catalyst loading. This environmentally benign biphasic catalytic system can be applied to the Wacker oxidation of various alkenes. Furthermore, the PdCl2-mediated oxidation of styrene was preferentially converted into benzaldehyde using a biphasic scCO2/PEG system. The PEG could effectively immobilize and stabilize the catalysts. The present biphasic system could facilitate product separation and catalyst recycling. The effects of the reaction parameters such as solvent and CO2 pressure were also investigated in detail.
Aptamer-based microfluidic biosensors (2009)

Micro- and nanofabrication has allowed the creation of ultra-sensitive, miniaturized, and inexpensive biosensors. These devices generally utilize chemical or biological receptors which recognize a particular compound of interest and transduce this recognition event into a measurable signal. Recent advances in RNA and DNA synthesis have enabled the use of aptamers, which are in-vitro generated oligonucleotides offering high affinity biomolecular recognition to a theoretically limitless variety of analytes. DNA and RNA aptamers have become increasingly popular in the biosensor community, to the extent that they have begun competing with more established affinity ligands including enzymes, lectins, and most immunoreceptors such as antibodies. We present an overview of our recent research effort in developing an aptamer-functionalized microfluidic platform that by design exploits the specificity and temperature-dependent reversibility of aptamers to enable enhanced biosensing. Using the specificity of aptamers, we demonstrate highly selective capture and enrichment of biomolecules. Employing thermally induced, reversible disruption of aptamer-target binding, we accomplish isocratic elution of the captured analytes and regeneration of the aptamer aptamer-functionalized surfaces, thereby eliminating the use of potentially harsh reagents. Using integrated microfluidic control, the eluted analytes are detected in a label-free fashion by mass spectrometric methods.
Preparation and Adsorption Behavior of Aminated Electrospun Polyacrylonitrile Nanofiber Mats for Heavy Metal Ion Removal (2010)

Polyacrylonitrile (PAN) nanofiber mats were prepared by electrospinning and they were further modified to contain amidino diethylenediamine chelating groups on their surface via heterogeneous reaction with diethylenetriamine (DETA). The obtained aminated PAN (APAN) nanofiber mats were evaluated for their chelating property with four types of metal ions, namely Cu(II), Ag(I), Fe(II), and Pb(II) ions. The amounts of the metal ions adsorbed onto the APAN nanofiber mats were influenced by the initial pH and the initial concentration of the metal ion solutions. Increasing the contact time also resulted in a monotonous increase in the adsorbed amounts of the metal ions, which finally reached equilibria at about 10 h for Cu(II) ions and about 5 h for Ag(I), Fe(II), and Pb(II) ions. The maximal adsorption capacities of the metal ions on the APAN nanofiber mats, as calculated from the Langmuir model, were 150.6, 155.5, 116.5, and 60.6 mg g(-1), respectively. Lastly, the spent APAN nanofiber mats could be facilely regenerated with a hydrochloric acid (HCl) aqueous solution.
A versatilein vivoandin vitroeukaryotic expression vector for protein engineering (1988)

Journal Article A versatile in vivo and in vitro eukaryotic expression vector for protein engineering Get access Stephen Green, Stephen Green Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Faculté de Médecine11 rue Humann, 67085 Strasbourg, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Isabelle Issemann, Isabelle Issemann Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Faculté de Médecine11 rue Humann, 67085 Strasbourg, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Elisabeth Sheer Elisabeth Sheer Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Faculté de Médecine11 rue Humann, 67085 Strasbourg, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 1, 11 January 1988, Page 369, https://doi.org/10.1093/nar/16.1.369 Published: 11 January 1988 Article history Accepted: 27 October 1987 Published: 11 January 1988
Healing of experimentally produced lesions in articular cartilage following chondrocyte transplantation (1987)

Articular cartilage is known to have limited ability to heal once injured, and attempts to heal lesions in cartilage have yielded equivocal results. The following experiments were performed to investigate healing in cartilage transplantation of chondrocytes grown in vitro. The knee joint of the New Zealand White rabbit was used as the experimental model. An initial baseline study was made to determine the intrinsic capability of cartilage for healing defects that do not fracture the subchondral plate. A second experiment examined the effects of autologous in vitro grown chondrocytes on the healing rates of these defects. The results were evaluated by qualitative and quantitative light microscopy. In control defects not grafted with chondrocytes, 6 weeks after the initial defect was created, there was little repair. Macroscopic and histological findings were consistent with an osteoarthritic pathology such as synovitis and "cell nests." Macroscopic results from grafted specimens displayed a marked decrease in synovitis and other degenerative changes. Defects which had received transplants had a significant amount of cartilage reconstituted (82%) compared to ungrafted controls (18%). Controls showed a healing rate comparable to that obtained in the initial baseline study.
Stimuli-Responsive Polymersomes for Programmed Drug Delivery (2009)

In the past decade, polymersomes (also referred to as polymeric vesicles) have attracted rapidly growing interest based on their intriguing aggregation phenomena, cell and virus-mimicking dimensions and functions, as well as tremendous potential applications in medicine, pharmacy, and biotechnology. Unlike liposomes self-assembled from low molecular weight lipids, polymersomes are in general prepared from macromolecular amphiphiles of various architectures including amphiphilic diblock, triblock, graft and dendritic copolymers. Polymersomes exhibit very unique features highlighted with high stability, tunable membrane properties, versatility, and capacity of transporting hydrophilic as well as hydrophobic species such as anticancer drugs, genes, proteins, and diagnostic probes. Recently, much effort has been directed to the development of intelligent polymersomes that respond to internal or external stimuli, in particular, pH, temperature, redox potential, light, magnetic field, and ultrasound, either reversibly or nonreversibly. Stimuli-sensitive polymersomes have emerged as novel programmable delivery systems in which the release of the encapsulated contents can be readily modulated by the stimulus. The stimuli-responsive release may result in significantly enhanced therapeutic efficacy and minimized possible side effects. It is also feasible to form and disassemble polymersomes in water simply by applying an appropriate stimulus. In this article, recent advances in stimuli-sensitive polymersomes have been reviewed, and perspectives on future developments have been discussed.
DNA methylation: The nuts and bolts of repression (2007)

DNA methylation is an epigenetic modification which plays an important role in chromatin organization and gene expression. DNA methylation can silence genes and repetitive elements through a process which leads to the alteration of chromatin structure. The mechanisms which target DNA methylation to specific sites in the genome are not fully understood. In this review, we will discuss the mechanisms which lead to the long-term silencing of genes and will survey the progression that has been made in determining the targeted mechanisms for de novo DNA methylation.
Animals and Their Models Do Their Locomotions (1995)

Journal Article Animals and their models do their locomotions: Biologists probe mechanics and energetics of animal motion Get access William H. Allen William H. Allen Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 45, Issue 6, June 1995, Pages 381–383, https://doi.org/10.2307/1312715 Published: 01 June 1995
Susceptibility towards intramolecular disulphide-bond formation affects conformational stability and folding of human basic fibroblast growth factor (1998)

The conformational stability and the folding properties of the all-beta-type protein human basic fibroblast growth factor (hFGF-2) were studied by means of fluorescence spectroscopy. The results show that the instability of the biological activity of hFGF-2 is also reflected in a low conformational stability of the molecule. The reversibility of the unfolding and refolding process was established under reducing conditions. Determination of the free-energy of unfolding in the presence of reducing agents revealed that the conformational stability of hFGF-2 (DeltaGH2Oapp congruent with21 kJ. mol-1, 25 degreesC) is low compared with other globular proteins under physiological conditions (20-60 kJ.mol-1). However, the conformational stability of hFGF-2 is particularly low under non-reducing conditions. This instability is attributed to intramolecular disulphide-bond formation, rendering the molecule more susceptible to denaturant-induced unfolding. In addition, denaturant-induced unfolding of hFGF-2 renders the protein more susceptible to irreversible oxidative denaturation. Experimental evidence is provided that the irreversibility of the unfolding and refolding process in the absence of reducing agents is linked to the formation of an intramolecular disulphide bond involving cysteines 96 and 101.
Design and implementation of a lip reading system in smart phone environment (2009)

This study proposes a real-time lip-reading method in smart phone environment. In smart-phone environment where the resources are limited compared to existing PC environment, it is hard to operate lip-reading in real-time. To solve this problem, this study proposes the lip area detection method and feature extraction method suitable for smart-phone environment. First, to find the accurate lip area, the face area is detected by means of face color information, and the eyes are located to detect the lip area with the geometrical relation. To extract the outstanding features of the lip area in terms of changes in light according to the changes of surroundings, histogram matching, lip folding, and RASTA filter are applied, and the extracted data of features by means of PCA are used in recognition. As a result of the experiment, the changes were recognized almost in real-time, and 30 words of 50 were recognized, which indicates 60% recognition rates.
The APC gene I1307K variant is rare in Norwegian patients with familial and sporadic colorectal or breast cancer. (1998)

Recently, a T-to-A transversion creating an 8-base mononucleotide tract in the APC gene, resulting in substitution of lysine for isoleucine at codon 1307 (I1307K), was found in a subset of Ashkenazi Jews. This sequence variant was most frequent in colorectal cancer patients with a positive family history of colorectal cancer. To determine whether the I1307K variant plays a role in colorectal or breast cancer predisposition in the Norwegian population, we have analyzed blood samples from 210 colorectal cancer patients and 183 breast cancer patients by PCR and direct sequencing. Thirty-seven of the colorectal cancer patients had a positive family history of cancer. Among the breast cancer patients, 24 had a family history of colorectal cancer and 75 a family history of breast and/or ovarian cancer. Only one colorectal cancer patient who belonged to a Jewish family was found to carry the A variant. Our data show that the I1307K variant is rare in the Norwegian population and should not be viewed as a candidate for susceptibility testing for colorectal cancer.
Fast transparent migration for virtual machines (2005)

This paper describes the design and implementation of a system that uses virtual machine technology [1] to provide fast, transparent application migration. This is the first system that can migrate unmodified applications on unmodified mainstream Intel x86-based operating system, including Microsoft Windows, Linux, Novell NetWare and others. Neither the application nor any clients communicating with the application can tell that the application has been migrated. Experimental measurements show that for a variety of workloads, application downtime caused by migration is less than a second. 1
Injection locking in distributed feedback semiconductor lasers (1991)

Injection locking properties of distributed feedback semiconductor lasers are studied systematically. Due to the high side mode suppression, these devices show different locking properties when compared to lasers with Fabry-Perot structures. The main result is the identification of four regimes for different injection levels. In particular, a symmetrical locking band at low optical injection level is confirmed. The presence of this symmetrical band can be exploited in some applications. As examples, the measurement of the linewidth enhancement factor and the phase-shift-keying modulation capability are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
T-cell subsets and suppressor cells in human bone marrow (1992)

To characterize immune suppressive and hematopoietic features of enriched subsets of human marrow cells, we separated these cells on Percoll density gradients. CD4+ and CD8+ T cells (CD3+) were enriched in the high-density marrow cell fractions and reduced in low-density fractions. CD4-CD8- (CD3+) T cells expressing the alpha beta T-cell antigen receptor were at least 10 times less numerous than the CD4+ and CD8+ T cells in all fractions. Purified populations of the CD4-CD8- alpha beta + T cells obtained by flow cytometry suppressed the mixed leukocyte reaction (MLR). Another population of suppressor cells that expressed neither T-cell (CD3) nor natural killer cell (CD16) surface markers was also identified. The latter cells had the phenotypic and functional characteristics of “natural suppressor” cells. Suppressor cell activity was enriched in the low-density fractions along with hematopoietic progenitors (colony-forming unit-granulocyte-macrophage and burst-forming unit-erythroid). The progenitor and suppressor cell activities were depleted in high-density fractions. The latter fractions made vigorous responses in the MLR. The low-density fractions, which accounted for less than 10% of the input marrow cells, suppressed the MLR and did not respond. Further evaluation of the low-density fractions may be of value in allogeneic bone marrow transplantation due to the reduction of CD4+ and CD8+ T cells and the enrichment of hematopoietic progenitors as well as immune suppressor cells that may inhibit graft-versus-host disease.
Fusion Proteins for Combined Analysis of Autoantibodies to the 65-kDa Isoform of Glutamic Acid Decarboxylase and Islet Antigen-2 in Insulin-dependent Diabetes Mellitus (2001)

Autoantigens such as GAD65 and IA2 can be combined successfully in a fusion protein of similar immune reactivity. This allows simultaneous detection of GAD65- and IA2-abs in a one-step screening assay and cost-effective identification of positive individuals at risk of diabetes or at onset of disease.
Effects of temporal modelling on the statistical uncertainty of spatiotemporal distributions estimated directly from dynamic SPECT projections (2002)

Artefacts can result when reconstructing a dynamic image sequence from inconsistent single photon emission computed tomography (SPECT) projection data acquired by a slowly rotating gantry. The artefacts can lead to biases in kinetic parameters estimated from time-activity curves generated by overlaying volumes of interest on the images. Insufficient sampling and truncation of projections by cone-beam collimators can cause additional artefacts. To overcome these sources of bias in conventional image based dynamic data analysis, we have been investigating the estimation of time-activity curves and kinetic model parameters directly from dynamic SPECT projection data by modelling the spatial and temporal distribution of the radiopharmaceutical throughout the projected field of view. In the present work, we perform Monte Carlo simulations to study the effects of the temporal modelling on the statistical variability of the reconstructed spatiotemporal distributions. The simulations utilize fast methods for fully four-dimensional (4D) direct estimation of spatiotemporal distributions and their statistical uncertainties, using a spatial segmentation and temporal B-splines. The simulation results suggest that there is benefit in modelling higher orders of temporal spline continuity. In addition, the accuracy of the time modelling can be increased substantially without unduly increasing the statistical uncertainty, by using relatively fine initial time sampling to capture rapidly changing activity distributions.