gebhart/patrepeval huggingface dataset:
Reptation of a Polymer Chain in the Presence of Fixed Obstacles (1971)

We discuss possible motions for one polymer molecule P (of mass M) performing wormlike displacements inside a strongly cross-linked polymeric gel G. The topological requirement that P cannot intersect any of the chains of G is taken into account by a rigorous procedure: The only motions allowed for the chain are associated with the displacement of certain “defects” along the chain. The main conclusions derived from this model are the following: (a) There are two characteristic times for the chain motion: One of them (Td) is the equilibration time for the defect concentration, and is proportional to M2. The other time (Tr) is the time required for complete renewal of the chain conformation, and is proportional to M3. (b) The over-all mobility and diffusion coefficients of the chain P are proportional to M−2. (c) At times t &amp;lt; Tr the mean square displacement of one monomer of P increases only like 〈(rt − r0)2〉 = const t1/4. These results may also turn out to be useful for the (more difficult) problem of entanglement effects in unlinked molten polymers.
Three‐Dimensional Fabrication by Reaction‐Diffusion: “Remote” Fabrication via Three‐Dimensional Reaction‐Diffusion: Making Complex Core‐and‐Shell Particles and Assembling Them into Open‐Lattice Crystals (Adv. Mater. 19/2009) (2009)

Reaction-diffusion processes initiated from the surfaces of small gel or polymer particles can fabricate complex three-dimensional structures inside these particles. Bartosz Grzybowski and co-workers show on page 1911 that the core/shell particles thus prepared can be further modified “remotely” by electrochemical exchange reactions. The image shows four cubical particles, each having a spherical core fabricated by reaction-diffusion and comprising copper nanoparticles.
Expression and role of acidic mammalian chitinase and eotaxin-3 in chronic rhinosinusitis with nasal polyps. (2011)

Our results reveal that AMCase and eotaxin-3 may be important mediators in the pathogenesis of nasal polyps. The increased AMCase and eotaxin-3 might lead to nasal polyp formation and growth. Future studies are needed to determine the potential of AMCase and eotaxin-3 as therapeutic targets in CRSwNPs.
Probing Intramolecular Förster Resonance Energy Transfer in a Naphthaleneimide−Peryleneimide−Terrylenediimide-Based Dendrimer by Ensemble and Single-Molecule Fluorescence Spectroscopy (2005)

We report on the ensemble and single-molecule (SM) dynamics of Förster resonance energy transfer (FRET) in a multichromophoric rigid polyphenylenic dendrimer (triad) with spectrally different rylene chromophores featuring distinct absorption and emission spectra which cover the whole visible spectral range: a terrylenediimide (TDI) core, four perylenemonoimides (PMIs) attached at the scaffold, and eight naphthalenemonoimides (NMIs) at the rim. For FRET from PMI to TDI taking place with an efficiency of 99.5%, single triad molecules optically excited at 490 nm show fluorescence exclusively from the TDI side in the beginning of their emission. On 360-nm excitation, NMI chromophores transfer their excitation energy either directly or in a stepwise fashion to the core TDI, the latter case involving scaffold-substituted PMIs as intermediate acceptors. Indeed, SM experiments on 360-nm excitation evidence highly efficient FRET from NMI chromophores to the TDI core since individual triad molecules show fluorescence exclusively either from TDI or from an intermediate (oxidized) species but never from PMI. Because PMI and TDI are chromophores with high fluorescence quantum yields and high resistance to photobleaching compared to NMI, 360-nm excitation of a single triad molecule leads to bleaching of NMI chromophores with no chance for PMI to be observed. The spatial positioning and the spectral properties of the chosen rylene chromophores make this multichromophoric system an efficient light collector, able to capture light over the whole visible spectral range and to transfer it finally to the core TDI, the latter releasing it as red fluorescence.
Inhibition of the replication of hepatitis B virus in vitro by 2',3'-dideoxy-3'-thiacytidine and related analogues. (1991)

Several 2',3'-dideoxy-3'-thiapyrimidine nucleosides were studied for their ability to inhibit hepatitis B virus (HBV) DNA replication in a HBV-transfected cell line (2.2.15). 2',3'-Dideoxy-3'-thiacytidine (SddC) and 5-fluoro-2',3'-dideoxy-3'-thiacytidine(5-FSddC) were found to be the most potent anti-HBV compounds of those examined. Both compounds resulted in nearly complete cessation of viral DNA replication at 0.5 microM, as monitored by the absence of both intracellular episomal and secreted viral DNAs. The HBV-specific RNAs were not reduced at concentrations that completely blocked HBV DNA replication, suggesting that the inhibitory target is HBV DNA synthesis. The antiviral action of SddC and 5-FSddC was reversible. The concentration of SddC and 5-FSddC required to inhibit 50% of 4-day cell growth in culture was 37 microM and more than 200 microM, respectively. Unlike 2',3'-dideoxycytidine, these two compounds do not affect mitochondrial DNA synthesis in cells at concentrations lower than that required to inhibit cell growth. In view of the potent and selective antiviral activity, both SddC and 5-FSddC should be further evaluated for the treatment of human HBV infection.
Targeted Delivery of DNA Encoding Cytotoxic Proteins through High-Affinity Fibroblast Growth Factor Receptors (1998)

Nonviral DNA delivery strategies for gene therapy have generally been limited by a lack of specificity and efficacy. However, ligand-mediated endocytosis can specifically deliver DNA in vitro to cells bearing the appropriate cognate receptors. Similarly, in order to circumvent problems related to efficacy, DNA must encode proteins with high intrinsic activities. We show here that the ligand basic fibroblast growth factor (FGF2) can target FGF receptor-bearing cells with DNA encoding therapeutic proteins. Delivery of genes encoding saporin, a highly potent ribosomal inactivating protein, or the conditionally cytotoxic herpes simplex virus thymidine kinase, a protein that can kill cells by activating the prodrug ganciclovir, is demonstrated. The saporin gene was codon optimized for mammalian expression and demonstrated to express functional protein in a cell-free assay. FGF2-mediated delivery of saporin DNA or thymidine kinase DNA followed by ganciclovir treatment resulted in a 60 and 75% decrease in cell number, respectively. Specificity of gene delivery was demonstrated in competition assays with free FGF2 or with recombinant soluble FGF receptor. Alternatively, when histone H1, a ligand that binds to cell surface heparan sulfate proteoglycans ("low-affinity" FGF receptors), was used to deliver DNA encoding thymidine kinase, no ganciclovir sensitivity was observed. These findings establish the feasibility of using ligands such as FGF2 to specifically deliver genes encoding molecular chemotherapeutic agents to cells.
Infection by the Retrovirus Associated with the Acquired Immunodeficiency Syndrome (1985)

Peripheral mononuclear cells from more than 160 persons from groups at risk for the acquired immunodeficiency syndrome (AIDS) have yielded AIDS-associated retroviruses (ARV). Antibodies to ARV can also be found in these risk groups. Antibody-negative, virus-positive persons have been identified with early infection or possible viremia with immune complex formation. Established lines of human T and B cells, monocytes, and promyelocytes have been infected with ARV. Moreover, infectious virus has been recovered from macrophages cultured from the blood of some persons with AIDS. The cytopathic effects of ARV in T cells is associated with the accumulation of unintegrated viral forms in the infected cells. The ARV has also been isolated from plasma, serum, saliva, semen, urine, cerebrospinal fluid, and brain tissue. All these results reflect the wide host range of ARV and support its role in neurologic abnormalities seen in some patients. Molecular studies of independent ARV isolates indicate a polymorphism of nucleotide sequences, particularly in the viral envelope region. All these features place ARV in the lentivirus subfamily of human retroviruses.
Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species (1990)

Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
Expression and localization of the fibronectin receptor in the mouse nervous system (1988)

Cell surface receptors for extracellular matrix components have recently been characterized as integral membrane complexes with common features in their structural and functional properties. We have investigated the expression of the mammalian fibronectin receptor in the mouse nervous system using immunocytological and immunochemical methods. The fibronectin receptor was detectable on immature oligodendrocytes and immature and mature astrocytes in culture, while central nervous system neurons did not reveal detectable levels of fibronectin receptor at the developmental stages studied. In the peripheral nervous system both glia and neurons were found to express the fibronectin receptor. The receptor complex in both peripheral and central nervous system has an apparent molecular weight of approximately 140 kD under reducing conditions and resolves into two or three distinct protein bands under nonreducing conditions. The fibronectin receptor expresses the L2/HNK-1 epitope that is characteristic of several adhesion molecules, including L1, N-CAM, the myelin-associated glycoprotein, and J1 and thus is another member of the L2/HNK-1 family of adhesion molecules. The L2/HNK-1 carbohydrate epitope is expressed differently and independently of the fibronectin receptor protein backbone in that it is detectable in neonatal brain but not in adult brain. Our observations attribute a functional role to the fibronectin receptor and its L2/HNK-1 carbohydrate epitope during development and maintenance of cell interactions in the central and peripheral nervous systems.
An Autosome-Wide Scan for Linkage Disequilibrium–Based Association in Sporadic Breast Cancer Cases in Eastern Finland: Three Candidate Regions Found (2005)

Breast cancer is the most common of cancers among women in industrialized countries. Many of breast cancer risk factors are known, but the majority of the genetic background is still unknown. Linkage disequilibrium-based association is a powerful tool for mapping disease genes and is suitable for mapping complex traits in founder populations. We report the results of a two-stage, autosome-wide scan for LD with breast cancer. Our aim was to identify genetic risk factors for sporadic breast cancer in an eastern Finnish population. Our case-control set is from the province of northern Savo in the late-settlement area of eastern Finland. This population is relatively young and genetically homogeneous. We used 435 autosomal microsatellite markers spaced by an average of 10 cM in a set of 49 breast cancer cases and 50 controls. In the first-stage scan, we found 21 markers in LD with breast cancer (Ps = 0.003-0.046, Fisher's exact test). In the second-stage scan with markers flanking 21 positive loci, four significant markers were found (Ps = 0.013-0.046, Fisher's exact test). Haplotype analysis using global score method with two, three, or four markers also revealed four positive marker combinations (simulated P for global score = 0.003-0.021). Our results suggest breast cancer-associated regions on 3p26, 11q23, and 22q13.1 in an eastern Finnish population.
CD47: A Cell Surface Glycoprotein Which Regulates Multiple Functions of Hematopoietic Cells in Health and Disease (2013)

Interactions between cells and their surroundings are important for proper function and homeostasis in a multicellular organism. These interactions can either be established between the cells and molecules in their extracellular milieu, but also involve interactions between cells. In all these situations, proteins in the plasma membranes are critically involved to relay information obtained from the exterior of the cell. The cell surface glycoprotein CD47 (integrin-associated protein (IAP)) was first identified as an important regulator of integrin function, but later also was shown to function in ways that do not necessarily involve integrins. Ligation of CD47 can induce intracellular signaling resulting in cell activation or cell death depending on the exact context. By binding to another cell surface glycoprotein, signal regulatory protein alpha (SIRPα), CD47 can regulate the function of cells in the monocyte/macrophage lineage. In this spotlight paper, several functions of CD47 will be reviewed, although some functions may be more briefly mentioned. Focus will be on the ways CD47 regulates hematopoietic cells and functions such as CD47 signaling, induction of apoptosis, and regulation of phagocytosis or cell-cell fusion.
Efficacy of infliximab in the treatment of uveitis that is resistant to treatment with the combination of azathioprine, cyclosporine, and corticosteroids in behçet's disease: An open‐label trial (2005)

The results of this trial suggest that infliximab is effective in suppressing the occurrence of uveitis attacks, has a corticosteroid-sparing effect, and has favorable implications for the visual prognosis of patients with resistant Behçet's uveitis.
Detection of trojans using a combined ring oscillator network and off-chip transient power analysis (2013)

Verifying the trustworthiness of Integrated Circuits (ICs) is of utmost importance, as hardware Trojans may destroy ICs bound for critical applications. A novel methodology combining on-chip structure with external current measurements is proposed to verify whether or not an IC is Trojan free. This method considers Trojans' impact on neighboring cells and on the entire IC's power consumption, and effectively localizes the measurement of dynamic power. To achieve this, we develop a new on-chip ring oscillator network structure distributed across the entire chip and place each ring oscillator's components in different rows of a standard-cell design. By developing novel statistical data analysis, the effect of process variations on the ICs' transient power will be separated from the effect of Trojans. Simulation results using 90nm technology and experimental results on Xilinx Spartan-6 FPGAs demonstrate the efficiency of our proposed method.
The functional significance of vitamin K action. Difference in phospholipid binding between normal and abnormal prothrombin (1975)

In comparison to normal prothrombin, the abnormal prothrombin produced in response to vitamin K antagonists has been found to bind much less tightly, if at all, to phospholipid surfaces. As a consequence, the activation of abnormal prothrombin by Factor Xa and Ca2+ is not accelerated by the addition of phospholipid to the mixture while the activation of normal prothrombin under these conditions is greatly accelerated by phospholipid addition. In the absence of phospholipid, however, the rate of activation of abnormal prothrombin by Factor Xa and Ca2+ in both the presence and absence of Factor Va is indistinguishable from that of normal prothrombin. The distribution of the partial proteolysis products during activation by Factors Xa, Va, and Ca2+ also appears to be the same for both prothrombins. These observations provide an explanation for the function in prothrombin activation of the gamma-carboxyglutamate residues formed in the vitamin K-dependent carboxylation of prothrombin.
Motion adaptive error resilient encoding for MPEG-4 (2002)

Optimising delivery of video codecs such as MPEG-4 is vital to ensure that acceptable quality can be offered to 3G network customers. The error prone nature of mobile channels means that the video codec that is employed must be fairly robust. In the past, such research has required alteration to existing standards. Given the imminent implementation of 3G technologies, changing the standards is not a convenient option. This paper presents a technique for altering MPEG-4 encoding parameters to increase the error robustness of the output bitstream. It exploits the fact that frames with a high degree motion are often more sensitive to error than those with low amounts of motion. Using a simple model, the video packet length and number of adaptive intra refresh (AIR) blocks are varied according to the amount of motion in a frame. Simulations using a GPRS channel are presented to confirm the benefits of the proposed scheme.
Multimodality Cardiovascular Molecular Imaging, Part I (2008)

In Part I of this consensus article, the imaging methodology, evolving imaging technology, and development of novel targeted molecular probes relevant to the developing field of cardiovascular molecular imaging were reviewed. Novel reporter gene and reporter probe imaging approaches for tracking of cardiac transgene expression were also discussed and have important future implications for evaluation of gene- and cell-based therapies for the failing heart. The current role of metabolic and receptor imaging was also briefly reviewed, as these represent the beginning of our clinical application of molecular imaging within the cardiovascular system. Part II will summarize the available targeted imaging probes as well as specific future applications of molecular imaging for identification and evaluation of critical pathophysiological processes of the cardiovascular system.
Drusen associated with aging and age‐related macular degeneration contain proteins common to extracellular deposits associated with atherosclerosis, elastosis, amyloidosis, and dense deposit disease (2000)

Age-related macular degeneration (AMD), a blinding disorder that compromises central vision, is characterized by the accumulation of extracellular deposits, termed drusen, between the retinal pigmented epithelium and the choroid. Recent studies in this laboratory revealed that vitronectin is a major component of drusen. Because vitronectin is also a constituent of abnormal deposits associated with a variety of diseases, drusen from human donor eyes were examined for compositional similarities with other extracellular disease deposits. Thirty-four antibodies to 29 different proteins or protein complexes were tested for immunoreactivity with hard and soft drusen phenotypes. These analyses provide a partial profile of the molecular composition of drusen. Serum amyloid P component, apolipoprotein E, immunoglobulin light chains, Factor X, and complement proteins (C5 and C5b-9 complex) were identified in all drusen phenotypes. Transcripts encoding some of these molecules were also found to be synthesized by the retina, retinal pigmented epithelium, and/or choroid. The compositional similarity between drusen and other disease deposits may be significant in view of the recently established correlation between AMD and atherosclerosis. This study suggests that similar pathways may be involved in the etiologies of AMD and other age-related diseases.
Exogenous Carbohydrate Spares Muscle Glycogen in Men and Women during 10 h of Exercise (2007)

The ingestion of CHO during long-duration exercise decreases net muscle glycogen use while better maintaining whole-body carbohydrate oxidation, and potentially increasing performance in field settings. There are limited differences in sex-specific substrate oxidation.
Neural network based edge detection for CBCT segmentation (2015)

Edge detection is an important task in image processing, many times as part of the segmentation process. When segmentation is performed in medical imaging, one of the preferred tools is neural networks, because of their capabilities of adaptive learning and non-linear mapping. We present in this paper the neural network tools used for edge detection and we propose one that is able to perform edge detection in dental Cone Beam Computer Tomography (CBCT) images, a necessary step for the teeth 3D reconstruction.
Gene Targeting in Stem Cells from Individuals with Osteogenesis Imperfecta (2004)

Adult stem cells offer the potential to treat many diseases through a combination of ex vivo genetic manipulation and autologous transplantation. Mesenchymal stem cells (MSCs, also referred to as marrow stromal cells) are adult stem cells that can be isolated as proliferating, adherent cells from bones. MSCs can differentiate into multiple cell types present in several tissues, including bone, fat, cartilage, and muscle, making them ideal candidates for a variety of cell-based therapies. Here, we have used adeno-associated virus vectors to disrupt dominant-negative mutant COL1A1 collagen genes in MSCs from individuals with the brittle bone disorder osteogenesis imperfecta, demonstrating successful gene targeting in adult human stem cells.
Evidence of an immune response to Ureaplasma urealyticum in perinatal morbidity and mortality (1986)

Ureaplasma urealyticum has been associated with spontaneous pregnancy loss, neonates requiring intensive care, neonatal death and more recently respiratory disease. Due to high colonization rates it has been difficult to determine whether Ureaplasmas cause infection in humans. Therefore in this overview sera from over 300 cases were assessed to determine the prevalence of an elevated antibody response to U. urealyticum. Prospectively 22 cases of stillbirth, 75 neonatal deaths and 46 normal cases were studied, in addition to 259 retrospective cases of neonates with respiratory disease of which 56 were term gestations. An antibody response greater than or equal to 1:32 to at least 1 of the 8 serovars of U. urealyticum occurred in 77.3% of stillbirths, 58.3% of respiratory disease cases, 69.3% of neonatal deaths and 80.4% of term neonates, compared to 6.5% of well term neonates (P less than 0.001 each). Elevated titers were detected in the mothers in 65.0, 54.7, 62.9, and 64.5% of each group, respectively, compared to 8.5% in mothers of healthy control cases (P less than 0.001 each). When all groups were combined the mortality rate was 61.3% among the 155 neonates who had at least one Ureaplasma titer of greater than or equal to 1:32 compared to 27.1% of 168 with a maximum titer of 1:16 (P less than 0.001). Thus in humans the prevalence of antibody response to any of 8 U. urealyticum serovars was significantly higher in potentially infected cases such as stillbirth and neonatal respiratory disease, particularly among those born at term or who die, compared to normal mothers and neonates. Presence of an elevated antibody response correlated significantly with an increased mortality rate.