gebhart/patrepeval huggingface dataset:
Chemically Modified Oligonucleotides as Probes and Inhibitors (1991)

Abstract Oligonucleotides bind specifically to single‐stranded nucleic acids to form a double helix if there is a complementary antiparallel nucleotide sequence. In addition, certain oligonucleotides bind specifically to a variety of proteins. Therefore, biological processes involving these nucleic acids or proteins can be modulated (normally inhibited) by addition of the respective oligonucleotides. The effects of these oligonucleotides and the fields of potential application can be broadened by the introduction of chemically modified nucleotides. For instance, replacing oligonucleotide phosphate groups by methylphosphonates results in the loss of one negative charge per nucleotide and the oligonucleotide becomes more lipophilic. An oligonucleotide carrying a reactive group can modify its binding partner. An oligonucleotide covalently linked to a dye can be localized in a biological specimen. Oligonucleotides attached to an enzyme can be detected in very small amounts since the enzyme can catalyze the formation of large amounts of the substance assayed (e.g., a fluorescent product). An important biochemical application is the detection and localization of a messenger RNA or its gene. Medical applications include the detection of bacterial or viral sequences. There is also great interest in inhibiting the translation of messenger RNA and the transcription and replication of DNA. So‐called antisense oligonucleotides are currently being used for the inhibition of protein biosynthesis and of reverse transcription of retroviruses.
In vivoimaging of irreversible electroporation by means of electrical impedance tomography (2009)

Electroporation, the increased permeability of cell membranes due to a large transmembrane voltage, is an important clinical tool. Both reversible and irreversible in vivo electroporation are used for clinical applications such as gene therapy and solid malignant tumor ablation, respectively. The primary advantage of in vivo electroporation is the ability to treat tissue in a local and minimally invasive fashion. The drawback is the current lack of control over the process. This paper is the first report of a new method for real-time three-dimensional imaging of an in vivo electroporation process. Using two needle electrodes for irreversible electroporation and a set of electrodes for reconstructing electrical impedance tomography (EIT) images of the treated tissue, we were able to demonstrate electroporation imaging in rodent livers. Histology analysis shows good correlation between the extent of tissue damage caused by irreversible electroporation and the EIT images. This new method may lead the way to real-time control over genetic treatment of diseases in tissue and tissue ablation.
Apple and Pear Peel and Pulp and Their Influence on Plasma Lipids and Antioxidant Potentials in Rats Fed Cholesterol-Containing Diets (2003)

The aim of this study was to assess the bioactive compounds of apple and pear peel and pulp in vitro and their influence on plasma lipids and antioxidant potentials in vivo. The antioxidant potentials measured by 1,1-diphenyl-2-picrylhydrazyl (DPPH), β-carotene bleaching (β-carotene), and nitric oxide inhibition radical scavenging (NO) tests in apple peel and pulp were significantly higher than in pear peel and pulp, respectively. The ethanol extract of apple peels showed the strongest inhibition of lipid peroxidation as a function of its concentration and was comparable to the antioxidant activity of butylated hydroxyanisole. The pear pulp extract had the weakest antioxidant ability, whereas other extracts such as apple pulp and pear peel were nearly equal. The antioxidant activities comprised contributions from polyphenols, phenolic acids, and flavonoids and correlated well with polyphenols and flavonoids. The correlation coefficients between polyphenols and antioxidant activities by DPPH, β-carotene, and NO were as follows: 0.9207, 0.9350, and 0.9453. Contrarily, the correlation coefficient between the content of dietary fiber and the antioxidant activities test was low. The content of all studied indices in apple and pear peel was significantly higher than in peeled fruits (p < 0.05). Diets supplemented with fruit peels exercised a significantly higher positive influence on plasma lipid levels and on plasma antioxidant capacity of rats than diets with fruit pulps. Keywords: Apple; pear; peel; pulp; bioactive compounds; rats
Using boronolectin in MALDI-MS imaging for the histological analysis of cancer tissue expressing the sialyl Lewis X antigen (2011)

Certain carbohydrate-based biomarkers are known to correlate with cancer formation and progression. By targeting sialyl Lewis X, we have developed the first boronolectin-MS tag conjugate, which allows for MALDI-based imaging of cancer based on its cell surface carbohydrate.
Characterization and subcellular localization of the Clostridium thermocellum scaffoldin dockerin binding protein SdbA (1997)

This article reports the characterization of the Clostridium thermocellum SdbA protein thought to anchor the cellulosome to the bacterial cell surface. The NH2-terminal region of SdbA consists of a cohesin domain which specifically binds the dockerin domain of the cellulosomal scaffolding protein CipA. The COOH-terminal region consists of a triplicated segment, termed SLH repeats, which is present in the sequence of many bacterial cell surface polypeptides. The binding parameters of the interaction between the dockerin domain of CipA and the cohesin domain of SdbA were studied by using, as a probe, the chimeric polypeptide CelC-DSCipA, which carries the dockerin domain of CipA fused to endoglucanase CelC. In the presence of Ca2+, CelC-DSCipA bound to SdbA with an affinity constant of 1.26 x 10(7) M(-1). Binding of CelC-DSCipA to SdbA as a function of Ca2+ concentration was sigmoidal, corresponding to a Hill coefficient of 2 and an affinity constant for Ca2+ of 4 x 10(6) M(-2). This suggested the presence of two cooperatively bound Ca2+ ions in the cohesin-dockerin complex. Immunoblotting of C. thermocellum subcellular fractions and electron microscopy of immunocytochemically labeled cells indicated that SdbA is located on the cell surface and is a component of the cellulosome. Together, the data confirm that SdbA could mediate anchoring of the cellulosome to the surface of C. thermocellum cells by interacting with the dockerin domain of CipA.
Synthesis of Sulfotyrosine‐Containing Peptides by Incorporating Fluorosulfated Tyrosine Using an Fmoc‐Based Solid‐Phase Strategy (2015)

Tyrosine O-sulfation is a common protein post-translational modification that regulates many biological processes, including leukocyte adhesion and chemotaxis. Many peptides with therapeutic potential contain one or more sulfotyrosine residues. We report a one-step synthesis for Fmoc-fluorosulfated tyrosine. An efficient Fmoc-based solid-phase peptide synthetic strategy is then introduced for incorporating the fluorosulfated tyrosine residue into peptides of interest. Standard simultaneous peptide-resin cleavage and removal of the acid-labile side-chain protecting groups affords the crude peptides containing fluorosulfated tyrosine. Basic ethylene glycol, serving both as solvent and reactant, transforms the fluorosulfated tyrosine peptides into sulfotyrosine peptides in high yield.
Proliferin secreted by cultured cells binds to mannose 6-phosphate receptors. (1988)

Proliferin is a prolactin-related glycoprotein secreted by proliferating mouse cell lines and by mouse placenta. In an attempt to identify target sites for proliferin action, we looked for proliferin receptors in murine fetal and maternal tissues during pregnancy using proliferin purified from the conditioned medium of a constructed Chinese hamster ovary cell line carrying amplified copies of proliferin cDNA. Purified proliferin bound to membrane preparations from fetal or maternal liver and from placenta with a Kd of 1 to 2 nM. The amount of proliferin bound per microgram of membrane protein varied markedly during pregnancy; maximal binding to day 16 fetal liver membranes was approximately 25 times that to liver membranes from adult animals. Binding to fetal and maternal receptors was specifically and completely inhibited by mannose 6-phosphate, with half-maximal inhibition at 10 microM. Furthermore, non-glycosylated proliferin did not inhibit the binding of the glycosylated protein. A approximately 300 Kd proliferin receptor was purified from the liver of pregnant mice using a proliferin affinity column and elution with mannose 6-phosphate. This receptor reacted with antibodies directed against the rat cation-independent mannose 6-phosphate receptor. We conclude that 1) proliferin secreted by cultured cell binds to cation-independent mannose 6-phosphate receptors and therefore may be a lysosomal protein or targeted to lysosomes, and 2) the concentration or activity of mannose 6-phosphate receptors in murine fetal and maternal liver and in placenta is regulated during pregnancy.
Growth, conductivity, and vapor response properties of metal ion-carboxylate linked nanoparticle films (2003)

Nanoparticles of metals (Au, Ag, Pd, alloys) in the size range 1-3 nm diameter can be stabilized against aggregation of the metal particles by coating the metal surface with a dense monolayer of ligands (thiolates). The stabilization makes it possible to analytically define the nanoparticle composition (for example, Au140(hexanethiolate)53, I) and to elaborate the chemical functionality of the protecting monolayer (for example, Au140(C6)35(MUA)18, II, where C6 = hexanethiolate and MUA = mercaptoundecanoic acid). Network polymer films (IIfilm) on interdigitated array electrodes can be prepared from II, based on cation coordination (i.e., Cu2+, Zn2+, Ag+, methyl viologen) by the carboxylates of MUA. The electronic conductivity of the IIfilm network polymer films occurs by electron hopping between the Au140 nanoparticle cores, and offers an avenue for investigation of metal-to-metal nanoparticle electron transfer chemistry. The report begins with a brief summary of what is known about metal nanoparticle electron transfer chemistry. The investigation goes on to assess factors that influence the dynamics of film formation as well as film conductivity, in the interest of better understanding the parameters affecting electron hopping rates in IIfilm network polymer films. Finally, sorption of organic vapors into IIfilm causes a decreased electronic conductivity and increased mass that can be assessed using quartz crystal microbalance measurements. The change in electronic conductivity can be exploited for the sensing of organic vapors.
Bone disease in adolescents with acne fulminans and severe cystic acne: radiologic and scintigraphic findings. (1994)

Lytic lesions in the bones of the anterior chest wall and in the epiphyseal growth plates are common in patients with acne fulminans, but do not seem to occur in patients with severe cystic acne. The prognosis of bone disease associated with acne fulminans appears to be good, and the chronic sequelae, if any, are mild sclerosis and hyperostosis of the affected bones. Acne fulminans should be added to the list of dermatoses associated with bone lesions detectable by radiologic and scintigraphic methods.
SPX: global authentication using public key certificates (2002)

SPX, a reference implementation of an open distributed authentication service architecture based on ISO Standard 9594-9/CCITT X.509 directory public key certificates and hierarchically organized certification authorities, is described. SPX manages the end system state and provides the run-time environment enabling applications to mutually authenticate on the basis of a global principal identity. SPX scales well in that it does not require online trusted components, and permits management of global trust relationship policy in arbitrarily large distributed environments. Conceptual, component, and protocol descriptions are provided.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regularized Sampling of Multiband Signals (2010)

This paper presents a regularized sampling method for multiband signals, that makes it possible to approach the Landau limit, while keeping the sensitivity to noise and perturbations at a low level. The method is based on band-limited windowing, followed by trigonometric approximation in consecutive time intervals. The key point is that the trigonometric approximation “inherits” the multiband property, that is, its coefficients are formed by bursts of elements corresponding to the multiband components. It is shown that this method can be well combined with the recently proposed synchronous multirate sampling (SMRS) scheme, given that the resulting linear system is sparse and formed by ones and zeroes. The proposed method allows one to trade sampling efficiency for noise sensitivity, and is specially well suited for bounded signals with unbounded energy like those in communications, navigation, audio systems, etc. Besides, it is also applicable to finite energy signals and periodic band-limited signals (trigonometric polynomials). The paper includes a subspace method for blindly estimating the support of the multiband signal as well as its components, and the results are validated through several numerical examples.
Mechanisms of Lipid Transport Involved in Organelle Biogenesis in Plant Cells (2009)

Chloroplasts are the defining organelle of photoautotrophic plant cells. Photosynthetic light reactions and electron transport are the functions of an elaborate thylakoid membrane system inside chloroplasts. The lipid composition of photosynthetic membranes is characterized by a substantial fraction of nonphosphorous galactoglycerolipids reflecting the need of sessile plants to conserve phosphorus. Lipid transport and assembly of glycerolipids play an essential role in the biogenesis of the photosynthetic apparatus in developing chloroplasts. During chloroplast biogenesis, fatty acids are synthesized in the plastid and are exported to the endoplasmic reticulum, where they are incorporated into membrane lipids. Alternatively, lipids can also be assembled de novo at the inner envelope membrane of plastids in many plants. A rich repertoire of lipid exchange mechanisms involving the thylakoid membranes, the chloroplast inner and outer envelope membranes, and the endoplasmic reticulum is emerging. Studies of thylakoid biogenesis provide new insights into the general mechanisms of intermembrane lipid transfer.
Diffraction and interface losses in broadband ultrasound attenuation measurements of the calcaneum (1998)

Ultrasonic investigation of bone disease most frequently involves measurements on the heel, and the parameter most often used for this is the broadband ultrasound attenuation (BUA) which is the slope of the attenuation as a function of frequency between 0.2 and 0.6 MHz. In this study, the possible losses in the BUA measurement due to diffraction and interfaces have been discussed and evaluated using existing data and a standard diffraction model. The loss due to diffraction was found to depend critically upon whether a contact or immersion technique is used. For a contact method, we estimate that the diffraction loss can be greater than 10 dB MHz-1, whereas insertion devices typically will have losses of up to 0.6 dB MHz-1, and it not always clear whether or how manufacturers have attempted to correct for this. Dispersion which is found in the os calcis has only a small effect on the diffraction loss, but it can cause a frequency dependent interface loss of about 0.2 dB MHz-1. It may be impossible to correct for these discrepancies in vivo as the necessary data for the individual components of the heel are not known. However the losses should be borne in mind as factors limiting the accuracy of the measurements and, in the case of in vitro investigations, may merit further study.
Maternal use of cannabis and pregnancy outcome (2002)

The results of this study suggest that the use of cannabis during pregnancy was not associated with increased risk of perinatal mortality or morbidity in this sample. However, frequent and regular use of cannabis throughout pregnancy may be associated with small but statistically detectable decrements in birthweight.
Glucocorticoid-Related Molecular Signaling Pathways Regulating Hippocampal Neurogenesis (2012)

Stress and glucocorticoid hormones regulate hippocampal neurogenesis, but the molecular mechanisms underlying their effects are unknown. We, therefore, investigated the molecular signaling pathways mediating the effects of cortisol on proliferation, neuronal differentiation, and astrogliogenesis, in an immortalized human hippocampal progenitor cell line. In addition, we examined the molecular signaling pathways activated in the hippocampus of prenatally stressed rats, characterized by persistently elevated glucocorticoid levels in adulthood. In human hippocampal progenitor cells, we found that low concentrations of cortisol (100 nM) increased proliferation (+16%), decreased neurogenesis into microtubule-associated protein 2 (MAP2)-positive neurons (-24%) and doublecortin (Dcx)-positive neuroblasts (-21%), and increased differentiation into S100β-positive astrocytes (+23%). These effects were dependent on the mineralocorticoid receptor (MR) as they were abolished by the MR antagonist, spironolactone, and mimicked by the MR-agonist, aldosterone. In contrast, high concentrations of cortisol (100 μM) decreased proliferation (-17%) and neuronal differentiation into MAP2-positive neurons (-22%) and into Dcx-positive neuroblasts (-27%), without regulating astrogliogenesis. These effects were dependent on the glucocorticoid receptor (GR), blocked by the GR antagonist RU486, and mimicked by the GR-agonist, dexamethasone. Gene expression microarray and pathway analysis showed that the low concentration of cortisol enhances Notch/Hes-signaling, the high concentration inhibits TGFβ-SMAD2/3-signaling, and both concentrations inhibit Hedgehog signaling. Mechanistically, we show that reduced Hedgehog signaling indeed critically contributes to the cortisol-induced reduction in neuronal differentiation. Accordingly, TGFβ-SMAD2/3 and Hedgehog signaling were also inhibited in the hippocampus of adult prenatally stressed rats with high glucocorticoid levels. In conclusion, our data demonstrate novel molecular signaling pathways that are regulated by glucocorticoids in vitro, in human hippocampal progenitor cells, and by stress in vivo, in the rat hippocampus.
Evaluation of ricin A chain-containing immunotoxins directed against the CD30 antigen as potential reagents for the treatment of Hodgkin's disease. (1990)

Five monoclonal CD30 antibodies and two Fab' fragments were linked to deglycosylated ricin A chain (dgA), and their potential as immunotoxins for the treatment of Hodgkin's disease was evaluated. Cross-blocking experiments demonstrated that HRS-1, HRS-3, HRS-4, and Ber-H2 recognize the same epitope on the CD30 antigen and that Ki-1 binds to a different epitope. Scatchard analyses showed that HRS-3, HRS-4, and Ber-H2 bound strongly to L540 Hodgkin cells (Kd 15, 7, and 14 nM, respectively), whereas HRS-1 and Ki-1 bound more weakly (Kd 160 and 380 nM, respectively). The different affinities of the antibodies correlated closely with their cytotoxic potency as immunotoxins. HRS-3.dgA, HRS-4.dgA, and Ber-H2.dgA inhibited the protein synthesis of L540 cells by 50% at concentrations of 0.9-2.0 x 10(-10) M, whereas HRS-1.dgA and Ki-1.dgA were about 100 times less potent with 50% inhibitory concentrations of 0.8-1.0 x 10(-8) M. The most effective immunotoxins, HRS-3.dgA and HRS-4.dgA, were only 15 times less toxic than ricin itself. HRS-3 Fab'.dgA and HRS-4 Fab'.dgA were 7.8 and 3 times less potent than their IgG.dgA counterparts with 50% inhibitory concentrations of 7 x 10(-10) and 3 x 10(-10) M, respectively. Staining of human tissues revealed an unexpected cross-reactivity of HRS-4 with pancreatic cells of malignant and nonmalignant origin. HRS-1, HRS-3, Ber-H2, and Ki-1 showed very little cross-reactivity with any normal human tissues. It is concluded that HRS-3.dgA and HRS-3 Fab'.dgA are the immunotoxins of choice for in vivo therapy.
Line capacity expansion schemes in photonic switching (1990)

Design considerations for capacity expansion are described, and requirements for photonic switch matrices, optical memories, and tunable-wavelength filters are examined. The present status of photonic switching devices and system experiments is discussed, covering space-, wavelength-, and time-division switches. Hybrid switching systems and coherent optical detection are considered as examples of system technology that will facilitate line capacity expansion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Simultaneous Activity of MRP1 and Pgp Is Correlated With In Vitro Resistance to Daunorubicin and With In Vivo Resistance in Adult Acute Myeloid Leukemia (1999)

In adult acute myeloid leukemia (AML), the weight of the contribution of the combined activity of Pgp and MRP1 to drug resistance is not known. To address this question, we compared the activity of these proteins to the in vitro resistance to daunorubicin (DNR), etoposide, and cytosine arabinoside (Ara-C), using the calcein-AM uptake and the 3-[4, 5-di-methyl-thiazol-2, 5-diphenyl] tetrazolium bromide (MTT) assay in 80 adult AML patients. We found no correlation or only a weak correlation between the in vitro drug resistance to DNR and etoposide and MRP1 or Pgp expression or function when tested separately. However, a strong correlation was observed between the simultaneous activity of MRP1 and Pgp (quantified as the modulation of calcein-AM uptake by cyclosporin A and probenecid) and the LC50 of DNR (r =.77, P <.0001). This emphasized the role of these two proteins, not separately, but together in the resistance to DNR. In contrast, Mvp/LRP expression did not correlate with the LC50 of DNR. A high level of simultaneous activity of Pgp and MRP1 was predictive of a poor treatment outcome (for achievement of CR [P =.008], duration of relapse-free survival [RFS; P =.01], and duration of overall survival [OS; P =.02]). In addition, high LC50 of DNR and high LC50 of etoposide together were also predictive of a poor treatment outcome (for duration of RFS [P =.02] and duration of OS [P =.02]). The unfavorable cytogenetic category was more closely associated with the combined activity of both MRP1 and Pgp (P =.002) than with the activity of Pgp or MRP1 separately. This could explain the poor prognosis and the in vitro resistance to daunorubicin in this group of patients. These data suggest that treatment outcome may be improved when cellular DNR and etoposide resistance can be circumvented or modulated. Modulation of not only Pgp but also MRP1 could be essential to attain this aim in adult AML.
Efficient color histogram indexing for quadratic form distance functions (1995)

In image retrieval based on color, the weighted distance between color histograms of two images, represented as a quadratic form, may be defined as a match measure. However, this distance measure is computationally expensive and it operates on high dimensional features (O(N)). We propose the use of low-dimensional, simple to compute distance measures between the color distributions, and show that these are lower bounds on the histogram distance measure. Results on color histogram matching in large image databases show that prefiltering with the simpler distance measures leads to significantly less time complexity because the quadratic histogram distance is now computed on a smaller set of images. The low-dimensional distance measure can also be used for indexing into the database.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>