gebhart/patrepeval huggingface dataset:
Dendritic cells use macropinocytosis and the mannose receptor to concentrate macromolecules in the major histocompatibility complex class II compartment: downregulation by cytokines and bacterial products. (1995)

We have previously demonstrated that human peripheral blood low density mononuclear cells cultured in granulocyte/macrophage colony-stimulating factor (GM-CSF) and interleukin (IL)-4 develop into dendritic cells (DCs) that are extremely efficient in presenting soluble antigens to T cells. To identify the mechanisms responsible for efficient antigen capture, we studied the endocytic capacity of DCs using fluorescein isothiocyanate-dextran, horseradish peroxidase, and lucifer yellow. We found that DCs use two distinct mechanisms for antigen capture. The first is a high level of fluid phase uptake via macropinocytosis. In contrast to what has been found with other cell types, macropinocytosis in DCs is constitutive and allows continuous internalization of large volumes of fluid. The second mechanism of capture is mediated via the mannose receptor (MR), which is expressed at high levels on DCs. At low ligand concentrations, the MR can deliver a large number of ligands to the cell in successive rounds. Thus, while macropinocytosis endows DCs with a high capacity, nonsaturable mechanism for capture of any soluble antigen, the MR gives an extra capacity for antigen capture with some degree of selectivity for non-self molecules. In addition to their high endocytic capacity, DCs from GM-CSF + IL-4-dependent cultures are characterized by the presence of a large intracellular compartment that contains high levels of class II molecules, cathepsin D, and lysosomal-associated membrane protein-1, and is rapidly accessible to endocytic markers. We investigated whether the capacity of DCs to capture and process antigen could be modulated by exogenous stimuli. We found that DCs respond to tumor necrosis factor alpha, CD40 ligand, IL-1, and lipopolysaccharide with a coordinate series of changes that include downregulation of macropinocytosis and Fc receptors, disappearance of the class II compartment, and upregulation of adhesion and costimulatory molecules. These changes occur within 1-2 d and are irreversible, since neither pinocytosis nor the class II compartment are recovered when the maturation-inducing stimulus is removed. The specificity of the MR and the capacity to respond to inflammatory stimuli maximize the capacity of DCs to present infectious non-self antigens to T cells.
Gene expression variability across cells and species shapes innate immunity (2018)

As the first line of defence against pathogens, cells mount an innate immune response, which varies widely from cell to cell. The response must be potent but carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here we characterize the innate immune response's transcriptional divergence between species and variability in expression among cells. Using bulk and single-cell transcriptomics in fibroblasts and mononuclear phagocytes from different species, challenged with immune stimuli, we map the architecture of the innate immune response. Transcriptionally diverging genes, including those that encode cytokines and chemokines, vary across cells and have distinct promoter structures. Conversely, genes that are involved in the regulation of this response, such as those that encode transcription factors and kinases, are conserved between species and display low cell-to-cell variability in expression. We suggest that this expression pattern, which is observed across species and conditions, has evolved as a mechanism for fine-tuned regulation to achieve an effective but balanced response.
Rational screening of oligonucleotide combinatorial libraries for drug discovery (1993)

Combinatorial strategies offer the potential to generate and screen extremely large numbers of compounds and to identify individual molecules with a desired binding specificity or pharmacological activity. We describe a combinatorial strategy for oligonucleotides in which the library is generated and screened without using enzymes. Freedom from enzymes enables the use of oligonucleotide analogues. This dramatically extends the scope of both the compounds and the targets that may be screened. We demonstrate the utility of the method by screening 2'-O-Methyl and phosphorothioate oligonucleotide analogue libraries. Compounds have been identified that bind to the activated H-ras mRNA and that have potent antiviral activity against the human herpes simplex virus.
Modulation of Bacterial Type III Secretion System by a Spermidine Transporter Dependent Signaling Pathway (2007)

Cumulatively, these data have depicted a novel spermidine transporter-dependent signaling pathway, which appears to play an essential role in modulation of T3SS expression in P. aeruginosa.
Solid-Phase Oligosaccharide Synthesis:  Preparation of Complex Structures Using a Novel Linker and Different Glycosylating Agents (1999)

[formula: see text] A beta-(1-->4)-linked trisaccharide was prepared in 53% yield on a polymer support using glycosyl phosphates and released by cross-metathesis of a novel linker to reveal the anomeric n-pentenyl glycoside. Heptasaccharide 33 was prepared in 9% yield in 14 steps.
Fine Needle Aspiration Cytology of Endodermal Sinus Tumor of the Ovary - A Case Report - (1995)

We report a case of fine needle aspiration cytology of endodermal sinus tumor of the ovary. A 13-year-old girl complained of abdominal mass and pain. The abdominal sonography revealed a well-demarcated huge mass, which was solid and multiseptated. Percutaneous fine needle aspiration was performed from the mass. The smears revealed moderate cellularity, which was arranged in sheets or clumps of pleomorphic malignant cells on mucoid background The valuable characteristic features of tumor cells were papillary configuration, vacuolated cytoplasm and intracellular and extracellular hyaline globules. The diagnosis was confirmed later by histologic study of surgical resection of the specimen.
Measurement of cell-mediated immunity with a varicella-zoster virus-specific interferon-? ELISPOT assay: Responses in an elderly population receiving a booster immunization (2003)

An interferon-gamma ELISPOT assay has been developed for assessment of cellular immune responses to Varicella-Zoster Virus (VZV) in large, multi-center clinical vaccine trials. We show that the assay performed best when testing peripheral blood mononuclear cells (PBMCs) that had been isolated and then frozen on the same day as blood was drawn, and that freezing PBMCs from blood that was stored overnight before processing resulted in dramatically reduced responses. This assay was used to monitor cell-mediated immunity (CMI) in response to a booster immunization with an investigational live, attenuated VZV vaccine in an elderly population that had been vaccinated 8-10 years previously. The booster vaccine elicited a 1.6- to 1.7-fold rise in the VZV-specific cellular immune response as measured by the ELISPOT assay. The increase from pre to post booster vaccination response was more pronounced (approximately 2.2-fold rise) in a subset of subjects who had received two prior immunizations with a live, attenuated vaccine.
Human breast cancer-associated fibroblasts (CAFs) show caveolin-1 down-regulation and RB tumor suppressor functional inactivation: Implications for the response to hormonal therapy (2008)

It is becoming increasingly apparent that the tumor microenvironment plays a critical role in human breast cancer onset and progression. Therefore, we isolated cancer-associated fibroblasts (CAFs) from human breast cancer lesions and studied their properties, as compared with normal mammary fibroblasts (NFs) isolated from the same patient. Here, we demonstrate that 8 out of 11 CAFs show dramatic downregulation of caveolin-1 (Cav-1) protein expression; Cav-1 is a well-established marker that is normally decreased during the oncogenic transformation of fibroblasts. Next, we performed gene expression profiling studies (DNA microarray) and established a CAF gene expression signature. Interestingly, the expression signature associated with CAFs encompasses a large number of genes that are regulated via the RB-pathway. The CAF gene signature is also predictive of poor clinical outcome in breast cancer patients that were treated with tamoxifen mono-therapy, indicating that CAFs may be useful for predicting the response to hormonal therapy. Finally, we show that replacement of Cav-1 expression in CAFs (using a cell-permeable peptide approach) is sufficient to revert their hyper-proliferative phenotype and prevent RB hyper-phosphorylation. Taken together, these studies highlight the critical role of Cav-1 downregulation in maintaining the abnormal phenotype of human breast cancer-associated fibroblasts.
A Non-Maxima Suppression Method for Edge Detection with Sub-Pixel Accuracy (1995)

In this article we present a two dimensional edge detector which gives the edge position in an image with a sub-pixel accuracy. The method presented here gives an excellent accuracy (the position bias mean is almost zero and the standard deviation is less than one tenth of a pixel) with a low computational cost, and its implementation is very simple since it is derivated from the well-known Non-Maxima Suppression method [2, 4]. We also justify the method by showing that it gives the exact result in a theoretical one dimensional example. We have tested the accuracy and robustness of the edge extractor on several synthetic and real images and both qualitative and quantitative results are reported in this paper.
Driver assistance system for backward maneuvers in passive multi-trailer vehicles (2012)

Drivers of vehicles with one or several passive trailers, like truck-and-trailer or articulated luggage carriers, have difficulties in backward maneuvers due to jackknife and lack of visibility. Advanced driver assistance systems (ADAS) can be helpful to improve both safety and driver comfort in these complex operations. In this paper, we propose an ADAS that adopts our curvature limitation method for backward multi-trailer vehicles, where the last trailer is considered a virtual tractor and steering limits are established to avoid jackknife and inter-unit collisions. In the proposed solution, when the driver puts the vehicle in reverse, the steering wheel and pedals can be used as if the vehicle was driven from the back of the last trailer with visual feedback from a camera. This system can be implemented in drive-by-wire vehicles, where the steering-wheel feedback force can be customized for the curvature limitation of a given combination of one or several trailers. The system has been tested to tele-operate a mobile robot with two off-axle trailers.
Property Distributions:  Differences between Drugs, Natural Products, and Molecules from Combinatorial Chemistry (2002)

The differences between three different compound classes, natural products, molecules from combinatorial synthesis, and drug molecules, were investigated. The major structural differences between natural and combinatorial compounds originate mainly from properties introduced to make combinatorial synthesis more efficient. These include the number of chiral centers, the prevalence of aromatic rings, the introduction of complex ring systems, and the degree of the saturation of the molecule as well as the number and ratios of different heteroatoms. As drug molecules derive from both natural and synthetic sources, they cover a joint area in property space of natural and combinatorial compounds. A PCA-based scheme is presented that differentiates the three classes of compounds. It is suggested that by mimicking certain distribution properties of natural compounds, combinatorial products might be made that are substantially more diverse and have greater biological relevance.
Effects of hyperthermia on the peripheral nervous system: a review (2004)

The present paper overviews the current knowledge about effects of hyperthermia at temperatures used in clinical oncology on the peripheral nervous system. From the experimental studies it may be concluded that the heat sensitivity of the nerve is determined by the sensitivity of the nerve vasculature. These studies show that in order to avoid induction of severe neuropathy, application of heat to the peripheral nerves should not be in excess of doses of 30 min at 44 degrees C or equivalent. Using modern equipment for application of loco-regional hyperthermia the incidence of even mild neurological complications is very low. In hyperthermic isolated limb perfusion (HILP) neurotoxicity is an often-mentioned side effect, this is in spite of the fact that in all studies a relatively mild hyperthermic temperature is used that, based on the experimental studies, should be well tolerated by the nerves and other normal tissues in the limbs. It seems that the neurotoxicity observed after HILP results from thermal enhancement of drug toxicity, very probably combined with effects of a high tourniquet pressure that is used to isolate the blood flow in the leg. Whole body hyperthermia (WBH), using anesthesia and appropriate monitoring to avoid cardiovascular stress is at present considered a safe procedure. Still in the recent past cases of neuropathy after treatment have been described. When chemotherapy, and notably cisplatin, is administered before or during hyperthermia there are several clinical and experimental observations that indicate a limited tolerance of the peripheral nervous tissue in such case. Also previous radiotherapy may limit the tolerance of nerves to hyperthermia, notably when radiation is applied with a large field size. Experimental studies show that combined treatment with radiation and heat leads to enhancement of effects of radiation (enhancement ratio approximately 1.5 at 60 min at 44 degrees C). A clear contraindication for the application of hyperthermia in patients is the presence of a neurodegenerative disease, such as multiple sclerosis. Vigilance is also required in the treatment of diabetic patients with hyperthermia, this based on experimental animal studies, but so far no clear clinical data are available.
Mitochondrial cytopathy in adults: what we know so far. (2001)

Mitochondrial cytopathies are a diverse group of inherited and acquired disorders that result in inadequate energy production. They can be caused by inheritable genetic mutations, acquired somatic mutations, exposure to toxins (including some prescription medications), and the aging process itself. In addition, a number of well-described diseases can decrease mitochondrial energy production; these include hyperthyroidism, hypothyroidism, and hyperlipidemia.
Terms of Engraftment: Umbilical Cord Blood Transplants Arouse Enthusiasm (1995)

AN EVER-GROWING number of transplants using blood harvested from the placenta and umbilical cord of newborn infants are pointing the way toward a new approach for treating cancer, serious blood disorders, and perhaps a range of other illnesses, from inherited diseases to AIDS. The reason cord blood holds such promise is that it contains the same vital stem and progenitor hematopoietic cells found in bone marrow. These key cells, whether from marrow or cord blood, have the potential to "self-renew," or regenerate themselves, and to differentiate into the entire menagerie of blood cells required by the body. However, there is increasing evidence that cord blood provides some distinct advantages, both logistic and biological, over bone marrow transplants. For example, cord blood can be obtained noninvasively at the time of delivery and stored for months or years, available on demand for later use—either by the donor, if he or she later
Residues 1-254 of anthrax toxin lethal factor are sufficient to cause cellular uptake of fused polypeptides. (1993)

Anthrax lethal toxin is a complex of protective antigen (PA, 735 amino acids) and lethal factor (LF, 776 amino acids) that lyses certain eukaryotic cells. LF interacts with PA to gain access to the cytosol to assert its toxicity. The internalization of LF requires that PA bind to a specific membrane receptor and be cleaved by a cell-surface protease (probably furin), so as to expose a site on PA to which LF binds with high affinity. To localize LF functional domains, amino, carboxyl, and internal deletions of LF were made. Toxicity was eliminated by deletion of 40 and 47 residues from the amino and carboxyl termini, respectively. Similarly, deleting the first of the four imperfect repeats of 19 amino acids located at residues 308-383 made LF non-toxic, showing that this region is also essential for activity. To identify the minimum region of LF which is required for binding to PA, varying amino-terminal portions of LF were fused to the ADP-ribosylation domain of Pseudomonas exotoxin A. Fusion proteins containing residues 1-254 of LF were toxic when administered with PA, while those having only residues 1-198 of LF were inactive, showing that the PA-binding domain of LF lies within residues 1-254.
ZrB2 Substrate for Nitride Semiconductors (2002)

Zirconium diboride (ZrB2) has excellent properties as an electrically conductive substrate for nitride semiconductors. In this paper, the bulk growth of ZrB2 by a floating-zone method and some properties of ZrB2, together with a brief summary of heteroepitaxial growth of gallium nitride (GaN) by molecular beam epitaxy (MBE) and metalorganic vapor phase epitaxy (MOVPE), are presented. By optimizing the bulk growth conditions, a 20-mm-diameter ZrB2 single crystal was obtained. The cleavage direction of the ZrB2 (0001) substrate was confirmed to be parallel to [1120], which is parallel to that of GaN (0001). Epitaxial growth by both MBE and MOVPE was demonstrated. The grown n-type GaN/ZrB2 structure exhibited ohmic-like current–voltage behavior. These results indicate that ZrB2 has potential for application to the substrate for nitride semiconductors.
Controlled-release oxycodone relieves neuropathic pain: a randomized controlled trial in painful diabetic neuropathy (2003)

CR oxycodone is effective and safe for the management of painful diabetic neuropathy and improves QOL.
Escherichia coli gal operon proteins made after prophage lambda induction (1981)

Expression of the EScherichia coli gal operon under the control of the prophage lambda promoter pL leads to gross discoordinacy of gal expression. Expression of the most promoter-distal cistron galK is much greater than expression of the promoter-proximal cistron galE. We had previously shown that transcription of the gal operon is coordinate after prophage induction. A survey of protein synthesized after prophage induction indicated that lack of expression of galE is due to a failure of translation of the galE sequence in the pL-gal transcript. This failure of translation of the galE sequence may be due to extensive dyad symmetry present in the vicinity of the gal promoter region of the pL-gal transcript. This symmetry could result in a ribonucleic acid stem-loop structure, blocking the attachment of ribosomes at the Shine-Dalgarno sequence of galE. To test this model, strains bearing the IS1 or IS2 insertion, deletion, or new promoter mutation within the symmetrical region were constructed. The restoration of some galE expression after such disruptions of the symmetrical region indicated that the ribonucleic acid stem-loop structure did play a role in the discoordinate expression of gal from pL. However, failure to obtain galE expression coordinated with high levels of galK expression suggested that other components were involved, perhaps other symmetries between galE and the pL transcript.
Two edged role of mannose binding lectin in rheumatoid arthritis: a cross sectional study. (2000)

Presence of MBL variant alleles was associated with early onset of RA. MBL deficiency may, therefore, accelerate the disease. However, in patients with late onset and advanced disease our results indicate that the A/A type may be associated with additional inflammation different from that seen in carriers of variant alleles.
Effect of Antacid on Absorption of Enteric-Coated Aspirin (1974)

<h3>To the Editor.—</h3> Modification of the gastrointestinal absorption of one drug by another may be an important factor in patients receiving multiple drug therapy, especially with the increasing use of over-the-counter medications. We report the influence of administration of antacids on the release of aspirin from an entericcoated formulation. Enteric-coated aspirin (Ecotrin) was administered to six healthy subjects (aged 21 to 32 years) with and without coadministration of a magnesium and aluminum hydroxide oral suspension (Maalox) in a crossover manner. At least one week separated each study. After an overnight fast and one hour prior to the administration of the aspirin, 15 ml of antacid suspension was taken with 85 ml of water. At the time of aspirin administration, 15 ml of antacid suspension was again administered with 85 ml ofwater. The control studies consisted of administration of 100 ml of water one hour prior to and concomitantly with
ChemInform Abstract: AMINOETHYNYL METALATIONS. 11. REACTION OF SILYLATED AND STANNYLATED YNAMINES WITH CARBODIIMIDES (1983)

Abstract Die Reaktion der Titelverbindungen (I) und (II) führt zu den Chinolinderivaten (III′a)‐(IIIe) und den Propiolamidinen (IVa) und (IVb), die über eine gemeinsame zwitterionische Vorstufe durch Cyclisierung an der ortho‐Stellung eines Arylrings bzw. durch 1,3‐Verschiebung des Restes Zund Hydrolyse der dadurch gebildeten Einlagerungsprodukte entstehen.
Exploration, normalization, and summaries of high density oligonucleotide array probe level data (2003)

In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip arrays. We display some familiar features of the perfect match and mismatch probe (PM and MM) values of these data, and examine the variance-mean relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the PM and MM using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure that is a robust multi-array average (RMA) of background-adjusted, normalized, and log-transformed PM values. We evaluate the four expression summary measures using the dilution study data, assessing their behavior in terms of bias, variance and (for MBEI and RMA) model fit. Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data. We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities.