gebhart/patrepeval huggingface dataset:
Glucose transporters are abundant in cells with "occluding" junctions at the blood-eye barriers. (1990)

We studied the distribution of the "erythroid/brain" glucose transporter protein in the human and rat eye by immunocytochemistry with monoclonal and polyclonal antibodies to the C terminus of the human erythrocyte glucose transporter. We found intense immunocytochemical staining in the endothelium of microvessels of the retina, optic nerve, and iris but not in microvessels of the choroid, ciliary body, sclera, and other retro-orbital tissues. In addition, we found marked immunocytochemical staining of retinal pigment epithelium, ciliary body epithelium, and posterior epithelium of the iris. The common feature of all those endothelial and epithelial cells that stained intensely for the glucose transporter is the presence of "occluding" intercellular junctions, which constitute the anatomical bases of the blood-eye barriers. We propose that a high density of the glucose transporter is a biochemical concomitant of epithelial and endothelial cells with barrier characteristics, at least in tissues that have a high metabolic requirement for glucose.
Ultrastructural localization of proteinase 3, the target antigen of anti-cytoplasmic antibodies circulating in Wegener's granulomatosis. (1990)

To investigate the distribution of proteinase 3, the target antigen of anti-cytoplasmic antibodies (ACPA or C-ANCA), within the organelles of resting normal human polymorphonuclear leukocytes and monocytes, the authors used immunocytochemical techniques on thin frozen sections. To obtain valuable tools for immunolabeling, two murine monoclonal antibodies (MAbs) directed against the ACPA antigen were produced. In neutrophils, the authors observed immunogold label for the ACPA antigen, predominantly in myeloperoxidase-positive azurophil granules, and in smaller amounts on the plasma membrane. In monocytes, the ACPA antigen could be detected in small granules, which occasionally also contained myeloperoxidase, and rare labeling was found on the monocyte membrane. The finding that the ACPA antigen is expressed on the plasma membrane of neutrophils and monocytes, thereby becoming accessible to circulating autoantibodies, supports the supposition that ACPA are not only markers of disease activity, but also are involved in the pathogenesis of Wegener's granulomatosis.
Yeast farnesyl-diphosphate synthase: site-directed mutagenesis of residues in highly conserved prenyltransferase domains I and II. (1994)

Prenyltransferases that catalyze the fundamental chain elongation reaction in the isoprenoid biosynthetic pathway contain several highly conserved amino acids, including two aspartate-rich regions thought to be involved in substrate binding and catalysis. We report a study of site-directed mutants for yeast farnesyl-diphosphate synthase (FPPSase; geranyl-diphosphate:isopentenyl-diphosphate, EC 2.5.1.10), a prenyltransferase that catalyzes the sequential 1'-4 coupling of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate and geranyl diphosphate. A recombinant form of FPPSase extended by a C-terminal -Glu-Glu-Phe alpha-tubulin epitope (EEF in single-letter amino acid code) was engineered to facilitate rapid purification of the enzyme by immunoaffinity chromatography and to remove traces of contaminating activity from wild-type FPPSase in the Escherichia coli host. Ten site-directed mutants were constructed in FPPSase::EEF. The six aspartates in domain I (at positions 100, 101, and 104) and domain II (at positions 240, 241, and 244) were changed to alanine (mutants designated D100A, D101A, D104A, D240A, D241A, and D244A); three arginine residues were changed, Arg-109 and Arg-110 to glutamine and Arg-350 to alanine (mutants designated R109Q, R110Q, and R350A); and Lys-254 was converted to alanine (mutant designated K254A). Mutations of the aspartatic residues and nearby arginine residues in domain I and Asp-240 and Asp-241 in domain II drastically lowered the catalytic activity of FPPSase::EEF. The D244A and K254A mutants were substantially less active, while kcat and the Michaelis constants for the R350A mutant were similar to those of FPPSase::EEF. Addition of an -EEF epitope to the C terminus of wild-type FPPSase resulted in a 14-fold increase of KmIPP and a 12-fold decrease of kcat, suggesting that the conserved hydrophilic C terminus of the enzyme may have a role in substrate binding and catalysis.
A novel antisense oligonucleotide targeting survivin expression induces apoptosis and sensitizes lung cancer cells to chemotherapy. (2000)

Survivin, an inhibitor of apoptosis protein, deserves attention as a selective target for cancer therapy because it lacks expression in differentiated adult tissues but is expressed in a variety of human tumors. We designed 20-mer phosphorothioate antisense oligonucleotides targeting different regions of survivin mRNA and investigated their ability to down-regulate survivin mRNA and induce apoptosis in the lung adenocarcinoma cell line A549. Oligonucleotide 4003, which targets nucleotides 23-251 of survivin mRNA, was identified as the most potent compound. As measured by real-time PCR, 4003 down-regulated survivin mRNA in a dose-dependent manner with an IC50 of 200 nM. Its maximum effect was achieved at a concentration of 400 nM, at which mRNA was down-regulated by 70%. As revealed by increased caspase-3-like protease activity, nuclear condensation and fragmentation, and trypan blue uptake, treatment with 4003 induced apoptosis and sensitized tumor cells to the chemotherapeutic agent etoposide. Oligonucleotide 4003 did not reduce the viability of normal blood leukocytes with marginal levels of survivin mRNA.
Tumor necrosis factor-related apoptosis-inducing ligand's antitumor activity in vivo is enhanced by the chemotherapeutic agent CPT-11. (1999)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can induce apoptosis in a wide variety of transformed human cells in vitro. In this study, the antitumor activity of recombinant TRAIL was analyzed in mice bearing human colon carcinoma tumors. We found that these tumors displayed a differential sensitivity to TRAIL in vivo that paralleled their susceptibility to TRAIL-induced apoptosis in vitro. Treatment of TRAIL-sensitive tumors 3 days after tumor challenge resulted in a dose-dependent inhibition of growth and the elimination of tumors in many mice. Colon carcinoma cell lines could be further sensitized to TRAIL-induced apoptosis in vitro by the addition of the chemotherapeutic agent camptothecin. Moreover, the combination of TRAIL and CPT-11, a water-soluble analogue of camptothecin, greatly enhanced the antitumor activity of TRAIL in vivo. TRAIL plus CPT-11 treatment of both 3- and 10-day established TRAIL-sensitive tumors resulted in both a significant inhibition of tumor growth and a high proportion of complete tumor regressions. Treatment of TRAIL-resistant tumors with TRAIL and CPT-11 dramatically slowed tumor growth and induced a transient tumor regression. These data demonstrate that TRAIL alone is a potent antitumor agent in vivo, and its activity can be significantly enhanced in combination with the chemotherapeutic agent CPT-11.
Trends in real-world clinical outcomes among patients (pts) with metastatic pancreatic adenocarcinoma (mPDAC) treated with liposomal irinotecan based regimens in the United States (US). (2020)

e16751 Background: The NAPOLI-1 study, a randomized phase 3 study in pts with mPDAC previously treated with gemcitabine-based therapy, demonstrated an improvement in overall survival (OS) with liposomal irinotecan + 5-fluorouracil/ leucovorin (5-FU/LV) vs. 5-FU/LV. In this analysis we describe the trends in pt characteristics, real-world OS (rwOS), and real-world time to-treatment failure (rwTTF) among pts with mPDAC treated with liposomal Irinotecan based regimens overall and stratified by tx initiation prior to 2018 (pre-2018) or after 2018 (post-2018). Methods: This retrospective observational study used de-identified data from Flatiron Health EHR database from over 280 cancer clinics in the US. Pt characteristics, rwOS, and rwTTF were assessed in adult pts diagnosed with mPDAC who received liposomal irinotecan treatment (tx) between January 1, 2016 and October 31, 2019. Results: Of the 590 pts treated with liposomal irinotecan based regimens, 53% were male, 56% were initially diagnosed with Stage IV disease, 92% were treated in the community setting, and median age at tx initiation was 69 (IQR: 62 – 75) years. Among pts with available ECOG scores (N = 435), 77% had a score of 0 or 1. 43% (n = 254) initiated tx pre-2018 and 57% (n = 336) post-2018. Pre-2018, 106 (42%) pts initiated liposomal irinotecan in the third line metastatic setting or later (3rd line+), 125 (49%) had ECOG score of 0-1, and median age was 68 (62–74) years. Post-2018, 36% of pts initiated tx in 3rd line+, 211 (63%) had ECOG score of 0-1, and median age was 70 (63 – 75) years. Median rwOS was 4.4 months [95% CI: 4.3–6.2] pre-2018 and 5.2 mos [4.3–6.2] post-2018. rwTTF was 1.6 mos [1.4–1.9] pre-2018 and 2.1 mos [1.6–2.5] among pts post-2018. Among pts treated in first- or second-line, pre-2018 rwOS was 5.3 mos [3.9–6.4] and post-2018 rwOS was 6.3 mos [5.0– 7.6]. Conclusions: In this descriptive real-world study of pts with mPDAC receiving liposomal irinotecan based regimens, pts initiating treatment post-2018 appear to be less pre-treated, older, and have better performance status than pts pre-2018. Pts treated post-2018 experienced numerically longer rwTTF and rwOS than pts treated pre-2018.
Importance of the Solvent-Exposed Residues of the Insulin B Chain α-Helix for Receptor Binding (2008)

Conjointly, the solvent-exposed residues of the central alpha-helix of the B chain form a well-defined ridge, which is flanked and partly overlapped by the two described insulin receptor binding surfaces on either side of the insulin molecule. To evaluate the importance of this interface in insulin receptor binding, we developed a new powerful method that allows us to introduce all the naturally occurring amino acids into a given position and subsequently determine the receptor binding affinities of the resulting insulin analogues. The total amino acid scanning mutagenesis was performed at positions B9, B10, B12, B13, B16, and B17, and the vast majority of the insulin analogue precursors were expressed and secreted in amounts close to that of the wild-type (human insulin) precursor. The analogue binding data revealed that positions B12 and B16 were the two positions most affected by the amino acid substitutions. Interestingly, the receptor binding affinities of the B13 analogues were also markedly affected by the amino acid substitutions, suggesting that GluB13 indeed is a part of insulin's binding surface. The B10 library screen generated analogues covering a wide range of (20-340%) of relative binding affinities, and the results indicated that a structural stabilization of the central alpha-helix and thereby a more rigid presentation of the binding epitope at the insulin receptor is important for receptor recognition. In conclusion, systematic amino acid scanning mutagenesis allowed us to confirm the importance of the B chain alpha-helix as a central recognition element serving as a linker of a continual binding surface.
Bone formation by three-dimensional stromal osteoblast culture in biodegradable polymer scaffolds (1997)

Bone formation was investigated in vitro by culturing stromal osteoblasts in three-dimensional (3-D), biodegradable poly(DL-lactic-co-glycolic acid) foams. Three polymer foam pore sizes, ranging from 150-300, 300-500, and 500-710 microns, and two different cell seeding densities, 6.83 x 10(5) cells/cm2 and 22.1 x 10(5) cells/cm2, were examined over a 56-day culture period. The polymer foams supported the proliferation of seeded osteoblasts as well as their differentiated function, as demonstrated by high alkaline phosphatase activity and deposition of a mineralized matrix by the cells. Cell number, alkaline phosphatase activity, and mineral deposition increased significantly over time for all the polymer foams. Osteoblast foam constructs created by seeding 6.83 x 10(5) cells/cm2 on foams with 300-500 microns pores resulted in a cell density of 4.63 x 10(5) cells/cm2 after 1 day in culture; they had alkaline phosphatase activities of 4.28 x 10(-7) and 2.91 x 10(-6) mumol/cell/min on Days 7 and 28, respectively; and they had a cell density that increased to 18.7 x 10(5) cells/cm2 by Day 56. For the same constructs, the mineralized matrix reached a maximum penetration depth of 240 microns from the top surface of the foam and a value of 0.083 mm for mineralized tissue volume per unit of cross sectional area. Seeding density was an important parameter for the constructs, but pore size over the range tested did not affect cell proliferation or function. This study suggests the feasibility of using poly(alpha-hydroxy ester) foams as scaffolding materials for the transplantation of autogenous osteoblasts to regenerate bone tissue.
FLEXIBLE POLYIMIDE FILM TECHNOLOGY FOR VIBRATION ENERGY HARVESTING (2009)

In this paper we present recent developments of an electromagnetic vibration energy harvester based on micro-machined flexible polyimide films and planar micro-coils. A range of different prototype resonator structures were successfully fabricated with resonance frequencies in the range of 200 Hz to 400 Hz. A fully assembled prototype generator device produced an output power of 5 µW (70 mV at 1000 Ω) of peak power from a harmonic input excitation of 9g (15 µm amplitude at 390 Hz).
3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds (2018)

Lithographic nanofabrication is often limited to successive fabrication of two-dimensional (2D) layers. We present a strategy for the direct assembly of 3D nanomaterials consisting of metals, semiconductors, and biomolecules arranged in virtually any 3D geometry. We used hydrogels as scaffolds for volumetric deposition of materials at defined points in space. We then optically patterned these scaffolds in three dimensions, attached one or more functional materials, and then shrank and dehydrated them in a controlled way to achieve nanoscale feature sizes in a solid substrate. We demonstrate that our process, Implosion Fabrication (ImpFab), can directly write highly conductive, 3D silver nanostructures within an acrylic scaffold via volumetric silver deposition. Using ImpFab, we achieve resolutions in the tens of nanometers and complex, non-self-supporting 3D geometries of interest for optical metamaterials.
Concepts of the cover coefficient-based clustering methodology (1985)

Document clustering has several unresolved problems. Among them are high time and space complexity, difficulty of determining similarity thresholds, order dependence, nonuniform document distribution in clusters, and arbitrariness in determination of various cluster intiators. To overcome these problems to some degree, the cover coefficient based clustering methodology has been introduced. The concepts used in this methodology have created certain new concepts, relationships, and measures such as the effect of indexing on clustering, an optimal vocabulary generation for indexing, and a new matching function. These new concepts are discussed. The result of performance experiments that show the effectiveness of the clustering methodology and the matching function are also included. In these experiments, it has been also observed that the majority of the documents obtained in a search are concentrated in a few clusters containing a low percentage of documents of the database.
Synthesis of new heterocyclic derivatives of retinoids (1998)

Abstract Reaction of α‐ and β‐ionones 1 and 2 with dialkylformamide/phosphorus oxychloride affords enamines 6 and 7 along with the expected chloro derivatives 4 and 5 . Reaction of 6a with hydrazines, hydroxylamine and guanidine furnished pyrazoles, isoxazole, pyrimidine 8–10 showing the potential of these enaminones as key intermediates in the synthesis of synthetic retinoids.
In situ DNA‐ hybridization chain reaction ( HCR ): a facilitated in situ HCR system for the detection of environmental microorganisms (2014)

In situ detection of microorganisms by fluorescence in situ hybridization (FISH) is a powerful tool for environmental microbiology, but analyses can be hampered by low rRNA content in target organisms, especially in oligotrophic environments. Here, we present a non-enzymatic, hybridization chain reaction (HCR)-based signal amplified in situ whole-cell detection technique (in situ DNA-HCR). The components of the amplification buffer were optimized to polymerize DNA amplifier probes for in situ DNA-HCR. In situ hybridization of initiator probes followed by signal amplification via HCR produced bright signals with high specificity and probe permeation into cells. The detection rates for Bacteria in a seawater sample and Archaea in anaerobic sludge samples were comparable with or greater than those obtained by catalyzed reporter deposition (CARD)-FISH or standard FISH. Detection of multiple organisms (Bacteria, Archaea and Methanosaetaceae) in an anaerobic sludge sample was achieved by simultaneous in situ DNA-HCR. In summary, in situ DNA-HCR is a simple and easy technique for detecting single microbial cells and enhancing understanding of the ecology and behaviour of environmental microorganisms in situ.
Cardiac Hormones as Diagnostic Tools in Heart Failure (2003)

In patients with heart failure, plasma levels of atrial natriuretic peptide (ANP), B-type natriuretic peptide (BNP), and the N-terminal fragments of their prohormones (N-ANP and N-BNP) are elevated, because the cardiac hormonal system is activated by increased wall stretch due to increased volume and pressure overload. Patients suspected of having heart failure can be selected for further investigations on the basis of having an elevated plasma concentration of N-ANP, BNP, and N-BNP. High levels of cardiac hormones identify those at greatest risk for future serious cardiovascular events. Moreover, adjusting heart failure treatment to reduce plasma levels of N-BNP may improve outcome. Cardiac hormones are most useful clinically as a rule-out test. In acutely symptomatic patients, a very high negative predictive value is coupled with a relatively high positive predictive value. Measurement of cardiac hormones in patients with heart failure may reduce the need for hospitalizations and for more expensive investigations such as echocardiography. However, there have also been conflicting reports on the diagnostic value of cardiac hormones, they are not specific for any disease, and the magnitude of the effects of age and gender on BNP in the normal subgroup suggests that these parameters need to be considered when interpreting cardiac hormone levels.
Characterization of Sodium‐Dependent [3H]GBR‐12935 Binding in Brain: A Radioligand for Selective Labelling of the Dopamine Transport Complex (1986)

High-affinity and saturable binding sites for the diphenyl-substituted piperazine derivative [3H]GBR-12935 have been characterized in crude synaptosomal membranes prepared from rat brain. The specific binding of [3H]GBR-12935 is sodium-dependent and is unevenly distributed among various brain regions, with the highest concentration of binding sites being found in the corpus striatum and nucleus accumbens. Sodium-dependent [3H]GBR-12935 binding in all other brain areas was 10% or less of the binding found in the striatum. The affinity of [3H]GBR-12935 for binding sites in the striatum is increased in the presence of Na+ but other cations, including K+, Ca2+, or Mg2+, inhibit specific binding. There is an excellent correlation (r = 0.96, p less than 0.01) between the potencies of a series of drugs in inhibiting [3H]GBR-12935 binding to striatal membranes and their potencies in inhibiting [3H]3,4-dihydroxyphenylethylamine ([3H]dopamine) uptake in synaptosomes. Agonists and antagonists of other neurotransmitter receptor or drug recognition sites have little or no effect on specific [3H]GBR-12935 binding to striatal membranes. In addition, prior intracerebroventricular administration of 6-hydroxydopamine results in a decrease in the number of specific [3H]GBR-12935 binding sites in the striatum. These data indicate that [3H]GBR-12935 is a selective radioligand of the presynaptic dopamine transport complex in brain.
Natural History of Sickle Cell Anemia in Saudi Arabs (1978)

We studied 270 Saudi Arabs with homozygous sickle cell anemia, using chart review, a register (since 1969), and home visiting in 42 cases. Average follow-up for the total group was 10 years. Seventy-four percent of those diagnosed by age 3 years presented on screening or with merely anemia; 26% presented with illness, abnormal physical findings, or pain. Compared with American or Jamaican blacks, serious complications occurred only 6% to 25% as frequently; leg ulcers did not occur at all; the mortality under age 15 years was 10% as great; mean levels of blood hemoglobin were higher (10 g/dl), reticulocyte count was lower (5% to 6%), and mean fetal hemoglobin (HbF), which was inversely correlated with reticulocytes, was higher (22% to 26.8%). The high HbF is believed to account for the very mild clinical manifestations.
Catecholaminergic microcircuitry controlling the output of airway-related vagal preganglionic neurons (2003)

In this study, we have investigated the ultrastructure and function of the catecholaminergic circuitry modulating the output of airway-related vagal preganglionic neurons (AVPNs) in ferrets. Immunoelectron microscopy was employed to characterize the nature of catecholaminergic innervation of AVPN at the ultrastructural level. In addition, immunofluorescence was used to examine the expression of the alpha(2A)-adrenergic receptor (alpha(2A)-AR) on AVPNs, and norepinephrine release within the rostral nucleus ambiguous (rNA) was measured by using microdialysis. Physiological experiments were performed to determine the effects of stimulation of the noradrenergic locus coeruleus (LC) cell group on airway smooth muscle tone. The results showed that 1) catecholaminergic nerve endings terminate in the vicinity of identified AVPNs but very rarely form axosomatic or axodendritic synapses with the AVPNs that innervate the extrathoracic trachea; 2) AVPNs express the alpha(2A)-AR; 3) LC stimulation-induced norepinephrine release within the rNA region was associated with airway smooth muscle relaxation; and 4) blockade of alpha(2A)-AR on AVPNs diminished the inhibitory effects of LC stimulation on airway smooth muscle tone. It is concluded that a noradrenergic circuit originating within the LC is involved in the regulation of AVPN activity within the rNA, and stimulation of the LC dilates the airways by the release of norepinephrine and activation of alpha(2A)-AR expressed by AVPNs, mainly via volume transmission.
Antitumour effects of single or combined monoclonal antibodies directed against membrane antigens expressed by human B cells leukaemia (2011)

Altogether these data suggest that the combined use of two mAbs, such as anti-HLA-DR and anti-CD5, may significantly enhance their therapeutic potential.
Kynurenate and 7‐Chlorokynurenate Formation in Chronically Epileptic Rats (2005)

These results demonstrate that the epileptic brain can synthesize glycine(B) receptor antagonists in situ. Astrogliosis probably accounts for their enhanced production in chronically epileptic rats. These results bode well for the use of 4-chlorokynurenine in the treatment of chronic seizure disorders.
Lecture d'un palimpseste urbain : la Suwayqat ‘Alī à Alep (1998)

Introduction Au Moyen-Orient, plus qu'ailleurs peut-être, les villes conservent des traces lisibles d'écritures partiellement effacées : villes de négociants, d'échange et de contact, elles sont rarement pour une longue durée, si l'on excepte les capitales, le siège d'un pouvoir fort, qui cherche à marquer l'espace public par une empreinte définitive, et souhaite effacer les signes des pouvoirs antérieurs. Même dans les capitales, la ville des citadins et l'espace du prince sont clairement sé...