gebhart/patrepeval huggingface dataset:
The MUC6 secretory mucin gene is expressed in a wide variety of epithelial tissues (1998)

Secretory mucins play an important role in the cytoprotection of epithelial surfaces and are used as tumour markers in a variety of cancers. The MUC6 secretory mucin was originally isolated from a gastric cDNA library. The aim was to determine the specific type and location of MUC6 mucin gene expression in a wide range of human adult and fetal epithelial tissues. In situ hybridization, RNA analysis, and immunohistochemistry were used to quantify and localize mucin gene expression. The data obtained show that MUC6 is highly expressed in gastric mucosa, duodenal Brunner's glands, gall bladder, seminal vesicle, pancreatic centroacinar cells and ducts, and periductal glands of the common bile duct; focal expression is seen in basal endometrial and endocervical glands. MUC6 epitopes were also highly expressed in 7/10 pancreatic cancers and 7/10 cholangiocarcinomas and focally expressed in 4/10 endocervical adenocarcinomas. Expression of MUC6 occurs early in fetal development and was observed in Brunner's glands and pancreatic ducts at 18-19 weeks and in gastric glands at 20 weeks' gestation. The tissue distribution of the MUC6 secretory mucin indicates that it may function to protect epithelial tissues from a wide range of substances. Expression of MUC6 is frequently preserved in pancreatic and bile duct adenocarcinomas, but it is only sparsely expressed in endocervical carcinomas.
Lipid Rafts and Apical Membrane Traffic (2004)

Lipid rafts are dynamic assemblies floating freely in the surrounding membranes of living cells. This membrane heterogeneity provides a useful concept for understanding processes as diverse as cell polarity, signal transduction, and membrane sorting. Individual rafts are small entities containing thousands of lipids but only a few proteins. Regulation of raft association and size is an elementary feature of interactions at the molecular level. By clustering small rafts into a bigger platform, proteins are brought together for modification. Oligomerization might transform a monomeric weakly raft-associated protein into an assembly with higher raft affinity. Lectins are multivalent glycoprotein-binding proteins and are likely to be key players in mediating the clustering of rafts in vivo. Glycosylation-dependent surface delivery in a polarized fashion is a feature conserved across evolution, and we expect lectins to be at the heart of the molecular machinery responsible for lipid raft delivery to the cell surface. Currently, we are evaluating candidate proteins by affinity chromatography, proteomics, and RNA interference.
Response to low‐dose ketoconazole and subsequent dose escalation to high‐dose ketoconazole in patients with androgen‐independent prostate cancer (2006)

LDK is associated with a PSA response rate comparable to HDK as secondary hormonal therapy in patients with AIPC, but with less toxicity. Although uncommon, additional durable responses occurred in some patients after dose escalation.
First pass TWT design success (2001)

Making use of an ensemble of computer codes, Hughes Electron Dynamics (HED) has achieved first pass success in the design of slow wave circuits for several traveling wave tubes (TWTs) during the last year. By first pass design success we mean that when tested, the first device fabricated achieved the design goals for RF output power, basic efficiency, gain and phase shift. The design goals are derived from the predictions of a computer model, based on the exact dimensions of the TWT. The establishment of accurate computer models for the TWT slow wave circuit has enabled the optimization of a new design on the computer, eliminating the need for several experimental iterations in the development process. This accomplishment has enabled HED to significantly reduce the time required to develop new devices and demonstrate new design concepts.
Iron-Chelation Therapy with Oral Deferiprone — Toxicity or Lack of Efficacy? (1998)

Red-cell transfusion therapy in patients with homozygous β-thalassemia (thalassemia major) decreases the complications of severe anemia and prolongs survival.1 However, the effectiveness of transfusions is limited by the tissue damage resulting from iron overload, a consequence of the body's limited capacity to excrete iron. Each 250 ml of transfused red cells adds about 250 mg of elemental iron to the body. The end-organ manifestations of iron overload in patients with β-thalassemia — cirrhosis, hepatocellular carcinoma, cardiac failure, diabetes mellitus, and hypopituitarism — are similar to those in patients with hereditary hemochromatosis, and they shorten life expectancy.1 There is a direct . . .
Global Correspondence Optimization for Non‐Rigid Registration of Depth Scans (2008)

Abstract We present a registration algorithm for pairs of deforming and partial range scans that addresses the challenges of non‐rigid registration within a single non‐linear optimization. Our algorithm simultaneously solves for correspondences between points on source and target scans, confidence weights that measure the reliability of each correspondence and identify non‐overlapping areas, and a warping field that brings the source scan into alignment with the target geometry. The optimization maximizes the region of overlap and the spatial coherence of the deformation while minimizing registration error. All optimization parameters are chosen automatically; hand‐tuning is not necessary. Our method is not restricted to part‐in‐whole matching, but addresses the general problem of partial matching, and requires no explicit prior correspondences or feature points. We evaluate the performance and robustness of our method using scan data acquired by a structured light scanner and compare our method with existing non‐rigid registration algorithms.
Protein-tyrosine Phosphatase ϵ (1995)

Transgenic mice that overexpress v-Ha-ras, c-myc, c-neu or int-2 proto-oncogenes in the mammary epithelium develop breast tumors with morphologies that are characteristic of each initiating oncogene. Since these morphological differences reflect distinctive patterns of tumor-specific gene expression, the identification of the products of these genes might shed light on the mechanisms of transformation and/or the identity of target cells that are transformed by specific classes of oncogenes. By focusing on the tyrosine phosphorylation pathway, we have found that the transmembranal protein-tyrosine phosphatase epsilon (PTP epsilon) is highly expressed in murine mammary tumors initiated by c-neu and v-Haras, but not in mammary tumors initiated by c-myc or int-2. This difference is striking and occurs both in primary tumors and in epithelial cells cultured from them. Moreover, PTP epsilon overexpression appears to be mammary tumor-specific in that it is not found in other ras-based tumors and cell lines. These observations suggest that PTP epsilon either plays a role in ras- and neu-mediated transformation of mammary epithelium or marks mammary epithelial cells particularly susceptible to transformation by these oncogenes. Because of its distinctive expression in these mammary tumors, we have further characterized murine PTP epsilon, cloning and determining the complete structures of its cDNAs and showing that it is a glycoprotein that is N-glycosylated in a tissue-specific manner.
Bisindolylmaleimides Linked to DNA Minor Groove Binding Lexitropsins:  Synthesis, Inhibitory Activity against Topoisomerase I, and Biological Evaluation (1996)

The synthesis, characterization, inhibitory activity against topoisomerase I, and biological evaluation of a series of oligopeptide-substituted bisindolylmaleimides 7-12 are described. Compounds 7-9, which contain a basic C-terminus function such as (dimethylamino)propyl and bind to DNA with C(50) values of 200, 160, and 135 microM, respectively, exhibited inhibition of topoisomerase I in a concentration dependent manner. Also, the relative order of observed topoisomerase I inhibition is 9 > 8 > 7 at < or = 100 microM concentration, corresponding to the increase of the number of pyrrole units in the oligopeptide moiety. Compounds 10-12, which contain an electrostatically neutral moiety, such as methyl ester, did not bind to DNA templates nor inhibit topoisomerase I. However, the cytotoxicity activities of these compounds were 1.5 times greater than those of compounds 7-9.
Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications (2018)

The MinION sequencer (Oxford Nanopore Technologies) is a paradigm shifting device allowing rapid, real time long read sequencing of nucleic acids. Yet external benchmarking of this technologies' capabilities has not been extensively reported, nor has thorough evaluation of its utility for field-based analysis with sub-optimal sample types been described. The aim of this study was to evaluate the capability of the MinION sequencer for bacterial genomic and metagenomic applications, with specific emphasis placed on the quality, yield, and accuracy of generated sequence data. Two independent laboratories at the National Microbiology Laboratory (Public Health Agency of Canada), sequenced a set of microbes in replicate, using the currently available flowcells, sequencing chemistries, and software available at the time of the experiment. Overall sequencing yield and quality improved through the course of this set of experiments. Sequencing alignment accuracy was high reaching 97% for all 2D experiments, though was slightly lower for 1D sequencing (94%). 1D sequencing provided much longer sequences than 2D. Both sequencing chemistries performed equally well in constructing genomic assemblies. There was evidence of barcode cross-over using both the native and PCR barcoding methods. Despite the sub-optimal nature of samples sequenced in the field, sequences attributable to B. anthracis the target organism used in this scenario, could none-the-less be detected. Together, this report showcases the rapid advancement in this technology and its utility in the context of genomic sequencing of microbial isolates of importance to public health.
[Resection of the Müller muscle. Indications, technique and results]. (1994)

From 1987 to 1992, 582 operations for blepharoptosis were performed in our department. Twenty-five cases of superior tarsal muscle resection in 22 patients were reviewed retrospectively and serve as the basis of the present study. The blepharoptosis was mild to moderate (up to 4 mm) in 20/25 cases. Preoperatively, the phenylephrine eye drops test was positive in 20/25 cases. The indication for both congenital and acquired blepharoptosis was independent of the activity of the levator muscle. The resection was performed by a conjunctival approach. Three techniques of muscle stump refixation were tested without any significant difference in the results. A satisfactory eyelid elevation of more than 2 mm was achieved in 16/25 operations. A moderate effect (1-2 mm) was measured in 5/25 and an unsatisfactory effect (< 1 mm) in 4/25 cases. In contrast to the Fasanella-Servat procedure, the above-mentioned technique leaves all other structures of the upper eyelid intact, especially the accessory lacrimal glands.
Nanoscale metal/self-assembled monolayer/metal heterostructures (1997)

We present the investigation of novel metal/organic monolayer/metal heterostructure diodes. Our technique provides well-defined, stable, and reproducible metallic contacts to a self-assembled monolayer of 4-thioacetylbiphenyl with nanoscale area. Electronic transport measurements show a prominent rectifying behavior arising from the asymmetry of the molecular heterostructure. Variable-temperature measurements reveal that thermal emission of electrons over a barrier of 0.22 eV dominates for electron injection from Ti into the organic layer while the transport for electron injection from Au into the organic layer satisfies the formula for hopping conduction.
Ethidium derivatives bind to G-quartets, inhibit telomerase and act as fluorescent probes for quadruplexes (2001)

The telomeric G-rich single-stranded DNA can adopt in\n vitro an intramolecular quadruplex structure, which has been\n shown to directly inhibit telomerase activity. The reactivation\n of this enzyme in immortalized and most cancer cells suggests that\n telomerase is a relevant target in oncology, and telomerase inhibitors\n have been proposed as new potential anticancer agents. In this paper,\n we describe ethidium derivatives that stabilize G-quadruplexes.\n These molecules were shown to increase the melting temperature of\n an intramolecular quadruplex structure, as shown by fluorescence\n and absorbance measurements, and to facilitate the formation of intermolecular\n quadruplex structures. In addition, these molecules may be used\n to reveal the formation of multi-stranded DNA structures by standard\n fluorescence imaging, and therefore become fluorescent probes of\n quadruplex structures. This recognition was associated with telomerase\n inhibition in vitro: these derivatives showed a\n potent anti-telomerase activity, with IC50 values of\n 18–100 nM in a standard TRAP assay.
Transforming growth factor-β: an important cytokine in the mucosal immune response (2000)

Cytokines are important mediators in the intestine regulating both oral tolerance and mucosal inflammation. Central to this immune-regulatory role is the cytokine transforming growth factor-beta (TGF-beta). Oral tolerance and inflammatory responses in the gut are regulated through the balance of the Th1, Th2, and Th3 lymphocyte responses--a balance influenced strongly by TGF-beta. TGF-beta also modulates B-cell responses by increasing the production of immunoglobulin A (IgA) while decreasing the production of IgG, IgM, and IgE. In intestinal epithelial cells, TGF-beta activates signal transduction pathways resulting in the inhibition of proliferation and tumorigenesis. Currently, these signaling pathways are being dissected at the molecular level.
ATP-Sensitive Potassium Channel Openers and 2,3-Dimethyl-2-Butylamine Derivatives (2006)

ATP-sensitive potassium (K(ATP)) channels have important functions through their coupling of cellular energetic networks and their ability to decode metabolic signals, and they are implicated in diseases of many organs. K(ATP) channels are formed by the physical association between the inwardly rectifier potassium channels (Kir6.x) and the regulatory sulfonylurea receptor subunit (SUR), which form a hetero-octameric complex. Different subtypes of K(ATP) channels exist in various tissues. K(ATP) channel openers (KCOs) are classified into nine chemical families according to their molecular structures: (1) benzopyrans, (2) cyanoguanidines, (3) thioformamides, (4) pyrimidine derivatives, (5) pyridine derivatives, (6) benzothiadiazines, (7) dihydropyridines, (8) nicotinamide derivatives, and (9) aliphatic amines. Although the model also predicts that KCOs have four co-binding areas, it was hypothesized that the main contribution lies in the binding domain of hydrophobicity of the side chain. A series of compounds containing the skeleton of the aliphatic secondary amines as a side chain was designed. It was found that N-isopropyl 2,3-dimethyl-2-butylamine (iptakalim, 91) is a novel KCOs. Iptakalim regulates the pore selectively of the inwardly rectifier potassium channel and dilates smaller arteries, but has little effect on vasodilatation of the aorta. Iptakalim administered p.o. has selective and long-lasting antihypertensive effects in hypertensive animals and does not induce tolerance, but has little effect on blood pressure in normotensive animals. Meanwhile, it also reverses cardiovascular remodeling and protects the brain and kidney against damage caused by hypertension in animal models. Iptakalim is in phase II clinical trials now and has a promising future as a treatment for hypertension.
Regions of the Mouse CD14 Molecule Required for Toll-like Receptor 2- and 4-mediated Activation of NF-κB (2002)

Regions of mouse CD14 required for Toll-like receptor 2 (TLR2)- and TLR4-mediated activation of NF-kappaB were studied in transiently transfected 293 cells. Wild-type CD14 enhanced lipopolysaccharide (LPS)-induced NF-kappaB-dependent reporter activity in cells expressing TLR4/MD-2, and deletion of amino acid regions 35-44, 144-153, 235-243, and 270-275 impaired the TLR4-mediated activation. Unlike human CD14, mouse CD14 truncated at amino acid 151 lost the activity. Deletion of amino acids 35-44 or 235-243 also abrogated TLR2-mediated activation of NF-kappaB, whereas mutants lacking 144-153 and 270-275 retained the activity. Deletion and alanine substitution experiments revealed that amino acids 151-153 and 273-275 were required for the TLR4-mediated activation. Both deletion mutants lacking amino acids 35-44 and 235-243 and alanine substitution mutants in regions 151-153 and 273-275 were expressed on the cell surface and retained the ability to associate with TLR4. A cross-linking study with photoreactive LPS showed that the labeling intensities to CD14 mutants/TLR4/MD-2 were paralleled by the ability of CD14 mutants to increase TLR4-mediated activation. These results indicate that different regions of mouse CD14 are required for TLR4- and TLR2-mediated activation of NF-kappaB and suggest that amino acids 35-44, 151-153, 235-243, and 273-275 of mouse CD14 play an important role in LPS binding and its transfer to TLR4/MD-2.
Spontaneous resolution of fetal nuchal cystic hygroma. (1991)

Complete resolution of the hygroma occurred in two fetuses with the mid-trimester ultrasound diagnosis of a nuchal cystic hygroma. Cytogenetic studies showed a normal 46,XX karyotype in one fetus, and a 47,XX, +18 in the other. Complete regression of cystic hygroma has been reported in fetuses with normal chromosomes, as well as in those with trisomy 21, and with Turner's syndrome. The incidence of spontaneous in utero resolution of fetal nuchal cystic hygroma is unknown. The natural history of cystic hygroma in utero cannot be correlated with the chromosome complement. An antenatal karyotype determination should be offered to any patient whose fetus has cystic hygroma, even to those with spontaneous resolution.
Carbon Monoxide-Releasing Molecules: A Pharmacological Expedient to Counteract Inflammation (2008)

Carbon monoxide (CO) mediates many of the biological effects that are attributed to heme oxygenase (HO), the enzyme responsible for CO production in mammals. Antioxidant and anti-inflammatory activities of HO-1, the inducible isoform of heme oxygenase, have been demonstrated in a variety of disease models and a therapeutic exploitation of this pathway is currently under scrutiny. In this context, the liberation of CO from CO-releasing molecules (CO-RMs) is extremely attractive as these compounds may form the basis of a new class of pharmaceuticals. Recent investigations indicate that HO-1 and CO modulate important processes in chronic inflammation; these include the control of immune responses, the production of inflammatory mediators and the mitigation of cartilage or bone destruction. As HO-1 is highly expressed in the joint tissues of patients affected by arthritic diseases, it is plausible to suggest that this pathway may play a protective role against joint degenerative diseases. Studies aimed at identifying the signaling pathways responsive to endogenous CO and CO-RMs in rheumatoid arthritis and other inflammatory states are currently in progress. This research will help to elucidate the molecular mechanisms underlying the pharmacological effects of CO-RMs and may lead to the development of novel therapeutic strategies for the treatment of acute and chronic inflammatory conditions.
Blood flow and muscle fatigue in SCI individuals during electrical stimulation (2003)

Our purpose was to measure blood flow and muscle fatigue in chronic, complete, spinal cord-injured (SCI) and able-bodied (AB) individuals during electrical stimulation. Electrical stimulation of the quadriceps muscles was used to elicit similar activated muscle mass. Blood flow was measured in the femoral artery by Doppler ultrasound. Muscle fatigue was significantly greater (three- to eightfold, P < or = 0.001) in the SCI vs. the AB individuals. The magnitude of blood flow was not significantly different between groups. A prolonged half-time to peak blood flow at the beginning of exercise (fivefold, P = 0.001) and recovery of blood flow at the end of exercise (threefold, P = 0.009) was found in the SCI vs. the AB group. In conclusion, the magnitude of the muscle blood flow to electrical stimulation was not associated with increased muscle fatigue in SCI individuals. However, the prolonged time to peak blood flow may be an explanation for increased fatigue in SCI individuals.
Hemorrhagic streptococcal pneumonia in newly procured research dogs. (1982)

An acute necrotizing hemorrhagic pneumonia syndrome was recognized among 14 newly arrived research dogs. Typically, there were acute deaths without clinical signs. Necropsy revealed diffuse hemorrhagic pneumonia, and Lancefield group C Streptococcus zooepidemicus was isolated consistently from the lungs. In many cases, septic thrombi were seen in the small vessels of the kidneys, lymph nodes, spleen, brain, and adrenal glands. The syndrome was reproduced by intratracheal inoculation of the isolant into a susceptible dog.
Wavelength dilated switches (WDS)-a new class of high density, suppressed crosstalk, dynamic wavelength-routing crossconnects (1992)

The concept of dilated space-division switches is generalized to the wavelength dimension, resulting in a new class of dynamic wavelength-routing crossconnects. These wavelength dilated switches (WDSs) are reconfigurable and feature suppressed crosstalk and denser wavelength-spacings. They are scalable, with switch-complexity of alpha N log/sub 2/ N where alpha is the dilation constant, typically 4-6, and N is the number of ports. A method for minimizing the crosstalk is described, and it is demonstrated with examples how the WDS can relax the crosstalk requirement of the wavelength routing devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chemometric Techniques for Quantitative Analysis (1999)

Basic approach creating some data classical least-squares inverse least-squares factor spaces principal component regression PCR in action partial least squares PLS in action appendix A - matrices and matrix operations appendix B - errors -some definitions of terminology appendix C - centering and scaling appendix D - F-tests for reduced eigenvalues appendix E - leverage and influence.
Activity-Guided Isolation of Triterpenoid Acyl CoA Cholesteryl Acyl Transferase (ACAT) Inhibitors from Ilex kudincha (1999)

Activity-guided fractionation of a methanol extract of the leaves of Ilex kudincha led to the isolation of seven acyl CoA cholesteryl acyl transferase (ACAT) inhibitory triterpenes. Four of them were identified by spectroscopic methods as ulmoidol (4), 23-hydroxyursolic acid (5), 27-trans-p-coumaroyloxyursolic acid (6), and 27-cis-p-coumaroyloxyursolic acid (7), and three were new compounds named ilekudinols A-C (1-3). The structures of these new triterpenoids were elucidated as 2alpha, 3beta-dihydroxy-24-nor-urs-4(23),11-dien-28,13beta- olide (1), 2alpha, 3beta-dihydroxy-24-nor-urs-4(23),12-dien-28-oic acid (2), and 3beta, 24,28-trihydroxylupane (3). Compounds 1-7 showed potent inhibitory activity in the ACAT assay.