gebhart/patrepeval huggingface dataset:
Inhibition of the classical and alternative pathways by amino acids and their derivatives. (1978)

Effects of various aminoacids and their derivatives on the classical pathway and alternative pathway of the complement were studied. Leupeptin, acetyl-leucyl-leucyl-arginal, inhibited CH50 and Cl-esterase, but did not inhibit the alternative pathway. When aminoacids of carbon chains of the order of seven were used, arginine and lysine had stronger effects than trans-aminomethyl cyclohexane carboxylic acid (t-AMCHA), cis-aminomethyl cyclohexane carboxylic acid (cis-AMCHA) and epsilon aminocaproic acid (EACA). SH-compounds, cysteine, homocysteine and glutathione, had the strongest inhibitory effects among these aminoacids on both classical and alternative pathways. When effects on Cl esterase were compared, arginine, lysine, t-AMCHA, cis-AMCHA and EACA had weak inhibition while SH-compounds showed strong inhibition. Poly-L-lysine, which had extremely strong inhibition of CH50, had no inhibition of Cl esterase. The inhibitory effects of antifibrinolytic agents, EACA and t-AMCHA, were weak but when effects on early parts of the classical pathway, C(1,4,2)H50 were tested, some inhibitory activities were recognized. Thus inhibitory effects of these agents were due to their activities on the early parts of the classical pathway.
Rapid prototyping of microfluidic systems using a PDMS/polymer tape composite (2009)

Rapid prototyping of microfluidic systems using a combination of double-sided tape and PDMS (polydimethylsiloxane) is introduced. PDMS is typically difficult to bond using adhesive tapes due to its hydrophobic nature and low surface energy. For this reason, PDMS is not compatible with the xurography method, which uses a knife plotter and various adhesive coated polymer tapes. To solve these problems, a PDMS/tape composite was developed and demonstrated in microfluidic applications. The PDMS/tape composite was created by spinning it to make a thin layer of PDMS over double-sided tape. Then the PDMS/tape composite was patterned to create channels using xurography, and bonded to a PDMS slab. After removing the backing paper from the tape, a complete microfluidic system could be created by placing the construct onto nearly any substrate; including glass, plastic or metal-coated glass/silicon substrates. The bond strength was shown to be sufficient for the pressures that occur in typical microfluidic channels used for chemical or biological analysis. This method was demonstrated in three applications: standard microfluidic channels and reactors, a microfluidic system with an integrated membrane, and an electrochemical biosensor. The PDMS/tape composite rapid prototyping technique provides a fast and cost effective fabrication method and can provide easy integration of microfluidic channels with sensors and other components without the need for a cleanroom facility.
Effect of Temperature and Ionic Strength on the Dissociation Kinetics and Lifetime of PNA−DNA Triplexes (2000)

Dissociation kinetics of triplexes formed by molecules of peptide nucleic acid (PNA) and DNA have been studied. The complexes consisted of oligomeric PNA containing 10 thymine bases and the dA(10) target incorporated in single-stranded (ssDNA) or double-stranded DNA (dsDNA). Their dissociation was followed by means of the gel mobility shift assay at various temperatures and sodium ion concentrations. In all experiments, the dissociation kinetics of triplexes were exponential; the effective lifetime of a triplex, tau, depended on temperature in accordance with the Arrhenius law. The tau values for T(10) PNA complexes with ss- and dsDNA were equal within the accuracy of experiments. The activation energy, U, value for T(10) PNA-DNA complexes did not change when the NaCl concentration was increased from 50 to 200 or 600 mM. Conversely, the tau values decreased with the increase in NaCl concentration. The equal lifetimes of the T(10) PNA-DNA triplexes containing ss- and dsDNA suggest that the loop formed in dsDNA does not noticeably affect the triplex structure. The decrease in the triplex lifetime tau with an increase in ionic strength was accounted for by the fact that the PNA backbone is neutral. The lack of relationship between the activation energy of dissociation and salt concentration suggests that the dissociation enthalpy does not depend on the ionic strength. Thus, the effect of ionic strength on the lifetime is entropic by its nature. Contrary to this, for complexes of ssDNA with bis-PNA 1743, which also consists of 10 thymine bases but contains 2 additional positive charges inside the sequence in 1 of the PNA arms, an increase of the dissociation enthalpy at low salt concentration was observed. We suggest that this effect is a result of a direct electrostatic interaction of the positive charges of the PNA with the DNA backbone. Finally, our results allow an estimate of the lifetime of a 10-mer triplex invasion complex in dsDNA at 37 degrees C in excess of several hundred days.
A Review of Targeted Pulmonary Arterial Hypertension-Specific Pharmacotherapy (2016)

Significant advances in the understanding of the pathophysiology of pulmonary arterial hypertension over the past two decades have led to the development of targeted therapies and improved patient outcomes. Currently, a broad armamentarium of pulmonary arterial hypertension-specific drugs exists to assist in the treatment of this complex disease state. In this manuscript, we provide a comprehensive review of the current Food and Drug Administration (FDA)-approved pulmonary arterial hypertension-specific therapies, and their supporting evidence for adults, targeting the nitric oxide, soluble guanylate cyclase, endothelin, and prostacyclin pathways.
Carbon source nutrition of rapamycin biosynthesis inStreptomyces hygroscopicus (1995)

Chemically-defined media were developed for rapamycin production by Streptomyces hygroscopicus. Thirty-five carbon sources were tested for their effect on production. Eight failed to support growth and seven appeared to repress or inhibit rapamycin formation. The best combination of two carbon sources were 2% fructose and 0.5% mannose. Acetate and propionate, which are known to contribute most of the carbon atoms of the lactone ring, were unsatisfactory for growth and/or rapamycin production.
Addressing the Rare Word Problem in Neural Machine Translation (2015)

Thang Luong, Ilya Sutskever, Quoc Le, Oriol Vinyals, Wojciech Zaremba. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
A mutant epidermal growth factor receptor common in human glioma confers enhanced tumorigenicity. (1994)

The development and neoplastic progression of human astrocytic tumors appears to result through an accumulation of genetic alterations occurring in a relatively defined order. One such alteration is amplification of the epidermal growth factor receptor (EGFR) gene. This episomal amplification occurs in 40-50% of glioblastomas, which also normally express endogenous receptors. Moreover, a significant fraction of amplified genes are rearranged to specifically eliminate a DNA fragment containing exons 2-7 of the gene, resulting in an in-frame deletion of 801 bp of the coding sequence of the extracellular domain. Here we used retroviral transfer of such a mutant receptor (de 2-7 EGFR) into glioblastoma cells expressing normal endogenous receptors to test whether the mutant receptor was able to augment their growth and malignancy. Western blotting analysis showed that these cells expressed endogenous EGFR of 170 kDa as well as the exogenous de 2-7 EGFR of 140-155 kDa. Although holo-EGFRs were phosphorylated on tyrosine residues only after exposure of the cells to ligand, de 2-7 EGFRs were constitutively phosphorylated. In tissue culture neither addition of EGF nor expression of the mutant EGFR affected the rate of cell growth. However, when cells expressing mutant EGFR were implanted into nude mice subcutaneously or intracerebrally, tumorigenic capacity was greatly enhanced. These results suggest that a tumor-specific alteration of the EGFR plays a significant role in tumor progression perhaps by influencing interactions of tumor cells with their microenvironment in ways not easily assayed in vitro.
Reflective coating for lightweight x-ray optics (2012)

X-ray reflective coating for next generation’s lightweight, high resolution optics for astronomy requires thin-film deposition that is precisely fine-tuned so that it will not distort the thin sub-mm substrates. Film of very low stress is required. Films with multi-layer or bi-layer can be deposited to give an effective low stress which cause negligible distortion. Alternatively, mirror distortion can be cancelled by precisely balancing the deformation by coating films on both sides of the substrates. We have been developing techniques to coat glass substrates that can provide good reflectivity in the soft x-ray band below 10 keV, and yet introduce negligible surface distortion for arc-second optics. These efforts include: low-stress deposition by magnetron sputtering and atomic layer deposition of the metals, balancing of gross deformation with two-layer depositions of opposite stresses and with depositions on both sides of the thin mirrors.
High internal phase emulsion templating as a route to well-defined porous polymers (2005)

The use of high internal phase emulsions (HIPEs) as templates to create highly porous materials (PolyHIPEs) is described. Polymerisation occurs around emulsion droplets, which create voids in the final material. The void fraction is very high and can reach levels of 0.99. Varying the emulsion composition can control features of the morphology of the resulting porous materials, such as the void diameter and degree of interconnection. Other parameters can also be varied, for example surface area can be increased from 3 to around 700 m2 g−1. Rubbery materials can be produced from hydrophobic elsatomers and PolyHIPEs with high thermo-oxidative stability are prepared from high performance materials such as poly(ether sulfone). The highly porous materials so produced are finding applications in areas such as solid supported organic chemistry, sensors, cell culturing and tissue engineering.
Addition of functional human telomeres to YACs (1994)

Linear mammalian artificial chromosomes (MACs) will require functional telomeres, a centromere and the ability to replicate autonomously. We are investigating the possibility of developing MACs from yeast artificial chromosomes (YACs). Retrofitting vectors have been constructed to replace YAC telomeres with cloned human telomeric DNA. A modified YAC was introduced into mammalian cells by spheroplast fusion and the frequency with which the retrofitted human telomeric DNA seeded the formation of a new telomere was determined by Bal31 digestion and cytogenetic analysis. The telomere adjacent to the selectable marker gene was functional in 5/46 clones (11%) while the telomere 200 kb away at the other end of the YAC was functional in 1/46 clones (2%). These results indicate that despite the in vivo modification of the end of the telomere by the addition of yeast sequences, human telomeres will function at a high enough frequency to allow the construction of MACs by this route.
T cell activation: in vivo veritas (2004)

Phenotypic changes in CD4(+) T cells undergoing antigen-dependent activation were compared in vivo and in vitro. The most obvious difference was in expression of CD25, the alpha chain of the high affinity receptor for IL-2. High level expression of CD25 in vivo is restricted to a small fraction of the cells at the leading edge of the cell division profile, whereas all activated cells express high levels of CD25 in cultures responding to antigen. Because IL-2 is known to upregulate expression of CD25 in preactivated T cells, this suggests a difference in IL-2 exposure in the two responses. A number of other markers, including CD54, show a similar difference in the pattern of expression in vivo and in vitro. Using 6-colour flow cytometry, it was demonstrated that the small percentage of cells expressing CD25 in vivo coexpresses a very high level of a number of other activation markers, including CD38, CD44 and Ly-6A/E, suggesting that these may also be upregulated by autocrine IL-2.
Physiology: The production of placental protein 14 by human uterine tubal epithelial cells in culture (1995)

Cells prepared from the mucosal layer obtained from the fimbrial, proximal ampullary and distal ampullary regions of the human uterine (Fallopian) tube have been grown in monolayer culture. Immunocytochemistry with anti-cytokeratin, anti-vimentin or anti-CD 45 antibodies indicated that the overwhelming number of cells were epithelial in nature and were free of fibroblasts and leukocytes. Basal and steroid-stimulated placental protein 14 (PP14) production was investigated in tissue obtained from nine patients undergoing hysterectomy, by addition of oestradiol and/or progesterone to confluent cultures. Basal PP14 production varied considerably between experiments, probably due to differences between individuals from whom the tissue had been obtained. However, there was no difference in basal PP14 production by cells prepared from the fimbrial, proximal ampullary and distal ampullary parts of the tube obtained from the same patient. When total PP14 production by cells obtained from an individual uterine tube was pooled both progesterone and oestradiol significantly (P < 0.05) stimulated the production of PP14 but the effect of progesterone either alone or in the presence of oestradiol was numerically greater than that of oestradiol alone. Considering PP14 production by cells prepared from the different regions of the tube showed that cells from the fimbrial region were more responsive to steroid stimulation than cells prepared from either the proximal or the distal ampullary regions. All combinations of hormonal supplementation stimulated PP14 production by cells from the fimbrial region on all days measured (P < 0.05 - P < 0.001).(ABSTRACT TRUNCATED AT 250 WORDS)
Alteration of a protease-sensitive region of Pseudomonas exotoxin prolongs its survival in the circulation of mice. (1992)

Pseudomonas exotoxin A (PE) is a single-chain 66-kDa polypeptide that kills eukaryotic cells by ADP-ribosylation of translational elongation factor 2. PE is composed of three major structural domains whose functions are binding of cells (I), translocation (II), and ADP-ribosylation (III). Here we describe a protease cleavage target that is located near arginine-490 on the surface of domain III. We made several different types of mutations near arginine-490. Deletion of arginine-490 or replacement of arginine-490 and -492 with serine and lysine or with two lysines resulted in protease-resistant molecules that were fully cytotoxic and had normal ADP-ribosylation activity. However, the half-life in mouse blood of the PE delta 490 mutant was 24 min whereas that of PE was 13 min. Furthermore, two PE mutants that were protease-hypersensitive, PEGlu246,247,249 and PEGlu57,246,247,249 (in which glutamate residues replace basic residues at the indicated positions), had very short half-lives. These data indicate that protease sensitivity is an important determinant in the half-life of PE in the circulation and suggest that the half-life of other proteins may be prolonged by removal of protease sites. Deletion of arginine-492 or the replacement of amino acids 486-491 with three glycines markedly diminished ADP-ribosylation activity and cytotoxicity, indicating that this region of domain III is also important for catalytic activity.
Identification of multiple nuclear localization signals in murine Elf3, an ETS transcription factor (2006)

We investigated nuclear localization signal (NLS) determinants within the AT-hook and ETS DNA-binding domains of murine Elf3 (mElf3), a member of the subfamily of epithelium-specific ETS transcription factors. Deletion mutants containing the AT-hook, ETS domain or both localized strictly in the nucleus, suggesting that these individual domains contain independent NLS motif(s). Within the AT-hook domain, four basic residues (244KRKR247) were critical for strong NLS activity, and two potent bipartite NLS motifs (236-252 and 249-267) were sufficient for nuclear import of mElf3, although less efficient than the full domain. In addition, one stretch of basic residues (318KKK320) within the ETS domain appears to be essential for mElf3 nuclear localization. Taken together, mElf3 contains multiple NLS motifs, which may function cooperatively to effect efficient nuclear transport.
Modulated Synthesis of Zr‐Based Metal–Organic Frameworks: From Nano to Single Crystals (2011)

We present an investigation on the influence of benzoic acid, acetic acid, and water on the syntheses of the Zr-based metal-organic frameworks Zr-bdc (UiO-66), Zr-bdc-NH(2) (UiO-66-NH(2)), Zr-bpdc (UiO-67), and Zr-tpdc-NH(2) (UiO-68-NH(2)) (H(2) bdc: terephthalic acid, H(2) bpdc: biphenyl-4,4'-dicarboxylic acid, H(2) tpdc: terphenyl-4,4''-dicarboxylic acid). By varying the amount of benzoic or acetic acid, the synthesis of Zr-bdc can be modulated. With increasing concentration of the modulator, the products change from intergrown to individual crystals, the size of which can be tuned. Addition of benzoic acid also affects the size and morphology of Zr-bpdc and, additionally, makes the synthesis of Zr-bpdc highly reproducible. The control of crystal and particle size is proven by powder XRD, SEM and dynamic light scattering (DLS) measurements. Thermogravimetric analysis (TGA) and Ar sorption experiments show that the materials from modulated syntheses can be activated and that they exhibit high specific surface areas. Water proved to be essential for the formation of well-ordered Zr-bdc-NH(2) . Zr-tpdc-NH(2), a material with a structure analogous to that of Zr-bdc and Zr-bpdc, but with the longer, functionalized linker 2'-amino-1,1':4',1''-terphenyl-4,4''-dicarboxylic acid, was obtained as single crystals. This allowed the first single-crystal structural analysis of a Zr-based metal-organic framework.
Efficient Preparation of Organic Substrate−RNA Conjugates via in Vitro Transcription (2005)

A concise synthetic way has been developed for the preparation of guanosine monophosphate derivatives carrying a decaethylene glycol spacer at their 5'-oxygen to which are attached a range of organic substrates. The four different compounds, prepared via a convergent synthetic strategy, carry a tethered benzylallyl ether residue (1a), an anthracene (1b), a benzyl carbamate residue (1c), or a primary amino group (1d), respectively. All four compounds have been successfully incorporated at the 5'-end of a 25-mer long RNA transcript via T7 RNA polymerase, and no inhibition of chain elongation could be observed. Under proper conditions, 1a and 1b can be incorporated up to 90-95% and 1c up to 68%. The amino-terminated initiator 1d is incorporated less efficiently although still up to 49%. These results show that the more hydrophobic the guanosine monophosphate derivative is, the higher is its enzymatic incorporation.
Editorial Commentary:The Many Faces ofPseudomonas aeruginosain Chronic Obstructive Pulmonary Disease (2008)

Bacterial infection of the airways plays a critical role in the course and pathogenesis of chronic obstructive pulmonary disease (COPD). Bacteria cause acute exacerbations that characterize the course of COPD, and these exacerbations are associated with substantial morbidity and mortality [1-3]. In addition, bacteria are present in the lower airways of many adults with COPD, even during clinically stable periods [4-6]. Bacteria in the airways contribute to the airway inflammation that is a hallmark of COPD [7-9]. The application of modern approaches in the past decade by research groups throughout the world has advanced our understanding of the role of bacterial infection in COPD. However, important gaps in our knowledge remain. Perhaps one of the largest gaps is understanding the role of Pseudomonas aeruginosa in COPD. The observation that P. aeruginosa is isolated from sputum samples from 4%15% of adults with COPD in many crosssectional studies suggests that the bacterium is a common cause of infection in this clinical context [10-12]. Indeed, P. aeruginosa is more likely to be isolated from patients with severe disease, particularly among patients who require mechanical ventilation for severe exacerbations [13-15]. However, these data are also consistent with an alternative explanation that is, P. aeruginosa in sputum is simply a colonizer and, thus, a marker for more-advanced lung disease. Individuals with advanced COPD are more likely to receive courses of antimicrobial therapy that selects antibiotic-resistant bacteria,
Prophylaxis for severe haemophilia: clinical and economical issues (2003)

Patients with severe haemophilia are treated either in case of bleeds only (on demand), or with regular infusions of clotting factor to prevent bleeds (prophylaxis). The introduction of prophylaxis has been hampered by issues of cost and viral safety. In order to compare results and treatment cost of different treatment strategies in adults, three cohorts of patients with severe haemophilia (born 1970-1980) were compared. 106 French patients were treated on demand, 49 Dutch patients were treated with intermediate dose prophylaxis, and 24 Swedish patients were treated with high dose prophylaxis. The annual number of joint bleeds, and the radiological Pettersson score were used to compare outcome, annual clotting factor consumption was used to compare costs. Prophylaxis reduced bleeds and arthropathy: patients treated on demand had a median of 11.5 joint bleeds/year and a median Pettersson score of 16 points, for intermediate dose prophylaxis median bleeds were 2.8 and Pettersson score was 7 points, and for high dose prophylaxis median bleeds were 0.5 joint bleeds and Pettersson score was 4 points. All differences were statistically significant, except the Pettersson scores in both prophylactic regimens. Treatment cost was only increased for high dose prophylaxis: mean clotting factor consumption was 1612 IU kg-1 yr-1 for on demand treatment, 1488 IU kg-1 yr-1 for intermediate dose prophylaxis, and 4012 IU kg-1 yr-1 for high dose prophylaxis. In young adults, the cost of intermediate dose prophylaxis is similar, but outcome is better than for on demand treatment. The cost of high dose prophylaxis is twofold higher, further improving outcome only slightly.
EGFR as a Target for Glioblastoma Treatment: An Unfulfilled Promise (2017)

The receptor for epidermal growth factor (EGFR) is a prime target for cancer therapy across a broad variety of tumor types. As it is a tyrosine kinase, small molecule tyrosine kinase inhibitors (TKIs) targeting signal transduction, as well as monoclonal antibodies against the EGFR, have been investigated as anti-tumor agents. However, despite the long-known enigmatic EGFR gene amplification and protein overexpression in glioblastoma, the most aggressive intrinsic human brain tumor, the potential of EGFR as a target for this tumor type has been unfulfilled. This review analyses the attempts to use TKIs and monoclonal antibodies against glioblastoma, with special consideration given to immunological approaches, the use of EGFR as a docking molecule for conjugates with toxins, T-cells, oncolytic viruses, exosomes and nanoparticles. Drug delivery issues associated with therapies for intracerebral diseases, with specific emphasis on convection enhanced delivery, are also discussed.