gebhart/patrepeval huggingface dataset:
5-hydroxymethylcytosine and its potential roles in development and cancer (2013)

Only a few years ago it was demonstrated that mammalian DNA contains oxidized forms of 5-methylcytosine (5mC). The base 5-hydroxymethylcytosine (5hmC) is the most abundant of these oxidation products and is referred to as the sixth DNA base. 5hmC is produced from 5mC in an enzymatic pathway involving three 5mC oxidases, Ten-eleven translocation (TET)1, TET2, and TET3. The biological role of 5hmC is still unclear. Current models propose that 5hmC is an intermediate base in an active or passive DNA demethylation process that operates during important reprogramming phases of mammalian development. Tumors originating in various human tissues have strongly depleted levels of 5hmC. Apparently, 5hmC cannot be maintained in proliferating cells. Furthermore, mutations in the TET2 gene are commonly observed in human myeloid malignancies. Since TET proteins and many lysine demethylases require 2-oxoglutarate as a cofactor, aberrations in cofactor biochemical pathways, including mutations in isocitrate dehydrogenase (IDH), may affect levels of 5hmC and 5mC in certain types of tumors, either directly or indirectly. We discuss current data and models of the function of 5hmC in general, with special emphasis on its role in mechanisms of development and cancer.
Mitochondrial Functions and Estrogen Receptor-dependent Nuclear Translocation of Pleiotropic Human Prohibitin 2 (2006)

Proteins with multiple cellular functions provide biological diversity to eukaryotic cells. In the current studies, we identified the mitochondrial functions of human prohibitin 2 (PHB2), which was initially identified as a repressor of estrogen-dependent transcriptional activity. The mitochondrial complex of PHB2 consists of PHB1, voltage-dependent anion channel 2, adenine nucleotide translocator 2, and the anti-apoptotic Hax-1, which is a novel binding partner for PHB2. RNA interference-mediated knockdown of PHB2 in HeLa cells resulted in caspase-dependent apoptosis through down-regulation of Hax-1 and fragmentation of mitochondria. We also found that, although PHB2 is predominantly expressed in the mitochondria of HeLa cells, it translocates to nucleus in the presence of estrogen receptor alpha and estradiol. Here, we first demonstrated the roles of mammalian PHB2 in mitochondria and the molecular mechanism of its nuclear targeting and showed that PHB2 is a possible molecule directly coupling nuclear-mitochondrial interaction.
Design and implementation of firewall based on web (2003)

This article does the basic research on the ways to build the firewall through the web pages in order to make this operation easily. Firstly it combines the technology of firewall with that of programming based on web, and then it introduces the design and implementation of firewall based on web. Finally it does some exploration on its commercial implementation.
Novel miktofunctional initiator for the preparation of an ABC‐type miktoarm star polymer via a combination of controlled polymerization techniques (2004)

Abstract An ABC‐type miktoarm star polymer was prepared with a core‐out method via a combination of ring‐opening polymerization (ROP), stable free‐radical polymerization (SFRP), and atom transfer radical polymerization (ATRP). First, ROP of ϵ‐caprolactone was carried out with a miktofunctional initiator, 2‐(2‐bromo‐2‐methyl‐propionyloxymethyl)‐3‐hydroxy‐2‐methyl‐propionic acid 2‐phenyl‐2‐(2,2,6,6‐tetramethyl‐piperidin‐1‐yl oxy)‐ethyl ester, at 110 °C. Second, previously obtained poly(ϵ‐caprolactone) (PCL) was used as a macroinitiator for SFRP of styrene at 125 °C. As a third step, this PCL–polystyrene (PSt) precursor with a bromine functionality in the core was used as a macroinitiator for ATRP of tert ‐butyl acrylate in the presence of Cu(I)Br and pentamethyldiethylenetriamine at 100 °C. This produced an ABC‐type miktoarm star polymer [PCL–PSt–poly( tert ‐butyl acrylate)] with a controlled molecular weight and a moderate polydispersity (weight‐average molecular weight/number‐average molecular weight &lt; 1.37). The obtained polymers were characterized with gel permeation chromatography and 1 H NMR. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4228–4236, 2004
Efficient and scalable method for scaling up cell free protein synthesis in batch mode (2005)

A novel method for general cell free system scale-up in batch mode was applied to expression of E. coli chloramphenicol acetyl transferase (CAT) and a GMCSF-scFv fusion protein being developed as a B-cell lymphoma vaccine candidate (GLH). Performance of two different E. coli based cell-free systems was evaluated using the new scale-up approach. Reaction volumes from 15 to 500 microL were tested for both products and both reaction systems. In each case, the new scale-up method preserved total, soluble, and active volumetric yields of GLH and CAT at every reaction volume. At the 500 microL reaction volume, the PANOx SP system produced 560 +/- 36 microg/mL of active CAT and 99 +/- 10 microg/mL of active GLH protein using the new thin film approach whereas 500 microL test tube reactions produced 250 +/- 42 microg/mL and 72 +/- 7 microg/mL of active CAT and GLH respectively. Similarly, 500 microL cell-free synthesis reactions with the Cytomim system produced 481 +/- 38 microg/mL of active CAT and 109 +/- 15 microg/mL active GLH respectively in thin films compared to 29 +/- 7 microg/mL of active CAT and 5 +/- 2 microg/mL of active GLH protein in 500 microL test tube reactions. The new thin film approach improves oxygen supply for the Cytomim system, and increases the availability of hydrophobic surfaces. Analysis suggests that these surfaces provide significant benefit for protein expression and folding. We believe that this approach provides a general reaction scale-up technology that will be suitable for any protein target, cell free system, and reaction volume.
A field evaluation of Nobi®‐Vac Atrophic Rhinitis vaccine (1987)

A field trial was carried out with Nobi-Vac AR vaccine in 11 swine breeding herds. One herd suffered from severe B. bronchiseptica (BB+) rhinitis in piglets, while no clinical Atrophic Rhinitis (AR) was observed. Ten herds were described as AR problem herds, because clinical AR was observed for at least 1 year in spite of the fact that medication of sows and piglets was carried out and adequate housing and management systems were available in most herds. BB+ was isolated in 9 of these 10 farms and the AR pathogenic P. multocida (PM+) in all these farms. The trial started when piglets were born of sows which had been vaccinated 3 times. All piglets between 7 and 10 weeks old were examined clinically for AR. Nasal swabs from 20 pigs on each farm were screened bacteriologically for BB+ and PM+ every other month. A severe reoccurrence of AR was found in 2 of the 10 AR problem farms. In these 2 herds the 'all in-all out' system was not applied in farrowing and weaning houses. In the 8 other AR problem herds the percentage of pigs with AR decreased significantly below the average level of 1% per year. The percentage of pigs infected with BB+ and PM+ also decreased significantly. PM+ was significantly related to the percentage of clinical AR piglets. Seasonal effects contributed to a minor extent to the percentage of AR piglets. After 2.5 years of this trial PM+ could not be isolated during the last 12 months in six of the remaining AR problems herds. The conclusion is that Nobi-Vac AR vaccination of the sow gave protection against clinical AR in piglets on those farms (80%) which provided adequate housing and management systems.
Steroid receptors and their associated proteins. (1993)

Those investigators involved in the purification and characterization of steroid receptors have been confronted with a number of difficulties, one being the expanding list of cellular proteins that can bind and copurify with these receptors. Research over the past 8-10 yr has established a high degree of acceptance for the concept that most inactive steroid receptors are sequestered in a complex with the 90-kilodalton (kDa) heat shock protein, hsp90 (see refs. 1, 2 for review). Initial observations on the copurification of this 90-kDa protein were confusing, and in some cases it was thought to be a contaminant or to actually be the receptor. Clarification of a receptor:hsp90 complex was provided by several approaches which mainly involved the use of antibodies to rapidly and gently isolate receptor complexes. That such a complex exists in the cell is supported primarily by three types of experiments The metabolic labeling studies of Howard and Distelhorst (3) argued that hsp90 binding was not simply occurring after cell lysis. Yeast mutants having an abnormally low level of hsp90 have been shown to be inefficient for the expression of functional steroid receptors (4). Most recently, Gehring and coworkers (5) have used chemical cross-linking in intact cells to show an association of glucocorticoid receptor with hsp90 and a second protein, p59. While a role of hsp90 in receptor structure is strongly supported, the topic of receptor-associated proteins is still quite confusing and uncertain. Most more recent members of this list (see Table 1) suffer from a lack of information regarding their identity and their presence or absence in a variety of receptor systems. Whether they truly represent intracellular receptor-associated proteins of significance to hormone action is unknown, and this represents a key topic for future research in this area. In this brief review, we will attempt to consolidate studies from a variety of systems, clarify some of the confusing terminology about receptor-associated proteins, and suggest some rationale for their participation
Isolation of an endotoxin–MD-2 complex that produces Toll-like receptor 4-dependent cell activation at picomolar concentrations (2004)

Host proinflammatory responses to minute amounts of endotoxins derived from many Gram-negative bacteria require the interaction of lipopolysaccharide-binding protein (LBP), CD14, Toll-like receptor 4 (TLR4) and MD-2. Optimal sensitivity to endotoxin requires an ordered series of endotoxin-protein and protein-protein interactions. At substoichiometric concentrations, LBP facilitates delivery of endotoxin aggregates to soluble CD14 (sCD14) to form monomeric endotoxin-sCD14 complexes. Subsequent interactions of endotoxin-sCD14 with TLR4 and/or MD-2 have not been specifically defined. This study reports the purification of a stable, monomeric, bioactive endotoxin-MD-2 complex generated by treatment of endotoxin-sCD14 with recombinant MD-2. Efficient generation of this complex occurred at picomolar concentrations of endotoxin and nanogram per milliliter doses of MD-2 and required presentation of endotoxin to MD-2 as a monomeric endotoxin-CD14 complex. TLR4-dependent delivery of endotoxin to human embryonic kidney (HEK) cells and cell activation at picomolar concentrations of endotoxin occurred with the purified endotoxin-MD-2 complex, but not with purified endotoxin aggregates with or without LBP and/or sCD14. The presence of excess MD-2 inhibited delivery of endotoxin-MD-2 to HEK/TLR4 cells and cell activation. These findings demonstrate that TLR4-dependent activation of host cells by picomolar concentrations of endotoxin occurs by sequential interaction and transfer of endotoxin to LBP, CD14, and MD-2 and simultaneous engagement of endotoxin and TLR4 by MD-2.
Gas Velocity above Sieve Trays (1993)

A knowledge of the single-phase flow pattern above sieve trays may lead to a better understanding of corresponding two-phase phenomena. Experimental work to determine velocity fields of gas flow issuing from the multiple jets of dry sieve trays without downcomers has therefore been carried out. The effects of hole spacing, tray thickness, tray spacing and the proximity of column walls on velocity profiles are presented and their possible influence on the behaviour of gas-liquid dispersions observed above sieve trays discussed. Unlike widely spaced holes the centre-line velocity distribution for relatively closely spaced holes appears almost independent of hole spacing, except at distances from the holes where velocity decay nears completion. Similarities in the flowfield to single jets are observed, but there are differences in the velocity and length scales, a tendency also seen in trays of different thickness. For trays closely spaced, the effective velocity in the jets may not decay to the superficial velocity before the velocity again approaches the hole velocity of the tray above.
Supported Lipid Bilayer Membranes for Water Purification by Reverse Osmosis (2010)

Some biological plasma membranes pass water with a permeability and selectivity largely exceeding those of commercial membranes for water desalination using specialized trans-membrane proteins aquaporins. However, highly selective transport of water through aquaporins is usually driven by an osmotic rather mechanical pressure, which is not as attractive from the engineering point of view. The feasibility of adopting biomimetic membranes for water purification driven by a mechanical pressure, i.e., filtration is explored in this paper. Toward this goal, it is proposed to use a commercial nanofiltration (NF) membrane as a support for biomimetic lipid bilayer membranes to render them robust enough to withstand the required pressures. It is shown in this paper for the first time that by properly tuning molecular interactions supported phospholipid bilayers (SPB) can be prepared on a commercial NF membrane. The presence of SPB on the surface was verified and quantified by several spectroscopic and microscopic techniques, which showed morphology close to the desired one with very few defects. As an ultimate test it is shown that hydraulic permeability of the SPB supported on the NF membrane (NTR-7450) approaches the values deduced from the typical osmotic permeabilities of intact continuous bilayers. This permeability was unaffected by the trans-membrane flow of water and by repeatedly releasing and reapplying a 10 bar pressure. Along with a parallel demonstration that aquaporins could be incorporated in a similar bilayer on mica, this demonstrates the feasibility of the proposed approach. The prepared SPB structure may be used as a platform for preparing biomimetic filtration membranes with superior performance based on aquaporins. The concept of SPBs on permeable substrates of the present type may also be useful in the future for studying transport of various molecules through trans-membrane proteins.
Physicochemically Tunable Polyfunctionalized RNA Square Architecture with Fluorogenic and Ribozymatic Properties (2014)

Recent advances in RNA nanotechnology allow the rational design of various nanoarchitectures. Previous methods utilized conserved angles from natural RNA motifs to form geometries with specific sizes. However, the feasibility of producing RNA architecture with variable sizes using native motifs featuring fixed sizes and angles is limited. It would be advantageous to display RNA nanoparticles of diverse shape and size derived from a given primary sequence. Here, we report an approach to construct RNA nanoparticles with tunable size and stability. Multifunctional RNA squares with a 90° angle were constructed by tuning the 60° angle of the three-way junction (3WJ) motif from the packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor. The physicochemical properties and size of the RNA square were also easily tuned by modulating the “core” strand and adjusting the length of the sides of the square via predictable design. Squares of 5, 10, and 20 nm were constructed, each showing diverse thermodynamic and chemical stabilities. Four “arms” extending from the corners of the square were used to incorporate siRNA, ribozyme, and fluorogenic RNA motifs. Unique intramolecular contact using the pre-existing intricacy of the 3WJ avoids relatively weaker intermolecular interactions via kissing loops or sticky ends. Utilizing the 3WJ motif, we have employed a modular design technique to construct variable-size RNA squares with controllable properties and functionalities for diverse and versatile applications with engineering, pharmaceutical, and medical potential. This technique for simple design to finely tune physicochemical properties adds a new angle to RNA nanotechnology.
Dysregulation of janus kinases and signal transducers and activators of transcription in cancer. (2011)

Despite their long recognised pivotal roles in immunological responses, Janus kinases (JAKs) and signal transducers and activators of transcription (STATs) are now seen as important players in cancer development and progression. Indeed, mutations in the JAKs are often found in myeloproliferative disorders (MPDs) and leukaemia, and the constitutive phosphorylation of STATs is a common occurrence in many solid and blood cancer cell lines and primary tumour specimens. More recently, we have also shown that JAKs likely have additional roles in promoting drug resistance in several cancer cell types. JAKs and STATs are thus molecules that may serve as useful targets in the clinic. This review will summarise studies that support this notion.
New Class of Bacterial Phenylalanyl-tRNA Synthetase Inhibitors with High Potency and Broad-Spectrum Activity (2004)

Phenylalanyl (Phe)-tRNA synthetase (Phe-RS) is an essential enzyme which catalyzes the transfer of phenylalanine to the Phe-specific transfer RNA (tRNA(Phe)), a key step in protein biosynthesis. Phenyl-thiazolylurea-sulfonamides were identified as a novel class of potent inhibitors of bacterial Phe-RS by high-throughput screening and chemical variation of the screening hit. The compounds inhibit Phe-RS of Escherichia coli, Haemophilus influenzae, Streptococcus pneumoniae, and Staphylococcus aureus, with 50% inhibitory concentrations in the nanomolar range. Enzyme kinetic measurements demonstrated that the compounds bind competitively with respect to the natural substrate Phe. All derivatives are highly selective for the bacterial Phe-RS versus the corresponding mammalian cytoplasmic and human mitochondrial enzymes. Phenyl-thiazolylurea-sulfonamides displayed good in vitro activity against Staphylococcus, Streptococcus, Haemophilus, and Moraxella strains, reaching MICs below 1 micro g/ml. The antibacterial activity was partly antagonized by increasing concentrations of Phe in the culture broth in accordance with the competitive binding mode. Further evidence that inhibition of tRNA(Phe) charging is the antibacterial principle of this compound class was obtained by proteome analysis of Bacillus subtilis. Here, the phenyl-thiazolylurea-sulfonamides induced a protein pattern indicative of the stringent response. In addition, an E. coli strain carrying a relA mutation and defective in stringent response was more susceptible than its isogenic relA(+) parent strain. In vivo efficacy was investigated in a murine S. aureus sepsis model and a S. pneumoniae sepsis model in rats. Treatment with the phenyl-thiazolylurea-sulfonamides reduced the bacterial titer in various organs by up to 3 log units, supporting the potential value of Phe-RS as a target in antibacterial therapy.
Coping With Somatic Comorbidities: Striving for Complete Recovery (2015)

Depression is increasingly being recognized as a common comorbid disorder in patients with severe and chronic medical conditions. However, patients with depression and anxiety frequently present with somatic complaints such as aches and pains, headache, and chronic fatigue. This leads to underrecognition and undertreatment of the psychiatric disorder in an attempt to identify the medical cause of the somatic complaint. Reports are demonstrating the efficacy of antidepressants in treating disorders other than depression and anxiety. Tricyclic antidepressants have shown their usefulness in the treatment of diabetic neuropathy, fibromyalgia, and headache. Controlled studies of several selective serotonin reuptake inhibitors have been shown to be efficacious in relieving the symptoms of premenstrual dysphoric disorder and fibromyalgia. Pilot studies have also been conducted with the serotonin and norepinephrine reuptake inhibitor venlafaxine for the treatment of diabetic neuropathy, fibromyalgia, migraine, premenstrual dysphoric disorder, and stroke. The results encourage further controlled studies.
Stoichiometry of recombinant cystic fibrosis transmembrane conductance regulator in epithelial cells and its functional reconstitution into cells in vitro. (1994)

We have generated several clones of Chinese hamster ovary, mouse epitheloid C127, and pig kidney epithelial LLCPK1 cells producing high levels of functional recombinant human cystic fibrosis transmembrane conductance regulator (CFTR). Processing of CFTR to the mature and fully glycosylated form in these cells is inefficient with only approximately 40% of all newly synthesized CFTR being converted to the mature form. Furthermore, expression of the most frequent mutant allele of the cystic fibrosis (CF) gene, the delta F508 mutant in these epithelial cells, indicated that it is biosynthetically arrested at the endoplasmic reticulum and fails to traffic to the plasma membrane. Using a combination of CFTR mutants and monoclonal antibodies, all the detectable recombinant CFTR in these cells was determined at least under the conditions used, to be present as a monomer. To demonstrate the feasibility of protein replacement therapy, we were able to effect the physical transfer of functional recombinant CFTR produced in Chinese hamster ovary cells to the plasma membranes of Ha3b fibroblasts, a cell line devoid of cAMP-stimulated chloride channels. Transfer of CFTR was mediated by the hemagglutinin viral fusion protein of influenza virus present on the Ha3b cells. Efficiency of transfer was up to 25% of the target cells, and CFTR chloride channel activity was detectable for up to 12 h post-fusion. Therefore, with the development of an appropriate formulation of fusogenic proteoliposome or virosome containing reconstituted purified CFTR, it should be feasible to introduce functional CFTR into CF-affected cells.
Protection of neutropenic mice from lethal Candida albicans infection by recombinant interleukin 1 (1988)

Natural and synthetic immunomodulators that increase nonspecific resistance to infection are also known to induce interleukin 1 (IL 1) production. Previous studies have demonstrated a protective effect of recombinant human IL 1 beta against death from infection caused by Pseudomonas aeruginosa. In the present study we investigated the effect of IL 1 beta or IL 1 alpha on the survival of neutropenic mice with a lethal Candida albicans infection. Mice with cyclophosphamide-induced neutropenia were injected with 3 X 10(5) C. albicans i.v. When 80 ng IL 1 beta was given as a single i.p. injection 24 h before the infection, survival compared to that in control animals was as follows: 100% vs. 97% at 24 h, 83% vs. 70% at 48 h and 70% vs. 23% at 72 h after the infection (p less than 0.01). The effect of IL 1 was also apparent when it was given 1/2 h before or 6 h after the infection. The results obtained with 80 ng IL 1 alpha given at 24 h before infection were similar to that obtained with IL 1 beta. The numbers of Candida cultured from the blood, liver, spleen, and kidney were not significantly different in IL 1 beta-treated and control animals. Passive transfer of serum obtained from mice pretreated with IL 1 to recipient mice did not provide protection against a subsequent lethal candidal infection. In conclusion, the present study demonstrates that IL 1 beta and IL 1 alpha prolong survival in neutropenic mice with a lethal C. albicans infection.
Mutations of p53 gene can be detected in the plasma of patients with large bowel carcinoma. (1998)

p53 gene mutations can be detected in the plasma of some patients with large bowel carcinoma and these are concordant with those in the primary carcinomas.