gebhart/patrepeval huggingface dataset:
Drastic rise of intracellular adenosine(5′)tetraphospho(5′)adenosine correlates with onset of DNA synthesis in eukaryotic cells (1984)

An assay of adenosine(5')tetraphospho(5')adenosine (Ap4A), based on the luciferin/luciferase method for ATP measurement, was developed, which allows one to determine picomolar amounts of unlabeled Ap4A in cellular extracts. In eukaryotic cells this method yielded levels of Ap4A varying from 0.01 microM to 13 microM depending on the growth, cell cycle, transformation, and differentiation state of cells. After mitogenic stimulation of G1-arrested mouse 3T3 and baby hamster kidney fibroblasts the Ap4A pools gradually increased 1000-fold during progression through the G1 phase reaching maximum Ap4A concentrations of about 10 microM in the S phase. Quiescent 3T3 cells reach a high level of Ap4A (1 microM) in a 'committed' but prereplicative state if exposed to an external mitogenic stimulant (excess of serum) and simultaneously to a synchronizer which inhibits entry into the S phase (hydroxyurea). When the block for DNA replication was removed at varying times after removal of the stimulant decay of commitment to DNA synthesis was found correlated with a shrinkage of the Ap4A pool. Cells lacking a defined G1 phase (V79 lung fibroblasts, Physarum) possess a constitutively high base level of Ap4A (about 0.3 microM) even during mitosis. From this high level, Ap4A concentration increases only about tenfold during the S phase. Temperature-down-shift experiments, using chick embryo cells infected with transformation-defective temperature-sensitive viral mutants(td-ts), have shown that the expression of the transformed state at 35 degrees C is accompanied by a tenfold increase of the cellular Ap4A pool. Treatment of exponentially growing human cells with interferon leads, concomitantly with an inhibition of DNA syntheses, to a tenfold decrease in intracellular Ap4A levels within 20 h. The possibility of Ap4A being a 'second messenger' of cell cycle and proliferation control is discussed in the light of these results and those reported previously demonstrating that Ap4A is a ligand of mammalian DNA polymerase alpha, triggers DNA replication in quiescent mammalian cells and is active in priming DNA synthesis.
Human Immunodeficiency Virus (HIV) Type 1 Strain MN Neutralizing Antibody in HIV-Infected Children: Correlation with Clinical Status and Prognostic Value (1993)

Protective immunity to human immunodeficiency virus (HIV) was examined in 228 serial sera from 58 HIV-infected children before and during antiretroviral therapy. Binding antibodies to putative protective V3 epitopes of HIV-1IIIB and HIV-1MN were investigated by a peptide ELISA, and neutralizing antibodies by inhibition of HIV-1MN cell-free viral infection. No difference in binding of total IgG or IgG subclasses was observed between patients with mild (group A) or advanced disease (group B). However, group A patients were more likely to possess neutralizing antibody titers > or = 225 (P = .040 after adjustment for CD4). This threshold titer also predicted clinical outcome in patients with age-adjusted CD4 count > 10% of normal median. Patients with titers < 225 more frequently encountered major clinical events during follow-up than did patients with titers > or = 225 (P = .0028). Epitopes other than the linear V3 loop contribute to this protective immune response. Identification of these epitopes should assist immune therapy of AIDS and HIV vaccine development.
Quantification of 5-Methylcytosine in DNA by the Chloroacetaldehyde Reaction (1999)

The study of changes in genome-wide levels of DNA methylation has become a key focus for understanding the epigenetic regulation of gene expression. Many procedures exist to study DNA methylation, falling into two categories: gene-specific and genome-wide. Genome-wide methylation analysis is best performed by DNA hydrolysis followed by HPLC; however, it requires access to an HPLC machine, which is not always available. Alternative procedures, such as the radioactive labeling of CpG sites using SssI DNA methyltransferase, have been developed to address this problem, but it can only monitor CpG methylation changes, and CpNpG methylation is not detected. Here, we present a method for the analysis of DNA methylation in any sequence context by fluorescent labeling. We present control analyses using synthetic oligonucleotides of known methylation levels and a comparison of genomic DNA from two transgenic tobacco lines known to differ in their methylation levels. The results indicate that hygromycin-induced hypermethylation acts equally on all classes of methylatable cytosine, perhaps indicating a common mechanism.
The UCSC Genome Browser database: 2015 update (2014)

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.
Anhydrobiotic Engineering of Gram-Negative Bacteria (2000)

Anhydrobiotic engineering aims to improve desiccation tolerance in living organisms by adopting the strategies of anhydrobiosis. This was achieved for Escherichia coli and Pseudomonas putida by osmotic induction of intracellular trehalose synthesis and by drying from trehalose solutions, resulting in long-term viability in the dried state.
Nonionic Surfactants: Polyoxyalkylene Block Copolymers (1996)

Synthesis and chemical modification of polyoxyalkylene block copolymers chemical analysis of polyoxyalkylene block copolymers physical chemistry of polyoxyalkylene block copolymers properties of polyoxyalkylene block copolymers applications of polyoxyalkylene block copolymers surfactants toxicology of polyoxyalkylene block copolymers biological activity of polyoxyalkylene block copolymers in the environment.
Current prodrug strategies for improving oral absorption of nucleoside analogues (2014)

Nucleoside analogues are first line chemotherapy in various severe diseases: AIDS (acquired immunodeficiency disease syndrome), cytomegalovirus infections, cancer, etc. However, many nucleoside analogues exhibit poor oral bioavailability because of their high polarity and low intestinal permeability. In order to get around this drawback, prodrugs have been utilized to improve lipophilicity by chemical modification of the parent drug. Alternatively, prodrugs targeting transporters present in the intestine have been applied to promote the transport of the nucleoside analogues. Valacyclovir and valganciclovir are two classic valine ester prodrugs transported by oligopeptide transporter 1. The ideal prodrug achieves delivery of a parent drug by attaching a non-toxic moiety that is stable during transport, but is readily degraded to the parent drug once at the target. This article presents advances of prodrug approaches for enhancing oral absorption of nucleoside analogues.
Storage of heart valve allografts in glycerol with subsequent antibiotic sterilisation. (1978)

Fresh allograft valves stored in a nutrient medium at +4 degrees C have a limited storage time of eight weeks. Dura mater has been stored in glycerol for longer periods, and this paper presents work on the glycerol storage of allograft heart valves. The elastic properties of the valve cusps showed a fall during storage in glycerol that was associated with an altered histological appearance of the cusp tissue. The loss in nuclearity in the histological sections of stored tissue was partially responsible for the observed decrease in viability during storage. All these changes during storage in glycerol, or glycerol and subsequent antibiotic treatment, were similar to the changes seen in valves stored in a nutrient medium. Glycerol therefore offers an alternative storage system to the cold nutrient medium but has no practical advantages. Glycerol alone will not sterilise the allograft tissue, and a post-storage treatment with antibiotics is essential.
Rapid one step detection of pathogenic bacteria in urine with sexually transmitted disease (STD) and prostatitis patient by multiplex PCR assay (mPCR). (2007)

We developed a multiplex PCR (mPCR) assay to simultaneously detect Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Ureaplasma urealyticum, Corynebacterium spp. and seudomona aeruginosa. This method employs a single tube and multiple specific primers which yield 200, 281, 346, 423, 542, and 1,427 bp PCR products, respectively. All the PCR products were easily detected by agarose gel electrophoresis and were sequenced to confirm the specificity of the reactions. To test this method, DNA extracted from urine samples was collected from 96 sexually transmitted disease or prostatitis patients at a local hospital clinical center, and were subjected to the mPCR assay. The resulting amplicons were cloned and sequenced to exactly match the sequences of known pathogenic isolates. N. gonorrhoeae and Corynebacterium spp. were the most frequently observed pathogens found in the STDs and prostatitis patients, respectively. Unexpectedly, P. aeruginosa was also detected in some of the STD and prostatitis samples. More than one pathogen species was found in 10% and 80.7% of STD and prostatitis samples, respectively, indicating that STD and prostatitis patients may have other undiagnosed and associates. The sensitivity of the assay was determined by sing purified DNA from six pathogenic laboratory strains and revealed that this technique could detect pathogenic DNA at concentrations ranging from 0.018 to 1.899 pg/ul. Moreover, the specificities of this assay were found to be highly efficient. Thus, this mPCR assay may be useful for the rapid diagnosis of causative infectious STDs and prostatitis. useful for the infectious STDs and prostatitis.
Melting properties of some structured lipids native to high stearic acid soybean oil (2004)

A number of structured lipids native to high stearic acid soybean oil were synthesized and their physical properties were determined by pulsed nuclear magnetic resonance (NMR), Mettler dropping point and differential scanning calorimetry (DSC). 1,3 Distearo-2-olein (SOS), 1,3 distearo-2-linolein (SLS) and1,3 distearo-2-linolenin (SlnS) were synthesized from pure 1,3 diacylglycerols and the appropriate fatty acid. Pulsed NMR determinations over the temperature range 10-50 ºC showed that the symmetrical triacylglycerols (SUS: where S = stearic, U = oleic, linoleic or linolenic) are high and sharply melting materials, all showing substantial amounts of solids at temperatures up to 33.3 ºC, yet are completely melted at only a few degrees higher. Mettler dropping points for SOS, SLS and SlnS were 44.1, 37.9 and 36.5 ºC respectively. The heats of fusion for the structured triacylglycerols were determined by DSC and shown to be of the order 29-32 cal/gm compared to 45 cal/gm for SSS. The heats of fusion were also calculated from Mettler dropping point determinations as admixtures with soybean oil and showed consistent agreement with the DSC data.
Smart cards provide very high security and flexibility in subscribers management (1990)

It is pointed out that in smart-card-based pay television, the security secrets reside solely in inexpensive and easily replaceable plastic cards-the same size as a credit card, with a secure computer microchip. The decoder no longer holds any secrets. Replacement smart cards can be sent to each subscriber periodically, or whenever there is reason to believe the system security has been breached. With each batch of new cards, algorithms or secret keys can be changed. Attacks on security are therefore extremely difficult to organize, and are not economically viable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Activation of ovarian sympathetic nerves in polycystic ovary syndrome. (1993)

Polycystic ovarian syndrome (PCOS) is one of the most common human ovarian pathologies affecting women of reproductive age. Despite extensive investigation, the etiology of PCOS remains poorly understood. Experimentally, a PCO-like syndrome can be induced in rodents by a single dose of the long-acting estrogen, estradiol valerate (EV). We have used this model to examine the possibility that PCOS is associated with derangement of the sympathetic control of the ovary. The release of newly incorporated norepinephrine (NE) from ovarian nerve terminals in response to transmural stimulation of the gland increased significantly before the formation of cysts (30 days after EV injection) and remained elevated at the time when cysts form (60 days). The increase in evoked NE release was accompanied by an augmented NE content and enhanced incorporation of [3H]NE into ovarian tissue; both of these changes had been initiated by 30 days after EV treatment and became unambiguous at the time of cyst formation. The overall increase in ovarian sympathetic outflow suggested by these alterations in catecholamine homeostasis was accompanied by a thecal cell-interstitial tissue selective down-regulation of beta-adrenergic receptors; the beta-adrenergic receptor concentration in these sympathetically innervated ovarian compartments was significantly lower in PCO than during the estrous phase of the estrous cycle, a time at which the beta-adrenergic receptor concentration reaches its lowest levels in normal cycling ovaries. Tyrosine hydroxylase activity was found to increase only when expressed per mg ovary, but not in absolute terms (i.e. per total ovary), suggesting regulation of enzyme activity by the enhanced catecholamine content. The results demonstrate that an activation of the sympathetic neurons innervating the ovary precedes the development of cysts in EV-induced PCOS and raise the possibility that a derangement of sympathetic inputs to the ovary contributes to the etiology of PCOS.
Optimization and quantification of protein synthesis inside liposomes (2009)

Synthetic biology aims at reprogramming existing, or creating new, biological systems, with the ultimate aim to obtain artificial cells whose functions can be tailored. For the latter, encapsulation of complex biochemical reactions into cell-sized compartments, such as liposomes, is required. Recently, several groups have demonstrated that proteins of interest can be produced de novo within liposomes by entrapping cell-free protein-synthesis systems and DNA templates inside liposomes. Although detectable, intraliposomal protein synthesis was generally poor. Here, we have optimized intraliposomal cell-free protein synthesis by changing several variables, including lipid composition as well as liposome, pyrophosphatase, and T7 RNA polymerase concentration. Further, by using an activity-based assay, we have quantified the amount of full-length protein that was produced from DNA templates inside liposomes before and after optimization of aforementioned variables. Based on the model protein beta-galactosidase, it is demonstrated that liposomal protein synthesis can yield microgram quantities of protein (30-40 microg/mL liposomes).
ON WORD BOUNDARY DETECTION IN DIGIT-BASED SPEAKER VERIFICATION (1998)

In an automatic speaker verification (ASV) system with prompted passwords, we use vocabulary-dependent hidden Markov models and rely on the ability to explicitly locate the corresponding words and their boundaries in the speech signal. In an experiment on 41 speakers in a Swedish telephone speech database, we compare the use of utterance segmentation produced by automatic and manual methods, and conclude that not much is lost in ASV performance with the automatic method compared to the manual.
MAT2A as Key Regulator and Therapeutic Target in MLLr Leukemogenesis (2020)

Epigenetic dysregulation plays a pivotal role in mixed-lineage leukemia (<i>MLL)</i> pathogenesis, therefore serving as a suitable therapeutic target. S-adenosylmethionine (SAM) is the universal methyl donor in human cells and is synthesized by methionine adenosyltransferase 2A (MAT2A), which is deregulated in different cancer types. Here, we used our human CRISPR/Cas9-<i>MLL</i>-rearranged (CRISPR/Cas9-<i>MLL</i>r) leukemia model, faithfully mimicking <i>MLL</i>r patients' pathology with indefinite growth potential <i>in vitro</i>, to evaluate the unknown role of MAT2A. Comparable to publicly available patient data, we detected MAT2A to be significantly overexpressed in our CRISPR/Cas9-<i>MLL</i>r model compared to healthy controls. By using non-<i>MLL</i>r and <i>MLL</i>r cell lines and our model, we detected an <i>MLL</i>r-specific enhanced response to PF-9366, a new MAT2A inhibitor, and small interfering (si) RNA-mediated knockdown of <i>MAT2A</i>, by alteration of the proliferation, viability, differentiation, apoptosis, cell cycling, and histone methylation. Moreover, the combinational treatment of PF-9366 with chemotherapy or targeted therapies against the SAM-dependent methyltransferases, disruptor of telomeric silencing 1 like (DOT1L) and protein arginine methyltransferase 5 (PRMT5), revealed even more pronounced effects. In summary, we uncovered MAT2A as a key regulator in <i>MLL</i> leukemogenesis and its inhibition led to significant anti-leukemic effects. Therefore, our study paves the avenue for clinical application of PF-9366 to improve the treatment of poor prognosis <i>MLL</i>r leukemia.
Engineering zonal cartilage through bioprinting collagen type II hydrogel constructs with biomimetic chondrocyte density gradient (2016)

Our results suggested that zonal engineered cartilage could be fabricated by bioprinting collagen type II hydrogel constructs with a biomimetic cell density gradient. Both the total cell density and the cell distribution pattern should be optimized to achieve synergistic biological effects.
CD8+Treg cells suppress CD8+T cell‐responses by IL‐10‐dependent mechanism during H5N1 influenza virus infection (2013)

Although Treg-cell-mediated suppression during infection or autoimmunity has been described, functions of Treg cells during highly pathogenic avian influenza virus infection remain poorly characterized. Here we found that in Foxp3-GFP transgenic mice, CD8(+) Foxp3(+) Treg cells, but not CD4(+) Foxp3(+) Treg cells, were remarkably induced during H5N1 infection. In addition to expressing CD25, the CD8(+) Foxp3(+) Treg cells showed a high level of GITR and produced IL-10. In an adoptive transfer model, CD8(+) Treg cells suppressed CD8(+) T-cell responses and promoted H5N1 virus infection, resulting in enhanced mortality and increased virus load in the lung. Furthermore, in vitro neutralization of IL-10 and studies with IL-10R-deficient mice in vitro and in vivo demonstrated an important role for IL-10 production in the capacity of CD8(+) Treg cells to inhibit CD8(+) T-cell responses. Our findings identify a previously unrecognized role of CD8(+) Treg cells in the negative regulation of CD8(+) T-cell responses and suggest that modulation of CD8(+) Treg cells may be a therapeutic strategy to control H5N1 viral infection.
Characterization of vaccinia virus DNA topoisomerase I expressed in Escherichia coli. (1988)

The putative structural gene encoding the vaccinia virus type I DNA topoisomerase (EC 5.99.1.2) was expressed in Escherichia coli under the control of a bacteriophage T7 promoter. Provision of T7 RNA polymerase resulted in the accumulation to high level of a Mr = 33,000 type I topoisomerase with the properties of the vaccinia enzyme. A simple purification scheme yielded approximately 8 mg of recombinant vaccinia topoisomerase from 400 ml of bacteria. DNA unwinding by the enzyme was stimulated by magnesium, manganese, calcium, cobalt, and spermidine, but inhibited by copper and zinc. Like eukaryotic cellular type I topoisomerases, but unlike the prokaryotic counterpart, the recombinant topoisomerase relaxed positively and negatively supercoiled DNA. The viral topoisomerase I was, however, resistant to the effects of camptothecin, a drug that specifically inhibits cellular type I topoisomerases.
Targeting ER stress–induced autophagy overcomes BRAF inhibitor resistance in melanoma (2014)

Melanomas that result from mutations in the gene encoding BRAF often become resistant to BRAF inhibition (BRAFi), with multiple mechanisms contributing to resistance. While therapy-induced autophagy promotes resistance to a number of therapies, especially those that target PI3K/mTOR signaling, its role as an adaptive resistance mechanism to BRAFi is not well characterized. Using tumor biopsies from BRAF(V600E) melanoma patients treated either with BRAFi or with combined BRAF and MEK inhibition, we found that BRAFi-resistant tumors had increased levels of autophagy compared with baseline. Patients with higher levels of therapy-induced autophagy had drastically lower response rates to BRAFi and a shorter duration of progression-free survival. In BRAF(V600E) melanoma cell lines, BRAFi or BRAF/MEK inhibition induced cytoprotective autophagy, and autophagy inhibition enhanced BRAFi-induced cell death. Shortly after BRAF inhibitor treatment in melanoma cell lines, mutant BRAF bound the ER stress gatekeeper GRP78, which rapidly expanded the ER. Disassociation of GRP78 from the PKR-like ER-kinase (PERK) promoted a PERK-dependent ER stress response that subsequently activated cytoprotective autophagy. Combined BRAF and autophagy inhibition promoted tumor regression in BRAFi-resistant xenografts. These data identify a molecular pathway for drug resistance connecting BRAFi, the ER stress response, and autophagy and provide a rationale for combination approaches targeting this resistance pathway.