gebhart/patrepeval huggingface dataset:
A New Arylsulfate Sulfotransferase Involved in Liponucleoside Antibiotic Biosynthesis in Streptomycetes (2010)

Sulfotransferases are involved in a variety of physiological processes and typically use 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as the sulfate donor substrate. In contrast, microbial arylsulfate sulfotransferases (ASSTs) are PAPS-independent and utilize arylsulfates as sulfate donors. Yet, their genuine acceptor substrates are unknown. In this study we demonstrate that Cpz4 from Streptomyces sp. MK730-62F2 is an ASST-type sulfotransferase responsible for the formation of sulfated liponucleoside antibiotics. Gene deletion mutants showed that cpz4 is required for the production of sulfated caprazamycin derivatives. Cloning, overproduction, and purification of Cpz4 resulted in a 58-kDa soluble protein. The enzyme catalyzed the transfer of a sulfate group from p-nitrophenol sulfate (K(m) 48.1 microM, k(cat) 0.14 s(-1)) and methyl umbelliferone sulfate (K(m) 34.5 microM, k(cat) 0.15 s(-1)) onto phenol (K(m) 25.9 and 29.7 mM, respectively). The Cpz4 reaction proceeds by a ping pong bi-bi mechanism. Several structural analogs of intermediates of the caprazamycin biosynthetic pathway were synthesized and tested as substrates of Cpz4. Des-N-methyl-acyl-caprazol was converted with highest efficiency 100 times faster than phenol. The fatty acyl side chain and the uridyl moiety seem to be important for substrate recognition by Cpz4. Liponucleosides, partially purified from various mutant strains, were readily sulfated by Cpz4 using p-nitrophenol sulfate. No product formation could be observed with PAPS as the donor substrate. Sequence homology of Cpz4 to the previously examined ASSTs is low. However, numerous orthologs are encoded in microbial genomes and represent interesting subjects for future investigations.
A Novel Glycinate-based Body Wash: Clinical Investigation Into Ultra-mildness, Effective Conditioning, and Improved Consumer Benefits. (2013)

The patented glycinate-containing body wash demonstrated better product mildness and patient-preferred attributes and clinical benefits.
Desmethyl(trifluormethyl)actinomycine (1990)

Demethyl(trifluoromethyl)actinomycins The synthesis of new 4‐(trifluoromethyl)benzoic acid derivatives 2 – 10 and their coupling with amino acids and peptides 12, 13, 15 is described. They serve as precursors for the synthesis of the hitherto unknown demethyl(trifluoromethyl)actinocin dimethyl esters 11 , demethyl‐trifluoromethyl‐actino‐cinyl peptides 14, 16, 18 and the demethyl‐trifluoromethyl‐actinomycins 17 . Although spacially comparable with the methyl residues, the 4‐ and 6‐trifluoromethyl groups have unexpected strong influences on the antibiotic and cytostatic properties of the actinomycins. The CH 3 /CF 3 exchange makes it possible to bring NMR‐analytically useful hetero nuclei into the centre of the actinomycin/DNA complex (Figure 1).
Higher titers of some H5N1 and recent human H1N1 and H3N2 influenza viruses in Mv1 Lu vs. MDCK cells (2011)

The yields of influenza subtype H1N1, H3N2, and H5N1 viruses can be higher in Mv1 Lu cells than in MDCK cells.
Interlayer cohesive energy of graphite from thermal desorption of polyaromatic hydrocarbons (2004)

We have studied the interaction of polyaromatic hydrocarbons (PAHs) with the basal plane of graphite using thermal desorption spectroscopy. Desorption kinetics of benzene, naphthalene, coronene, and ovalene at submonolayer coverages yield activation energies of 0.50 eV, 0.85 eV, 1.40 eV, and 2.1 eV, respectively. Benzene and naphthalene follow simple first order desorption kinetics while coronene and ovalene exhibit fractional order kinetics owing to the stability of two-dimensional adsorbate islands up to the desorption temperature. Preexponential frequency factors are found to be in the range ${10}^{14}$--${10}^{21}{\mathrm{s}}^{\ensuremath{-}1}$ as obtained from both Falconer-Madix (isothermal desorption) analysis and Antoine's fit to vapor pressure data. The resulting binding energy per carbon atom of the PAH is $52\ifmmode\pm\else\textpm\fi{}$5 meV and can be identified with the interlayer cohesive energy of graphite. The resulting cleavage energy of graphite is $61\ifmmode\pm\else\textpm\fi{}5$ meV/atom, which is considerably larger than previously reported experimental values.
Effect of lysophospholipids on signaling in the human Jurkat T cell line (1995)

Lysophospholipids have recently been demonstrated to induce activation and proliferation of fibroblasts and other cell lineages by interacting with high affinity cell surface receptors leading to specific intracellular signaling events. Platelet activation, likely at the site of injury or inflammation, results in increased production of lysophospholipids suggesting a possible source of lysophospholipids. We have recently demonstrated that high concentrations of lysophospholipids are present in ascites and plasma from ovarian cancer patients, suggesting that physiologically produced lysophospholipids could interact with cells present in these fluids, including lymphocytes, and alter their function. We demonstrate herein that lysophosphatidic acid (LPA), lysophosphatidylserine (LPS), and sphingosylphosphorylcholine (SPC) activate the Jurkat T cell line. Each of the lysophospholipids induced a transient increase in cytosolic free calcium ([Ca2+]i) in Jurkat cells. Increases in [Ca2+]i were cross-desensitized by LPA, LPS and SPC, suggesting that the lysophospholipids share the same receptor(s) or that their downstream signaling pathways converge or interact. Lysophosphatidylglycerol (LPG), a competitive inhibitor of the putative LPA receptor, inhibited the calcium releasing activity of LPA, but not that of LPS and SPC, suggesting that these lysophospholipids interact with different receptors and that desensitization is due to interactions in downstream signaling pathways. The ability of the lysophospholipids to induce increases in [Ca2+]i was attenuated, but not completely blocked, by increases in [Ca2+]i induced by activation of the thrombin receptor. In contrast, increases in [Ca2+]i induced by the lysophospholipids and cross-linking the CD3 component of the T cell receptor complex with the UCHT1 antibody did not undergo heterologous desensitization. Strikingly, LPA is sufficient to stimulate proliferation of Jurkat cells in serum-free medium or in synergy with low concentrations of fetal bovine serum. In addition, LPA also increased the production of the T cell growth factor, interleukin 2 (IL-2), by Jurkat cells treated with phorbol esters. LPS, in contrast, inhibited Jurkat proliferation while increasing IL-2 production and SPC inhibited both processes. Thus, although all three lysophospholipids were sufficient to induce a transient increase in [Ca2+]i in Jurkat cells, they induced markedly different physiological consequences.
CELL-MEDIATED-IMMUNITY AND IMMUNOTHERAPY IN OVARIAN-CANCER (REVIEW) (1995)

The natural containment of ovarian cancer to the peritoneal cavity makes this mileau attractive for examining the immune status within a 'malignant environment'. Such investigations have yielded further insight into host-tumor responses. Immunological strategies have been employed in ovarian cancer either as single agents or combined with chemotherapy and although achieving responses have limited success. The understanding of cytokine inter-relationships, refinement of monoclonal antibody therapy and the potential genetic manipulation will enhance immunological strategies. This review will address aspects of our present knowledge of immune status in ovarian cancer, examine clinical studies incorporating immune agents and potential future therapies.
Benzoic Acid, a Weak Organic Acid Food Preservative, Exerts Specific Effects on Intracellular Membrane Trafficking Pathways in Saccharomyces cerevisiae (2004)

Microbial spoilage of food causes losses of up to 40% of all food grown for human consumption worldwide. Yeast growth is a major factor in the spoilage of foods and beverages that are characterized by a high sugar content, low pH, and low water activity, and it is a significant economic problem. While growth of spoilage yeasts such as Zygosaccharomyces bailii and Saccharomyces cerevisiae can usually be retarded by weak organic acid preservatives, the inhibition often requires levels of preservative that are near or greater than the legal limits. We identified a novel synergistic effect of the chemical preservative benzoic acid and nitrogen starvation: while exposure of S. cerevisiae to either benzoic acid or nitrogen starvation is cytostatic under our conditions, the combination of the two treatments is cytocidal and can therefore be used beneficially in food preservation. In yeast, as in all eukaryotic organisms, survival under nitrogen starvation conditions requires a cellular response called macroautophagy. During macroautophagy, cytosolic material is sequestered by intracellular membranes. This material is then targeted for lysosomal degradation and recycled into molecular building blocks, such as amino acids and nucleotides. Macroautophagy is thought to allow cellular physiology to continue in the absence of external resources. Our analyses of the effects of benzoic acid on intracellular membrane trafficking revealed that there was specific inhibition of macroautophagy. The data suggest that the synergism between nitrogen starvation and benzoic acid is the result of inhibition of macroautophagy by benzoic acid and that a mechanistic understanding of this inhibition should be beneficial in the development of novel food preservation technologies.
Identification of herpes simplex virus type 1 genes required for origin-dependent DNA synthesis (1988)

The herpes simplex virus (HSV) genome contains both cis- and trans-acting elements which are important in viral DNA replication. The cis-acting elements consist of three origins of replication: two copies of oriS and one copy of oriL. It has previously been shown that five cloned restriction fragments of HSV-1 DNA together can supply all of the trans-acting functions required for the replication of plasmids containing oriS or oriL when cotransfected into Vero cells (M. D. Challberg, Proc. Natl. Acad. Sci. USA, 83:9094-9098, 1986). These observations provide the basis for a complementation assay with which to locate all of the HSV sequences which encode trans-acting functions necessary for origin-dependent DNA replication. Using this assay in combination with the data from large-scale sequence analysis of the HSV-1 genome, we have now identified seven HSV genes which are necessary for transient replication of plasmids containing either oriS or oriL. As shown previously, two of these genes encode the viral DNA polymerase and single-stranded DNA-binding protein, which are known from conventional genetic analysis to be essential for viral DNA replication in infected cells. The functions of the products of the remaining five genes are unknown. We propose that the seven genes essential for plasmid replication comprise a set of genes whose products are directly involved in viral DNA synthesis.
Transmissible toxin (hemolysin) plasmid in Streptococcus faecalis and its mobilization of a noninfectious drug resistance plasmid (1975)

Streptococcus faecalis strain DS-5 has been shown previously to contain three plasmids, pAMalpha1, pAMbeta1, and pAMgamma1. Mixed incubation of DS-5 with strain JH2-2, a plasmid-free S. faecalis recipient, results in the transfer of pAMalpha1 (which determines resistance to tetracycline) and/or pAMgamma1. Analyses of recipients carrying various combinations of these plasmids have revealed the pAMgamma1 codes for toxin (hemolysin) production and two bacteriocin activities. JH2-2 strains carrying both pAMalpha1 and pAMgamma1, or pAMgamma1 only, can donate their plasmids to other recipients, whereas strains carrying only pAMalpha1 cannot serve as donors. This indicates that pAMgamma1 actually mobilizes the otherwise nontransferable pAMalpha1.
DNA Ligases: Progress and Prospects (2009)

DNA ligases seal 5'-PO4 and 3'-OH polynucleotide ends via three nucleotidyl transfer steps involving ligase-adenylate and DNA-adenylate intermediates. DNA ligases are essential guardians of genomic integrity, and ligase dysfunction underlies human genetic disease syndromes. Crystal structures of DNA ligases bound to nucleotide and nucleic acid substrates have illuminated how ligase reaction chemistry is catalyzed, how ligases recognize damaged DNA ends, and how protein domain movements and active-site remodeling are used to choreograph the end-joining pathway. Although a shared feature of DNA ligases is their envelopment of the nicked duplex as a C-shaped protein clamp, they accomplish this feat by using remarkably different accessory structural modules and domain topologies. As structural, biochemical, and phylogenetic insights coalesce, we can expect advances on several fronts, including (i) pharmacological targeting of ligases for antibacterial and anticancer therapies and (ii) the discovery and design of new strand-sealing enzymes with unique substrate specificities.
Orphans of the HIV epidemic: Unmet needs in six US cities (1995)

In the United States, an estimated 72,000-125,000 children and adolescents will lose their mothers to AIDS by the year 2000. Six cities have been particularly hard hit: New York City, Newark, Miami, San Juan, Los Angeles, and Washington, DC. The most urgent unmet needs for children, their families and new guardians are for mental health services, including bereavement counselling; transitional services to help overcome the loss of AIDS-related benefits following the parent's death; legal services; housing supports, and appropriate evaluations and referrals by juvenile justice and school staff to community-based services. Professional staff need additional training and support. Public policies and legal standards should stress a preference for maintaining children in their extended families, broadly defined, whenever possible. Much more needs to be done to improve the lives and futures of these youth.
Glomerular Localization and Expression of Angiotensin-Converting Enzyme 2 and Angiotensin-Converting Enzyme (2006)

Angiotensin-converting enzyme 2 (ACE2) expression has been shown to be altered in renal tubules from diabetic mice. This study examined the localization of ACE and ACE2 within the glomerulus of kidneys from control (db/m) and diabetic (db/db) mice and the effect of chronic pharmacologic ACE2 inhibition. ACE2 co-localized with glomerular epithelial cell (podocyte) markers, and its localization within the podocyte was confirmed by immunogold labeling. ACE, by contrast, was seen only in glomerular endothelial cells. By immunohistochemistry, in glomeruli from db/db mice, strong ACE staining was found more frequently than in control mice (db/db 64.6 +/- 6.3 versus db/m 17.8 +/- 3.4%; P < 0.005). By contrast, strong ACE2 staining in glomeruli from diabetic mice was less frequently seen than in controls (db/db 4.3 +/- 2.4 versus db/m 30.6 +/- 13.6%; P < 0.05). For investigation of the significance of reduced glomerular ACE2 expression, db/db mice were treated for 16 wk with a specific ACE2 inhibitor (MLN-4760) alone or combined with telmisartan, a specific angiotensin II type 1 receptor blocker. At the end of the study, glomerular staining for fibronectin, an extracellular matrix protein, was increased in both db/db and db/m mice that were treated with MLN-4760. Urinary albumin excretion (UAE) increased significantly in MLN-4760-treated as compared with vehicle-treated db/db mice (743 +/- 200 versus 247 +/- 53.9 microg albumin/mg creatinine, respectively; P < 0.05), and the concomitant administration of telmisartan completely prevented the increase in UAE associated with the ACE2 inhibitor (161 +/- 56; P < 0.05). It is concluded that ACE2 is localized in the podocyte and that in db/db mice glomerular expression of ACE2 is reduced whereas glomerular ACE expression is increased. The finding that chronic ACE2 inhibition increases UAE suggests that ACE2, likely by modulating the levels of glomerular angiotensin II via its degradation, may be a target for therapeutic interventions that aim to reduce albuminuria and glomerular injury.
Gene-Expression Profiling for Rejection Surveillance after Cardiac Transplantation (2010)

Among selected patients who had received a cardiac transplant more than 6 months previously and who were at a low risk for rejection, a strategy of monitoring for rejection that involved gene-expression profiling, as compared with routine biopsies, was not associated with an increased risk of serious adverse outcomes and resulted in the performance of significantly fewer biopsies. (ClinicalTrials.gov number, NCT00351559.)
CaMKII inhibition rectifies arrhythmic phenotype in a patient-specific model of catecholaminergic polymorphic ventricular tachycardia (2013)

Induced pluripotent stem cells (iPSC) offer a unique opportunity for developmental studies, disease modeling and regenerative medicine approaches in humans. The aim of our study was to create an in vitro 'patient-specific cell-based system' that could facilitate the screening of new therapeutic molecules for the treatment of catecholaminergic polymorphic ventricular tachycardia (CPVT), an inherited form of fatal arrhythmia. Here, we report the development of a cardiac model of CPVT through the generation of iPSC from a CPVT patient carrying a heterozygous mutation in the cardiac ryanodine receptor gene (RyR2) and their subsequent differentiation into cardiomyocytes (CMs). Whole-cell patch-clamp and intracellular electrical recordings of spontaneously beating cells revealed the presence of delayed afterdepolarizations (DADs) in CPVT-CMs, both in resting conditions and after β-adrenergic stimulation, resembling the cardiac phenotype of the patients. Furthermore, treatment with KN-93 (2-[N-(2-hydroxyethyl)]-N-(4methoxybenzenesulfonyl)]amino-N-(4-chlorocinnamyl)-N-methylbenzylamine), an antiarrhythmic drug that inhibits Ca(2+)/calmodulin-dependent serine-threonine protein kinase II (CaMKII), drastically reduced the presence of DADs in CVPT-CMs, rescuing the arrhythmic phenotype induced by catecholaminergic stress. In addition, intracellular calcium transient measurements on 3D beating clusters by fast resolution optical mapping showed that CPVT clusters developed multiple calcium transients, whereas in the wild-type clusters, only single initiations were detected. Such instability is aggravated in the presence of isoproterenol and is attenuated by KN-93. As seen in our RyR2 knock-in CPVT mice, the antiarrhythmic effect of KN-93 is confirmed in these human iPSC-derived cardiac cells, supporting the role of this in vitro system for drug screening and optimization of clinical treatment strategies.
Evaluation of on screen navigational methods for a touch screen device (2010)

This study involves the design and evaluation of control methods for a touch screen device to enable effective navigation for UGVs (Unmanned Ground Vehicles). 6 different control methods were designed and evaluated. An experiment was conducted requiring participants to conduct navigational tasks. Analysis considers number of errors committed, task completion time and user preference.
MacroH2A1 downregulation enhances the stem-like properties of bladder cancer cells by transactivation of Lin28B (2015)

The histone variant, macroH2A1, has an important role in embryonic stem cell differentiation and tumor progression in various types of tumors. However, the regulatory roles of macroH2A1 on bladder cancer progression have not been fully elucidated. Here, we show that macroH2A1 knockdown promotes stem-like properties of bladder cancer cells. The knockdown of macroH2A1 in bladder cancer cells increased tumorigenicity, radioresistance, degeneration of reactive oxygen species, increased sphere formation capability and an increase in the proportion of side populations. We found that macroH2A1 is required for the suppression of Lin28B identified as a novel downstream target of macroH2A1 in bladder cancer. Loss of macroH2A1 expression significantly correlated with the elevated levels of Lin28B expression and subsequently inhibited the mature let-7 microRNA expression. Furthermore, the stable overexpression of Lin28B enhances the several phenotypes, including tumorigenicity and sphere-forming ability, which are induced by macroH2A1 depletion. Importantly, Lin28B expression was regulated by macroH2A1-mediated reciprocal binding of p300 and EZH2/SUV39H1. Our results suggest that Lin28B/let-7 pathway is tightly regulated by macroH2A1 and its cofactors, and have a pivotal role in the bladder tumor progression and the regulation of stem-like characteristics of bladder cancer cells.
Vaccination with the T Cell Antigen Mtb 8.4 Protects Against Challenge with Mycobacterium tuberculosis (2001)

The development of an effective vaccine against Mycobacterium tuberculosis is a research area of intense interest. Mounting evidence suggests that protective immunity to M. tuberculosis relies on both MHC class II-restricted CD4(+) T cells and MHC class I-restricted CD8(+) T cells. By purifying polypeptides present in the culture filtrate of M. tuberculosis and evaluating these molecules for their ability to stimulate PBMC from purified protein derivative-positive healthy individuals, we previously identified a low-m.w. immunoreactive T cell Ag, Mtb 8.4, which elicited strong Th1 T cell responses in healthy purified protein derivative-positive human PBMC and in mice immunized with recombinant Mtb 8.4. Herein we report that Mtb 8.4-specific T cells can be detected in mice immunized with the current live attenuated vaccine, Mycobacterium bovis-bacillus Calmette-Guérin as well as in mice infected i.v. with M. tuberculosis. More importantly, immunization of mice with either plasmid DNA encoding Mtb 8.4 or Mtb 8.4 recombinant protein formulated with IFA elicited strong CD4(+) T cell and CD8(+) CTL responses and induced protection on challenge with virulent M. tuberculosis. Thus, these results suggest that Mtb 8.4 is a potential candidate for inclusion in a subunit vaccine against TB.
Cytokine Therapy of Malignant Melanoma (1996)

Melanoma is a malignant neoplasia of melanocyte origin appearing mainly in the skin. About one third of all melanomas detected disseminate, with the metastatic spread occurring either via lymphatic or blood vessels. In the treatment of advanced melanoma the conventional chemotherapy or radiotherapy has not been very successful. Melanoma is known to have immunologically provocative features. In recent years immunological therapies, mainly cytokines, have been applied in the treatment of melanoma. The most widely used cytokines are Interferons and interleukin-2. These agents are used either alone or in combination with each other or with chemotherapeutics. Interferon and interleukin-2 therapies have yielded response rates of 15-20% on average, whereas combinations of immunotherapy and chemotherapy offer response rates as high as 50-60%. Unfortunately, average survival of patients with disseminated melanoma has been short, from 6 to 12 months. The immunotherapy approach has yielded some long-term responses and probably even a cure for a small proportion of patients. Understanding of basic mechanisms of tumour destruction by cytokines and new agents coming into clinical use will undoubtedly further improve treatment results.
Design verification for very large digital networks based on concurrent simulation and clock suppression (1983)

A methodology is presented for design verification of very large networks based on concurrent simulation and clock suppression. Concurrent case simulation consists of the concurrent injection and simulation of many input bit vectors into a given network model. This permits, relative to normal serial simulation, concurrent simulation of large numbers of cases of good machines at a very high speed. This speed advantage increases with the number of cases. Clock suppression is an auxiliary technique to avoid simulation slowdowns if networks with very large clock fanouts must be simulated. 11 references.