gebhart/patrepeval huggingface dataset:
Inhibition of the Staphylococcus aureusNADPH-dependent Enoyl-Acyl Carrier Protein Reductase by Triclosan and Hexachlorophene (2000)

Enoyl-acyl carrier protein reductase (FabI) plays a determinant role in completing cycles of elongation in type II fatty acid synthase systems and is an important target for antibacterial drugs. The FabI component of Staphylococcus aureus (saFabI) was identified, and its properties were compared with Escherichia coli FabI (ecFabI). ecFabI and saFabI had similar specific activities, and saFabI expression complemented the E. coli fabI(Ts) mutant, illustrating that the Gram-positive FabI was interchangeable with the Gram-negative FabI enzyme. However, ecFabI was specific for NADH, whereas saFabI exhibited specific and positive cooperative binding of NADPH. Triclosan and hexachlorophene inhibited both ecFabI and saFabI. The triclosan-resistant ecFabI(G93V) protein was also refractory to hexachlorophene inhibition, illustrating that both drugs bind at the FabI active site. Both the introduction of a plasmid expressing the safabI gene or a missense mutation in the chromosomal safabI gene led to triclosan resistance in S. aureus; however, these strains did not exhibit cross-resistance to hexachlorophene. The replacement of the ether linkage in triclosan by a carbon bridge in hexachlorophene prevented the formation of a stable FabI-NAD(P)(+)-drug ternary complex. Thus, the formation of this ternary complex is a key determinant of the antibacterial activity of FabI inhibitors.
Phenothiazine Neuroleptics Signal to the Human Insulin Promoter as Revealed by a Novel High-Throughput Screen (2010)

A number of diabetogenic stimuli interact to influence insulin promoter activity, making it an attractive target for both mechanistic studies and therapeutic interventions. High-throughput screening (HTS) for insulin promoter modulators has the potential to reveal novel inputs into the control of that central element of the pancreatic beta-cell. A cell line from human islets in which the expression of insulin and other beta-cell-restricted genes are modulated by an inducible form of the bHLH transcription factor E47 was developed. This cell line, T6PNE, was adapted for HTS by transduction with a vector expressing green fluorescent protein under the control of the human insulin promoter. The resulting cell line was screened against a library of known drugs for those that increase insulin promoter activity. Members of the phenothiazine class of neuroleptics increased insulin gene expression upon short-term exposure. Chronic treatment, however, resulted in suppression of insulin promoter activity, consistent with the effect of phenothiazines observed clinically to induce diabetes in chronically treated patients. In addition to providing insights into previously unrecognized targets and mechanisms of action of phenothiazines, the novel cell line described here provides a broadly applicable platform for mining new molecular drug targets and central regulators of beta-cell differentiated function.
The Influence of Various Chemical Additives on the Survival of Vesicular Exanthema Virus in Aerosols (1980)

The influence of relative humidity (r.h.) on the survival of vesicular exanthema virus (VEV) in aerosols at I s and during the next 5 min when generated from phosphate buffer solution containing polyhydroxy compounds, dimethyl sulphoxide, salt or protein has been examined. VEV was sensitive to r.h. in the range of 40 to 60% in the presence of bovine serum albumin, glucose, inositol or phosphate buffer. Addition of sodium chloride stabilized the virus in aerosols at mid-range r.h. both immediately after generation and after a period of storage for 5 min. In the presence of dimethyl sulphoxide or glycerol, virus survival was reduced at 20% r.h. at I s and at all r.h. during the first 5 min. Pre-humidification did not produce any significant difference in virus recovery.
Tumor rejection mediated by an amphotropic murine leukemia virus. (1983)

We studied the effects of murine leukemia virus infection on the growth of tumors in inbred strain 2 guinea pigs. Fibrosarcomas, induced by treatment of guinea pig fetal cells with chemical carcinogens, were exposed in vitro to the amphotropic murine leukemia virus, 4070A. Tumor cells exposed to murine leukemia virus 4070A in vitro expressed virus antigens, released both reverse transcriptase and infectious virus into supernatant fluids, and grew and regressed after injection into syngeneic animals. In contrast, uninfected tumor cells did not express virus antigens and grew progressively. Rejection of virus-infected tumor cells appeared to be a host-mediated event, since murine leukemia virus 4070A infection had no detectable cytopathic effect on fibrosarcoma cells. Rejection of virus-infected tumor cells occurred in guinea pigs unable to suppress the growth of the line 10 hepatoma at sites of injection of mycobacterial cell walls and unable to develop immunity to the line 10 hepatoma. Guinea pigs immunized with virus-infected tumor cells were unable to reject a challenge of uninfected tumor cells. The results are interpreted to mean that infection of guinea pig tumors in vitro by a murine leukemia virus led to synthesis of viral antigens by the tumor cells which in turn led to recognition of the tumor as foreign with consequent tumor destruction; tumor eradication occurred without development of immunity to cryptic, intrinsic tumor antigens.
<title>193-nm single-layer positive resists: building etch resistance into a high-resolution imaging system</title> (1995)

Our approach to the design of positive, single layer resists for 193 nm lithography is discussed. Phenolic resins, the archetype in positive photoresist materials, cannot be used at this wavelength due to optical opacity. Methacrylate polymers combine the required optical transparency at 193 nm with easily tailored properties, however. The methacrylate polymer materials used in our 193 nm resists are completely different from phenolics used in traditional (248 nm) chemically amplified resists but the imaging chemistry is very similar. With a design based on methacrylate terpolymers, we have recently developed a high resolution positive resist for 193 nm lithography with excellent imaging at both 193 and 248 nm. Our recent work has centered on gaining further insight into methacrylate polymer structure/property relationships, improving the imaging performance and finally increasing the etch resistance. Towards that end, we have developed a class of dissolution inhibitors for 193 nm resists that are combined with methacrylate polymers to provide 3-component resists. A family of B- steroid dissolution inhibitors that also increase etch resistance is described. Imaging and etch performance of four versions of our resist are disclosed. These methacrylate resists show resolution capability below 0.25 micron, etch rates 20% higher than novolak resins, good environmental stability in contrast to traditional DUV resists and dual wavelength (193/248) imaging.
Phosphorothioate analogs of (2'-5')(A)4: agonist and antagonist activities in intact cells (1990)

Metabolically stable phosphorothioate tetramer analogues of (2'-5')(A)n with Rp and/or Sp chirality in the 2'-5'-phosphodiester linkages constitute a new class of antiviral agents since they mimic the effects of interferons. Three of the diastereomeric 5'-monophosphates (i.e., pRpRpRp, pSpRpRp, and pRpSpSp) bind to and activate RNase L from extracts of HeLa cells. However, the pSpSpSp (2'-5')-(A)4-phosphorothioate is unique in that it binds to, but cannot activate, RNase L to cleave rRNA. When microinjected into the cytoplasm of HeLa cells followed by virus infection, the pRpRpRp, pSpRpRp, and pRpSpSp (2'-5')(A)4-phosphorothioates demonstrate antiviral activity, as does (2'-5')(A)4ox-red, an active (2'-5')(A)n analogue. When microinjected simultaneously with (2'-5')(A)nox-red, an active the pSpSpSp (2'-5')(A)4-phosphorothioate inhibits activation of RNase L in HeLa cells, thereby blocking direct protection of vesicular stomatitis virus. The agonist and antagonist properties of pRpRpRp and pSpSpSp, respectively, are transient probably as a consequence of the hydrolysis of the 5'-monophosphate and formation of the less active (2'-5')(A)4-phosphorothioate cores. The possible use of these (2'-5')(A)4-phosphorothioates as tools for dissecting the biological significance of the (2'-5')(A)n system or in antiviral chemotherapy is discussed.
Craniosynostosis - Recognition, clinical characteristics, and treatment (2017)

Craniosynostosis is a developmental craniofacial anomaly, resulting in impairment of brain development and abnormally shaped skull. The main cause of craniosynostosis is premature closure of one or more cranial sutures. It usually occurs as an isolated condition, but may also be associated with other malformations as part of complex syndromes. When left untreated, craniosynostosis can cause serious complications, such as developmental delay, facial abnormality, sensory, respiratory and neurological dysfunction, anomalies affecting the eye, and psychological disturbances. Thus, early diagnosis, expert surgical techniques, postoperative care, and adequate follow-up are of vital importance in treating craniosynostosis.
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements (2007)

CpG methylation is a key component of the epigenome architecture that is associated with changes in gene expression without a change to the DNA sequence. Since the first reports on deregulation of DNA methylation, in diseases such as cancer, and the initiation of the Human Epigenome Project, an increasing need has arisen for a detailed, high-throughput and quantitative method of analysis to discover and validate normal and aberrant DNA methylation profiles in large sample cohorts. Here we present an improved protocol using base-specific fragmentation and MALDI-TOF mass spectrometry that enables a sensitive and high-throughput method of DNA methylation analysis, quantitative to 5% methylation for each informative CpG residue. We have determined the accuracy, variability and sensitivity of the protocol, implemented critical improvements in experimental design and interpretation of the data and developed a new formula to accurately measure CpG methylation. Key innovations now permit determination of differential and allele-specific methylation, such as in cancer and imprinting. The new protocol is ideally suitable for detailed DNA methylation analysis of multiple genomic regions and large sample cohorts that is critical for comprehensive profiling of normal and diseased human epigenomes.
In Vitro Evaluations of Condoms with and Without Nonoxynol 9 As Physical and Chemical Barriers Against Chlamydia Trachomatis, Herpes Simplex Virus Type 2, and Human Immunodeficiency Virus (1989)

Simulated in vitro intercourse conditions demonstrated that unlubricated latex condoms provide an effective physical barrier to high concentrations of Chlamydia trachomatis, herpes simplex virus type 2, and human immunodeficiency virus. However, since condoms can be damaged after manufacturing inspection and prior to use, latex condoms alone should not be perceived as absolute protection against STDs. Nonoxynol 9 used in conjunction with condoms provided additional, yet still not foolproof, protection against the three viruses.
Comparison of the Relative Fibrinogenolytic, Fibrinolytic and Thrombolytic Properties of Tissue Plasminogen Activator and Urokinase in Vitro (1981)

The relative fibrinogenolytic, fibrinolytic and thrombolytic properties of human tissue plasminogen activator and human urokinase were compared in purified systems, in whole human plasma and in a system composed of a radioactive human blood clot (125I-fibrinogen) hanging in circulating human plasma. The human tissue plasminogen activator was highly purified from the culture fluid of a human melanoma cell line. In purified systems composed of fibrinogen of fibrin, plasminogen and alpha 2-antiplasmin as well as in whole plasma, tissue plasminogen activator digested fibrin without degrading fibrinogen significantly. Urokinase did not have this specific fibrinolytic effect. In the circulating plasma system, the degree of fibrinolysis was proportional to the amount of activator added, tissue plasminogen activator being about 10 times more efficient than urokinase. In addition, tissue plasminogen activator appeared to cause negligible fibrinogen degradation. Tissue plasminogen activator still induced significant thrombolysis at a concentration of 10 IU per ml whereas no effect of urokinase was observed at 20 IU per ml. Infusion of 100 IU (1 microgram) of tissue plasminogen activator per ml resulted in moderate activation of the fibrinolytic system as judged from a decrease of plasminogen and alpha 2-antiplasmin to 40-50 percent. Nevertheless, extensive fibrinolysis (50 to 80 percent of radioactivity released after 12 hrs) and only very limited fibrinogenolysis were observed. An equivalent amount of urokinase (100 IU per ml) only induced approximately 15 percent lysis in 12 hrs. At higher concentrations of urokinase (260 IU per ml or more) extensive activation of the fibrinolytic system was obtained as evidenced by a depletion of plasminogen, alpha 2-antiplasmin and fibrinogen. This was associated with extensive fibrinolysis (approximately 60 percent after 12 hrs). It is concluded that human tissue plasminogen activator is a more specific and effective fibrinolytic-thrombolytic agent than human urokinase.
Simultaneous fluorescence-activated cell sorter analysis of two distinct transcriptional elements within a single cell using engineered green fluorescent proteins. (1996)

Green fluorescent protein (GFP) is widely used as a reporter gene in both prokaryotes and eukaryotes. However, the fluorescence levels of wild-type GFP (wtGFP) are not bright enough for fluorescence-activated cell sorting or flow cytometry. Several GFP variants were generated that are brighter or have altered excitation spectra when expressed in prokaryotic cells. We engineered two GFP genes with different combinations of these mutations, GFP(S65T,V163A) termed GFP-Bex1, and GFP(S202F,T203I,V163A) termed GFP-Vex1. Both show enhanced brightness and improved signal-to-noise ratios when expressed in mammalian cells and appropriately excited, compared with wtGFP. Each mutant retains only one of the two excitation peaks of the wild-type protein. GFP-Bex1 excites at 488 nm (blue) and GFP-Vex1 excites at 406 nm (violet), both of which are available laser lines. Excitation at these wavelengths allows for the independent analyses of these mutants by fluorescence-activated cell sorting, permitting simultaneous, quantitative detection of expression from two different genes within single mammalian cells.
Specific, rapid synthesis of Phe-RNA by RNA (1999)

RNA 77, derived by selection amplification, accelerates its own conversion to Phe-RNA (relative to randomized RNA) more than 6 x 10(7)-fold, by using amino acid adenylates as substrate. A modified assay system allows measurement of slow rates of aa-RNA formation, which for disfavored amino acid substrates can be more than 10(4)-fold slower than phenylalanine. Thus unlike previously characterized self-aminoacylators, RNA 77 catalysis is highly amino acid selective. Remarkably, both rates of aminoacyl transfer and amino acid specificities are greater for RNA 77 than measured for protein PheRS. These data experimentally support the possible existence of an ancestral amino acid-specific translation system relying entirely on RNA catalysis. RNA 77 itself embodies a possible transitional evolutionary state, in which side-chain-specific aa-RNA formation and anticodon-codon pairing were invested in the same molecule.
Localization of a liver-specific enhancer in the apolipoprotein E/C-I/C-II gene locus (1993)

The sequences necessary for liver-specific expression of the apolipoprotein (apo) E gene have been shown to reside 3' to the gene, within the apoE/C-I/C-II gene cluster, but have not been precisely characterized. Utilizing a transient transfection reporter gene assay based on the apoC-II promoter, we have localized a liver-specific enhancer to its approximate limit dimension of 154 base pairs. This enhancer directed liver-specific expression of an apoE gene construction in transgenic mice. A DNaseI protection assay revealed two footprints over an inverted repeat of a known transcriptionally active motif, TGACCT. DNaseI-sensitive sites were present in three of six repeats of a motif (consensus GCAAACA) which has been postulated to represent the recognition sequence of a hepatic transcriptional activity, HNF-5. This region of DNA may function as a liver-specific enhancer for the entire apoE/C-I/C-II gene cluster.
Functionalized Monolayers on Ordered Mesoporous Supports (1997)

Mesoporous silica materials containing functionalized organic monolayers have been synthesized. Solid-state nuclear magnetic resonance suggests that a cross-linked monolayer of mercaptopropylsilane was covalently bound to mesoporous silica and closely packed on the surface. The relative surface coverage of the monolayers can be systematically varied up to 76 percent. These materials are extremely efficient in removing mercury and other heavy metals from both aqueous and nonaqueous waste streams, with distribution coefficients up to 340,000. The stability of these materials and the potential to regenerate and reuse them have also been demonstrated. The surface modification scheme reported here enables rational design of the surface properties of tailored porous materials and may lead to the synthesis of more sophisticated functionalized composites for environmental and industrial applications.
Standardized white spot syndrome virus (WSSV) inoculation procedures for intramuscular or oral routes (2006)

In the past, strategies to control white spot syndrome virus (WSSV) were mostly tested by infectivity trials in vivo using immersion or per os inoculation of undefined WSSV infectious doses, which complicated comparisons between experiments. In this study, the reproducibility of 3 defined doses (10, 30 and 90 shrimp infectious doses 50% endpoint [SID50]) of WSSV was determined in 3 experiments using intramuscular (i.m.) or oral inoculation in specific pathogen-free (SPF) Litopenaeus vannamei. Reproducibility was determined by the time of onset of disease, cumulative mortality, and median lethal time (LT50). By i.m. route, the 3 doses induced disease between 24 and 36 h post inoculation (hpi). Cumulative mortality was 100% at 84 hpi with doses of 30 and 90 SID50 and 108 hpi with a dose of 10 SID50. The LT50 of the doses 10, 30 and 90 SID50 were 52, 51 and 49 hpi and were not significantly different (p > 0.05). Shrimp orally inoculated with 10, 30 or 90 SID50 developed disease between 24 and 36 hpi. Cumulative mortality was 100% at 108 hpi with doses of 30 and 90 SID50 and 120 hpi with a dose of 10 SID50. The LT50 of 10, 30 and 90 SID50 were 65, 57 and 50 hpi; these were significantly different from each other (p < 0.05). A dose of 30 SID50 was selected as the standard for further WSSV challenges by i.m. or oral routes. These standardized inoculation procedures may be applied to other crustacea and WSSV strains in order to achieve comparable results among experiments.
Growth Inhibition of Macrophage-Like and Other Cell Types by Liposome-Encapsulated, Calcium-Bound, and Free BisphosphonatesIn Vitro (1994)

Bisphosphonates effectively inhibit osteoclastic bone resorption in diseases characterized by excessive bone loss. Liposome-encapsulated clodronate (dichloromethylene bisphosphonate) also is known to inactivate phagocytic cells in vivo, and inhibit the growth of macrophage-like RAW 264 cells in vitro. The macrophage suppressive effect of liposomal clodronate is of interest in autoimmune diseases, like rheumatoid arthritis, in which phagocytic cells are involved in inflammatory processes. Earlier in vivo studies suggested that liposomal clodronate is a far more potent inactivator of macrophages than liposomal forms of two other bisphosphonate compounds, pamidronate (3-amino-1-hydroxypropylidene bisphosphonate), and etidronate (1-hydroxyethylidene-1,1-bisphosphonate). We examined the growth inhibitory properties of these three bisphosphonates with macrophage-like RAW 264 cells and with other types of cells in vitro. All three bisphosphonates encapsulated in liposomes effectively inhibited the growth of RAW 264 and CV1-P cells, while free drugs were 20-1000 times less potent growth inhibitors. Also, high extracellular calcium concentrations enhanced the potency of bisphosphonates for RAW 264 cells, indicating that, in addition to liposomes, the uptake of bisphosphonates by macrophages is mediated also by calcium. In all formulations, pamidronate was the most potent compound for the cells, with the exception of CV1-P cells, for which liposomal clodronate was the most potent. The effects of liposomal drugs were selective for highly endocytotic cells. The results suggest that liposome-encapsulated bisphosphonates could provide a specific tool to affect the function of macrophages and all three of these bisphosphonates are potentially effective as macrophage suppressors in autoimmune diseases.
CD4 receptor binding peptides that block HIV infectivity cause human monocyte chemotaxis (1987)

The octapeptide Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr (peptide T) and two structural analogs are potent agonists of human monocyte chemotaxis, evincing identical rank potency orders as was previously shown for their inhibition of human immunodeficiency virus (HIV) envelope binding and T cell infectivity. Chemotactic activity could be inhibited by anti-CD4 monoclonal antibodies (Mabs), but not other mononuclear cell Mabs. The core peptide required for chemotactic activity is a pentapeptide related to the sequence Thr-Thr-Asn-Tyr-Thr. Homologous pentapeptides, identified by computer search, were detected in several other non-HIV-related viruses as well as the neuropeptide vasoactive intestinal polypeptide (VIP). The CD4 molecule, therefore, appears to be a recognition molecule for a small signal peptide ligand whose active sequence is a homolog of peptide T and which may be the neuropeptide VIP.
Cell-interactive Alginate Hydrogels for Bone Tissue Engineering (2001)

There is significant interest in the development of injectable carriers for cell transplantation to engineer bony tissues. In this study, we hypothesized that adhesion ligands covalently coupled to hydrogel carriers would allow one to control pre-osteoblast cell attachment, proliferation, and differentiation. Modification of alginate with an RGD-containing peptide promoted osteoblast adhesion and spreading, whereas minimal cell adhesion was observed on unmodified hydrogels. Raising the adhesion ligand density increased osteoblast proliferation, and a minimum ligand density (1.5-15 femtomoles/cm2) was needed to elicit this effect. MC3T3-E1 cells demonstrated increased osteoblast differentiation with the peptide-modified hydrogels, as confirmed by the up-regulation of bone-specific differentiation markers. Further, transplantation of primary rat calvarial osteoblasts revealed statistically significant increases of in vivo bone formation at 16 and 24 weeks with G4RGDY-modified alginate compared with unmodified alginate. These findings demonstrate that biomaterials may be designed to control bone development from transplanted cells.
Transformation of Tobacco, Tomato, Potato, and Arabidopsis thaliana Using a Binary Ti Vector System (1986)

Using a binary tumor-inducing (Ti) plasmid vector system, several plant species were transformed with a kanamycin resistance marker (neomycin phosphotransferase gene). Four Nicotiana species, seven tomato cultivars, two potato cultivars, and Arabidopsis thaliana were transformed by the binary vector transformation method. In this method, various plant organ pieces were co-cultivated with Agrobacterium tumefaciens cells carrying the binary vector, pGA472, and a helper Ti plasmid. We have also demonstrated that a wild type Ti plasmid can be used as a helper to obtain a transformed plant.