gebhart/patrepeval huggingface dataset:
On‐demand drug delivery from self‐assembled nanofibrous gels: A new approach for treatment of proteolytic disease (2011)

Local delivery of drugs offers the potential for high local drug concentration while minimizing systemic toxicity, which is often observed with oral dosing. However, local depots are typically administered less frequently and include an initial burst followed by a continuous release. To maximize efficiency of therapy, it is critical to ensure that drug is only released when needed. One of the hallmarks of rheumatoid arthritis, for example, is its variable disease activity consisting of exacerbations of inflammation punctuated by periods of remission. This presents significant challenges for matching localized drug delivery with disease activity. An optimal system would be nontoxic and only release drugs during the period of exacerbation, self-titrating in response to the level of inflammation. We report the development of an injectable self-assembled nanofibrous hydrogel, from a generally recognized as safe material, which is capable of encapsulation and release of agents in response to specific enzymes that are significantly upregulated in a diseased state including matrix metalloproteinases (MMP-2 and MMP-9) and esterases. We show that these self-assembled nanofibrous gels can withstand shear forces that may be experienced in dynamic environments such as joints, can remain stable following injection into healthy joints of mice, and can disassemble in vitro to release encapsulated agents in response to synovial fluid from arthritic patients. This novel approach represents a next-generation therapeutic strategy for localized treatment of proteolytic diseases.
Epigenetic Potentiation of NY-ESO-1 Vaccine Therapy in Human Ovarian Cancer (2014)

The cancer-testis/cancer-germline antigen NY-ESO-1 is a vaccine target in epithelial ovarian cancer (EOC), but its limited expression is a barrier to vaccine efficacy. As NY-ESO-1 is regulated by DNA methylation, we hypothesized that DNA methyltransferase (DNMT) inhibitors may augment NY-ESO-1 vaccine therapy. In agreement, global DNA hypomethylation in EOC was associated with the presence of circulating antibodies to NY-ESO-1. Pre-clinical studies using EOC cell lines showed that decitabine treatment enhanced both NY-ESO-1 expression and NY-ESO-1-specific CTL-mediated responses. Based on these observations, we performed a phase I dose-escalation trial of decitabine, as an addition to NY-ESO-1 vaccine and doxorubicin liposome (doxorubicin) chemotherapy, in 12 patients with relapsed EOC. The regimen was safe, with limited and clinically manageable toxicities. Both global and promoter-specific DNA hypomethylation occurred in blood and circulating DNAs, the latter of which may reflect tumor cell responses. Increased NY-ESO-1 serum antibodies and T cell responses were observed in the majority of patients, and antibody spreading to additional tumor antigens was also observed. Finally, disease stabilization or partial clinical response occurred in 6/10 evaluable patients. Based on these encouraging results, evaluation of similar combinatorial chemo-immunotherapy regimens in EOC and other tumor types is warranted.
Alopecia areata: More on Topical Sensitizers (1990)

Our experience on treating alopecia areata with topical sensitizers (diphencyprone, squaric acid dibutylester) is reported: staging, prognosis, side effects, follow-up, and psychological attitude of the patients towards this therapy and wigs are the focused aspects. The possible mechanisms of action of these allergens are discussed, reporting the case of a female patient with concomitant appearance of hair regrowth and psoriatic plaques in the same area after SADBE therapy.
Competitive exclusion of intestinal colonization of Escherichia coli in chicks. (1982)

A native gut microflora of chickens that protected chicks against Salmonella was evaluated against six pathogenic strains of Escherichia coli using similar methodology. Nalidixic-acid-resistant forms of the E. coli strains were derived for use in seeder-bird and individual-bird challenge tests. A substantial degree of exclusion of intestinal colonization of each of the six pathogenic strains of E. coli was secured in chicks that had been treated with native gut microflora. E. coli appeared to colonize chiefly the crop and cecum. Native gut microflora limited to a much lesser degree the "normal" E. coli present in the intestinal tract of test chicks. The mechanism of protection appears to be similar to that for Salmonella: native gut microflora and E. coli competed for sites of attachment.
A morphologically distinct candidate for an epithelial stem cell in mouse mammary gland (1988)

Transplantation studies demonstrate that an epithelial stem cell component must exist in the mouse mammary gland throughout life. Samples taken from any portion of the mammary gland at any age and at any developmental stage, including full functional differentiation, give rise to mammary epithelial outgrowths with complete developmental capacity. Cytological examination of mouse mammary gland explants revealed the presence of morphologically distinct cells distributed sporadically among the mammary epithelium, whose behaviour in vivo and in vitro suggested that they might represent a latent epithelial stem cell population. These pale-staining cells possessed large spherical nuclei, a clear cytoplasm and a round smooth-contoured shape. Electron microscopy confirmed their pale-staining characteristics and revealed a cytoplasm sparsely populated with organellar structures, such as mitochondria and endoplasmic reticulum. Their epithelial genealogy was demonstrated by the presence of terminal bars and tight junctions formed with their epithelial cell neighbours. In vivo, these cells were found among mammary epithelial cell populations in 16-day-old embryos onward in both ductal or lobular structures during all stages of pregnancy, lactation and involution. In explant cultures, these cells did not undertake a secretory morphology in the presence of lactogenic hormones, although occasionally they became immunologically positive for casein. They did not incorporate [3H]-thymidine into their nuclei under any of the experimental conditions used; however, they appeared to undergo mitosis within 4 h regardless of the presence or absence of hormone(s). At 24 h increased numbers of pale cells were found in pairs or in groups. At 72 h in the presence of IFPrl (medium containing insulin, hydrocortisone and prolactin), the pairs and groups of pale cells observed at 24 h were not found. Instead, individual pale cells were seen among groups of cytologically and functionally differentiated secretory epithelial cells. When lactogenic hormones were not present, groups of pale cells were still present in the explants at 72 h. These findings suggest that the pale cells are arrested at G2 phase of the cell cycle and that they give rise by mitosis to daughter cells capable of differentiating in the presence of lactogenic stimuli. Inhibition of DNA synthesis in the explants did not alter these cellular events.
Inhibition of the tumor-promoting action of 12-O-tetradecanoylphorbol-13-acetate by some oleanane-type triterpenoid compounds. (1988)

Since glycyrrhetinic acid was proved to suppress tumor promoter effects, several oleanane-type triterpenes which were chemically derived from oleanolic acid and hederagenin were tested in vitro and in vivo against the action of tumor promoter, 12-O-tetradecanoylphorbol 13-acetate. By in vitro experiment monitoring with 12-O-tetradecanoylphorbol-13-acetate-induced stimulation of 32Pi incorporation into phospholipids and an in vivo test on skin tumor formation in mice initiated with 7,12-dimethylbenz[a]anthracene and promoted with 12-O-tetradecanoylphorbol-13-acetate, 18 beta-olean-12-ene-3 beta,28-diol (= erythrodiol), 18 beta-olean-12-ene-3 beta,23,28-triol, 18 alpha-olean-12-ene-3 beta,28-diol, and 18 alpha-olean-12-ene-3 beta,23,28-triol showed remarkable suppressive effects. Especially 18 alpha-oleanane derivatives having a CH2OH grouping converted from the COOH group initially allocated at C-17 were 100 times more effective than glycyrrhetinic acid both in vitro and in vivo.
Long‐term continuous evolution of acetate resistant Acetobacter aceti (2003)

Elevated concentrations of cytotoxic acetate are found in many environmental niches, and few species are relatively resistant to acetate. In particular the high-level acetate resistance of so-called acetic acid bacteria that occurs in industrial settings must be constantly selected for. To investigate the nature of such high-level resistance, we grew the moderately acetate-resistant Acetobacter aceti wild-type and acetate-sensitive Escherichia coli in long-term continuous cultures with increasing acetate concentrations at near neutral pH. While E. coli did not acquire any significant resistance after 125 generations of selection, A. aceti evolved the capability to grow at acetate concentrations exceeding 50 g/L within 240 generations. This phenotype was found to be stable for several generations in the absence of selective pressure, hence must be genetically determined. Intracellular acetate concentrations were significantly lower in evolved A. aceti, when compared to wild-type A. aceti and E. coli, indicating that cytoplasmatic anion accumulation is an important component of acetate toxicity.
Some Challenging Typing Issues in Object-Oriented Languages (2003)

In this paper we discuss some of the remaining problems in the design of static type systems for object-oriented programming languages. We look at typing problems involved in writing a simple interpreter as a good example of a simple problem leading to difficult typing issues. The difficulties encountered seem to arise in situations where a programmer desires to simultaneously refine mutually interdependent classes and object types.
Prolonged Activation of the Baroreflex Abolishes Obesity-Induced Hypertension (2007)

Prolonged electrical activation of the carotid baroreflex produces sustained reductions in sympathetic activity and arterial pressure in normotensive dogs. The main goal of this study was to assess the influence of prolonged baroreflex activation on arterial pressure and neurohormonal responses in 6 dogs with obesity-induced hypertension. After control measurements, the diet was supplemented with cooked beef fat for 6 weeks, whereas sodium intake was held constant. After 4 weeks of the high-fat diet, there were increments in body weight from 25.8+/-0.7 to 38.6+/-1.0 kg, mean arterial pressure from 97+/-2 to 110+/-3 mm Hg, heart rate from 67+/-3 to 91+/-4 bpm, and plasma norepinephrine concentration from 141+/-35 to 280+/-52 pg/mL. Plasma glucose and insulin concentrations were elevated, but increases in plasma renin activity during the initial weeks of the high-fat diet were not sustained. During week 5, baroreflex activation resulted in sustained reductions in mean arterial pressure, heart rate, and plasma norepinephrine concentration; at the end of week 5, these values were 87+/-2 mm Hg, 77+/-4 bpm, and 166+/-45 pg/mL, respectively. These suppressed values returned to week 4 levels during a 7-day recovery period after baroreflex activation. There were no changes in plasma glucose or insulin concentrations, or plasma renin activity during prolonged baroreflex activation. These findings indicate that baroreflex activation can chronically suppress the sympathoexcitation associated with obesity and abolish the attendant hypertension while having no effect on hyperinsulinemia or hyperglycemia.
The structure of human lymphotoxin (tumor necrosis factor-beta) at 1.9-A resolution. (1992)

The three-dimensional structure of recombinant human lymphotoxin (residues 24-171 of the mature protein) has been determined by x-ray crystallography at 1.9-A resolution (Rcryst = 0.215 for I greater than 3 sigma (I)). Phases were derived by molecular replacement using tumor necrosis factor (TNF-alpha) as a search model. Like TNF-alpha, lymphotoxin (LT) folds to form a "jellyroll" beta-sheet sandwich. Three-fold related LT subunits form a trimer stabilized primarily by hydrophobic interactions. A cluster of 6 basic residues around the 3-fold axis may account for the acid lability of the trimer. Although the structural cores of TNF-alpha and LT are similar, insertions and deletions relative to TNF-alpha occur in loops at the "top" of the LT trimer and significantly alter the local structure and the overall shape trimer is highly conserved. The sites of two mutations (Asp-50 and Tyr-108) that abolish the cytotoxicity of LT are contained within poorly ordered loops of polypeptide chain that flank the cleft between neighboring subunits at the base of the molecule, suggesting that the receptor recognizes an intersubunit binding site.
Purified immunotoxins that are reactive with human lymphoid cells. Monoclonal antibodies conjugated to the ribosome-inactivating proteins gelonin and the pokeweed antiviral proteins. (1985)

Seven different monoclonal antibodies of the IgG class that are reactive with four different antigens on human lymphoid cells were utilized to form immunotoxins with the ribosome-inactivating proteins gelonin and the three known pokeweed antiviral proteins. Thirteen different immunotoxin combinations were prepared. The ribosome-inactivating proteins were modified with 2-iminothiolane. The sulfhydryl groups so introduced were reacted with maleimido groups or with dithiopyridyl groups that had been introduced into the antibodies. The toxin-antibody conjugates so formed were purified by affinity chromatography on protein A-Sepharose CL-4B, ion exchange chromatography, and by gel filtration and were characterized by polyacrylamide-dodecyl sulfate gel electrophoresis. The purified immunotoxins were free of nonconjugated monomeric proteins and aggregates of very high molecular weight. All the immunotoxins showed the specific binding of the component antibody as measured by indirect immunofluorescence binding assays. The activities of the ribosome-inactivating proteins were unaffected by conjugation where the cross-link to the antibody contained a disulfide bond and when assayed after reductive cleavage of the linker. Disulfide-linked immunotoxins with six of the antibodies were highly cytotoxic for the target cells. However, immunotoxins containing an anti-B1 antibody showed no cytotoxicity.
Natural and Azido Fatty Acids Inhibit Phosphate Transport and Activate Fatty Acid Anion Uniport Mediated by the Mitochondrial Phosphate Carrier (2001)

The electroneutral P(i) uptake via the phosphate carrier (PIC) in rat liver and heart mitochondria is inhibited by fatty acids (FAs), by 12-(4-azido-2-nitrophenylamino)dodecanoic acid (AzDA) and heptylbenzoic acid ( approximately 1 microm doses) and by lauric, palmitic, or 12-azidododecanoic acids ( approximately 0.1 mm doses). In turn, reconstituted E. coli-expressed yeast PIC mediated anionic FA uniport with a similar pattern leading to FA cycling and H(+) uniport. The kinetics of P(i)/P(i) exchange on recombinant PIC in the presence of AzDA better corresponded to a competitive inhibition mechanism. Methanephosphonate was identified as a new PIC substrate. Decanephosphonate, butanephosphonate, 4-nitrophenylphosphate, and other P(i) analogs were not translocated and did not inhibit P(i) transport. However, methylenediphosphonate and iminodi(methylenephosphonate) inhibited both electroneutral P(i) uptake and FA cycling via PIC. AzDA analog 16-(4-azido-2-nitrophenylamino)-[(3)H(4)]-hexadecanoic acid ((3)H-AzHA) bound upon photoactivation to several mitochondrial proteins, including the 30- and 34-kDa bands. The latter was ascribed to PIC due to its specific elution pattern on Blue Sepharose and Affi-Gel. (3)H-AzHA photolabeling of recombinant PIC was prevented by methanephosphonate and diphosphonates and after premodification with 4-azido-2-nitrophenylphosphate. Hence, the demonstrated PIC interaction with monovalent long-chain FA anions, but with divalent phosphonates of short chain only, indicates a pattern distinct from that valid for the mitochondrial uncoupling protein-1.
Characterization of [3H]‐(2S,2′R,3′R)‐2‐(2′,3′‐dicarboxy‐ cyclopropyl)glycine ([3H]‐DCG IV) binding to metabotropic mGlu2 receptor‐transfected cell membranes (1998)

1. The binding of the new selective group II metabotropic glutamate receptor radioligand, [3H]-(2S,2'R,3'R)-2-(2',3'-dicarboxycyclopropyl)glycine ([3H]-DCG IV), was characterized in rat mGlu2 receptor-transfected CHO cell membranes. 2. [3H]-DCG IV binding was pH-dependent, but was not sensitive to temperature. Saturation analysis showed the presence of a single binding site, with a Kd value of 160 nM and a Bmax value of 10 pmol mg(-1) protein. Binding was not sensitive to Na+-dependent glutamate uptake blockers or Cl-dependent glutamate binding inhibitors. Furthermore, up to concentrations of 1 mM, the glutamate ionotropic receptor agonists, N-methyl-D-aspartic acid (NMDA), (S)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate, did not affect [3H]-DCG IV binding. 3. Of the compounds observed to inhibit [3H]-DCG IV binding, the most potent were the recently described selective group II agonist, (+)-2-aminobicyclo-[3.1.0]hexane-2,6-dicarboxylate (LY 354740; Ki value 16 nM) and antagonist, 2-amino-2-(2-carboxycyclopropan-1-yl)-3-(dibenzopyran-4-yl) propanoic acid (LY 341495; Ki value 19 nM). As expected, for a G-protein-coupled receptor, guanosine-5'-O-(3-thiotriphosphate) (GTPgammaS) inhibited [3H]-DCG IV binding in a concentration-dependent manner, with an IC50 value of 12 nNM. 4. A highly significant correlation was observed between the potencies of compounds able to inhibit [3H]-DCG IV binding and potencies obtained for agonist activity in a GTPgamma35S binding functional assay. In addition, these studies identified a number of compounds with previously unknown activity at mGlu2 receptors, including L(+)-2-amino-3-phosphonopropionic acid (L-AP3), L(+)-2-amino-5-phosphonopentanoic acid (L-AP5), 3-((RS)-2-carboxypiperazin-4-yl)-propyl-1-phosphonic acid (R-CPP), N-acetyl-L-aspartyl-L-glutamic acid (NAAG) and (RS)-alpha-methylserine-O-phosphate (MSOP).
Oncogene-lnitiated Aberrant Signaling Engenders the Metastatic Phenotype: Synergistic Transcription Factor Interactions are Targets for Cancer Therapy (1996)

Certain p21GTPases (notably Ras) and some of their guanine nucleotide exchange factors (e.g., Ost, Dbl, Tiam) and downstream mediators (e.g., Raf, Myc) have the potential to promote the development of malignancies because they can enhance the transcription of genes that foster the tumorigenic and metastatic phenotype. Among these are genes that stimulate cell proliferation, confer immortality, and facilitate the invasion of normal tissues. Oncogenes upstream of Ras-cell surface receptors such as ErbB2/Neu, Met, or Trk (and their ligands), and nonreceptor cytoplasmic protein tyrosine kinases such as Src and Abl-not only can act through Ras but also contribute additional signals. This review presents a synopsis of our understanding of signaling pathways controlled by the p21GTPases, with a focus on transcription factors regulated by the pathways. Mutations in one or more of the elements in these signaling pathways are invariably found in cancer cells. Crosstalk among the pathways may explain how some forms of stress can contribute to the development of a malignancy. Abnormal signaling leads to modified cytoskeletal structures and permanently altered (i.e., self-sustaining or epigenetic) transcription of target genes. A common therne is that genes whose transcription is elevated to the greatest extent by Ras often have in their promoters juxtaposed binding sites for two different transcription factors (particularly those in the Fos/Jun, CREB/ATF, NFkB, and Ets families) each of which is activated and such that together they synergize to augment transcription substantially. Some of these transcription factors can also act as oncogenes in certain cell types when appropriately modified and expressed. This unifying theme among many different cancers suggests that strategies to restore the balance among the signaling pathways or to suppress synergistic interactions between transcription factors may prove broadly useful in reversing the malignant phenotype.
Text Linking and Retrieval Experiments for Textbook Components (1990)

Experiments are described designed to retrieve individual paragraphs of textbook material in answer to user-submitted queries. The retrieval strategies are based on the global comparison of paragraph texts, as well as on the local processing of text sentences. Furthermore, the retrieved items may be freely chosen, or may alternatively be restricted to certain areas in a clustered arrangement of book paragraphs. The retrieval results indicate that high retrieval values are obtainable for the more refined retrieval strategies, ranging between 0.70 and 0.80 in search precision.
Ganglioside GD3 promotes cell growth and invasion through p130Cas and paxillin in malignant melanoma cells (2005)

Although ganglioside GD3 levels are highly elevated in malignant melanomas, the role of GD3 in melanomas' malignant properties has not been clearly shown. To investigate this problem, we genetically generated GD3-positive (GD3+) transfectant cells from a GD3-negative (GD3-) mutant line SK-MEL-28-N1 and analyzed the phenotypic changes in the transfected cells. GD3+ cells showed markedly increased cell growth and invasive characteristics. Two bands that underwent stronger tyrosine phosphorylation in GD3+ cell lines than in controls after treatment with FCS were found with molecular masses of 130 and 68 kDa. They were identified as p130Cas and paxillin by sequential immunoprecipitation. Their roles in cell growth and invasion were analyzed with a small interfering RNA (siRNA) approach. Cell growth, as analyzed by BrdUrd uptake, was strongly suppressed in GD3+ cells to near the levels of GD3- cells when treated with siRNA for p130Cas but not when treated with siRNA for paxillin. However, treatment with siRNAs of either p130Cas or paxillin resulted in the marked suppression of the invasive activity of GD3+ cells almost to the levels of control cells. These results suggested that these two molecules function as effectors of GD3-mediated signaling, leading to such malignant properties as rapid cell growth and invasion.
Evaluation of a FRET-Peptide Substrate to Predict Virulence in Pseudomonas aeruginosa (2013)

Pseudomonas aeruginosa produces a number of proteases that are associated with virulence and disease progression. A substrate able to detect P. aeruginosa-specific proteolytic activity could help to rapidly alert clinicians to the virulence potential of individual P. aeruginosa strains. For this purpose we designed a set of P. aeruginosa-specific fluorogenic substrates, comprising fluorescence resonance energy transfer (FRET)-labeled peptides, and evaluated their applicability to P. aeruginosa virulence in a range of clinical isolates. A FRET-peptide comprising three glycines (3xGly) was found to be specific for the detection of P. aeruginosa proteases. Further screening of 97 P. aeruginosa clinical isolates showed a wide variation in 3xGly cleavage activity. The absence of 3xGly degradation by a lasI knock out strain indicated that 3xGly cleavage by P. aeruginosa could be quorum sensing (QS)-related, a hypothesis strengthened by the observation of a strong correlation between 3xGly cleavage, LasA staphylolytic activity and pyocyanin production. Additionally, isolates able to cleave 3xGly were more susceptible to the QS inhibiting antibiotic azithromycin (AZM). In conclusion, we designed and evaluated a 3xGly substrate possibly useful as a simple tool to predict virulence and AZM susceptibility.